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Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools

Browse Source
This commit is contained in:
Daniel Blankenberg
2019-07-11 17:04:17 -04:00
parent fd7f0d3d8f b415dfddfa
commit 56aab88923
225 changed files with 9321 additions and 8731 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.ci/flake8_blacklist.txt
+2
View File
@@ -15,3 +15,5 @@ lib/galaxy/util/jstree.py
lib/galaxy/web/proxy/js/node_modules
static/maps
static/scripts
build
dist
.gitignore
+11
View File
@@ -9,6 +9,17 @@ scripts/scramble/archives
.venv
.venv3
# Python build artifacts
build
dist
lib/galaxy.egg-info
.eggs
# Generated static content
lib/galaxy/web/framework/static/maps
lib/galaxy/web/framework/static/scripts
lib/galaxy/web/framework/static/style
# Database stuff
database/beaker_sessions
database/citations
.travis.yml
+1 -1
View File
@@ -14,7 +14,7 @@ install:
sh scripts/common_startup.sh
wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
mv db_gx_rev_0127.sqlite database/universe.sqlite
sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
sh manage_db.sh upgrade
elif [ "$TOX_ENV" == "py35-first_startup" ]; then
MINICONDA_URL="https://repo.anaconda.com/miniconda"
MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh"
client/galaxy/scripts/components/PluginList.vue
+10 -8
View File
@@ -2,14 +2,16 @@
<div class="ui-thumbnails">
<div v-if="error" class="alert alert-danger">{{ error }}</div>
<div v-else>
<input
class="search-query parent-width"
name="query"
placeholder="search visualizations"
autocomplete="off"
type="text"
v-model="search"
/>
<div class="search-input">
<input
class="search-query parent-width"
name="query"
placeholder="search visualizations"
autocomplete="off"
type="text"
v-model="search"
/>
</div>
<div v-for="plugin in plugins" :key="plugin.name">
<table v-if="match(plugin)">
<tr class="ui-thumbnails-item" @click="select(plugin)">
client/galaxy/scripts/entry/panels/admin-panel.js
-10
View File
@@ -93,16 +93,6 @@ const AdminPanel = Backbone.View.extend({
target: "__use_router__",
enabled: this.settings.is_tool_shed_installed
},
{
title: _l("Install new tools (Legacy)"),
url: "admin_toolshed/browse_tool_sheds",
enabled: this.settings.is_tool_shed_installed
},
{
title: "Install new tools (Beta)",
url: "admin_toolshed/browse_toolsheds",
enabled: this.settings.is_tool_shed_installed && this.config.enable_beta_ts_api_install
},
{
title: _l("Monitor installation"),
url: "admin_toolshed/monitor_repository_installation",
client/galaxy/scripts/entry/panels/tool-panel.js
+2 -2
View File
@@ -141,9 +141,9 @@ const ToolPanel = Backbone.View.extend({
<div class="toolSectionPad"/>
<div class="toolSectionPad"/>
<div class="toolSectionTitle" id="title_XXinternalXXworkflow">
<span>
<a>
${_l("Workflows")}
</span>
</a>
</div>
<div id="internal-workflows" class="toolSectionBody">
<div class="toolSectionBg"/>
client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
+2 -2
View File
@@ -1568,7 +1568,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
"</span>",
'<span class="title-info unpaired-info"></span>',
"</div>",
'<div class="unpaired-filter forward-unpaired-filter float-left">',
'<div class="unpaired-filter forward-unpaired-filter float-left search-input">',
'<input class="search-query" placeholder="',
_l("Filter this list"),
'" />',
@@ -1596,7 +1596,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
"</span>",
'<span class="title-info unpaired-info"></span>',
"</div>",
'<div class="unpaired-filter reverse-unpaired-filter float-left">',
'<div class="unpaired-filter reverse-unpaired-filter float-left search-input">',
'<input class="search-query" placeholder="',
_l("Filter this list"),
'" />',
client/galaxy/scripts/mvc/library/library-dataset-view.js
+16
View File
@@ -703,6 +703,12 @@ var LibraryDatasetView = Backbone.View.extend({
<td><%= _.escape(item.get("file_size")) %></td>
</tr>
<% } %>
<% if (item.get("update_time")) { %>
<tr>
<th scope="row">Date last updated (UTC)</th>
<td><%= _.escape(item.get("update_time")) %></td>
</tr>
<% } %>
<% if (item.get("date_uploaded")) { %>
<tr>
<th scope="row">Date uploaded (UTC)</th>
@@ -880,6 +886,12 @@ var LibraryDatasetView = Backbone.View.extend({
<td><%= _.escape(ldda.get("file_size")) %></td>
</tr>
<% } %>
<% if (ldda.get("update_time")) { %>
<tr>
<th scope="row">Date last updated (UTC)</th>
<td><%= _.escape(ldda.get("update_time")) %></td>
</tr>
<% } %>
<% if (ldda.get("date_uploaded")) { %>
<tr>
<th scope="row">Date uploaded (UTC)</th>
@@ -1006,6 +1018,10 @@ var LibraryDatasetView = Backbone.View.extend({
<th scope="row">Size</th>
<td><%= _.escape(item.get("file_size")) %></td>
</tr>
<tr>
<th scope="row">Date last updated (UTC)</th>
<td><%= _.escape(item.get("update_time")) %></td>
</tr>
<tr>
<th scope="row">Date uploaded (UTC)</th>
<td><%= _.escape(item.get("date_uploaded")) %></td>
client/galaxy/scripts/mvc/library/library-folderlist-view.js
+1 -1
View File
@@ -517,7 +517,7 @@ var FolderListView = Backbone.View.extend({
<span title="Sorted by Size" class="sort-icon-raw_size fa"></span>
</th>
<th style="width:160px;">
<a class="sort-folder-update_time" title="Click to reverse order" href='#'>Time Updated (UTC)</a>
<a class="sort-folder-update_time" title="Click to reverse order" href='#'>Date Updated (UTC)</a>
<span title="Sorted by Date" class="sort-icon-update_time fa"></span>
</th>
<th style="width:5%;">
client/galaxy/scripts/mvc/library/library-util.js
+26 -33
View File
@@ -1,45 +1,38 @@
/**
* Create alphabetical based two-argument comparator
* that takes into account that Folder comes before Dataset.
* Create alphabetical based two-argument comparator to handle library items (including folders)
* If sort_key is not present it is set to ''.
* @param {str} sort_key key to sort by
* @param {str} sort_order order to sort by (asc, desc)
* @return {function} two-argument comparator function
*/
var generateComparator = (sort_key, sort_order) => (itemA, itemB) => {
if (itemA.get("type") === itemB.get("type")) {
if (!itemA.has(sort_key) && !itemB.has(sort_key)) {
return 0;
} else if (!itemA.has(sort_key)) {
return 1;
} else if (!itemB.has(sort_key)) {
return -1;
}
var comparable_itemA_key;
var comparable_itemB_key;
if (typeof itemA.get(sort_key) === "number") {
comparable_itemA_key = itemA.get(sort_key);
comparable_itemB_key = itemB.get(sort_key);
}
else
{
comparable_itemA_key = itemA.get(sort_key).toLowerCase();
comparable_itemB_key = itemB.get(sort_key).toLowerCase();
}
if ( comparable_itemA_key > comparable_itemB_key) {
return sort_order === "asc" ? 1 : -1;
}
if (comparable_itemB_key > comparable_itemA_key) {
return sort_order === "asc" ? -1 : 1;
}
return 0; // equal
} else {
if (itemA.get("type") === "folder") {
return -1; // folder is always before dataset
}
if (!itemA.has(sort_key) && !itemB.has(sort_key)) {
return 0;
} else if (!itemA.has(sort_key)) {
return 1;
} else if (!itemB.has(sort_key)) {
return -1;
}
var comparable_itemA_key;
var comparable_itemB_key;
if (typeof itemA.get(sort_key) === "number") {
comparable_itemA_key = itemA.get(sort_key);
comparable_itemB_key = itemB.get(sort_key);
}
else
{
comparable_itemA_key = itemA.get(sort_key).toLowerCase();
comparable_itemB_key = itemB.get(sort_key).toLowerCase();
}
if ( comparable_itemA_key > comparable_itemB_key) {
return sort_order === "asc" ? 1 : -1;
}
if (comparable_itemB_key > comparable_itemA_key) {
return sort_order === "asc" ? -1 : 1;
}
return 0; // equal
};
export default {
generateComparator: generateComparator
client/galaxy/scripts/mvc/rules/rule-definitions.js
+13 -13
View File
@@ -42,7 +42,7 @@ const applyRegex = function(regex, target, data, replacement, groupCount) {
return null;
}
if (!replacement) {
groupCount = groupCount && parseInt(groupCount);
groupCount = groupCount && parseInt(groupCount, 10);
if (groupCount) {
if (match.length != groupCount + 1) {
failedCount++;
@@ -108,7 +108,7 @@ const RULES = {
}
},
save: (component, rule) => {
rule.start = parseInt(component.addColumnRownumStart);
rule.start = parseInt(component.addColumnRownumStart, 10);
},
apply: (rule, data, sources, columns) => {
let rownum = rule.start;
@@ -169,7 +169,7 @@ const RULES = {
const ruleValue = rule.value;
let newRow;
if (ruleValue.indexOf("identifier") == 0) {
const identifierIndex = parseInt(ruleValue.substring("identifier".length));
const identifierIndex = parseInt(ruleValue.substring("identifier".length), 10);
newRow = (row, index) => {
const newRow = row.slice();
newRow.push(sources[index]["identifiers"][identifierIndex]);
@@ -253,7 +253,7 @@ const RULES = {
component.addColumnRegexTarget = rule.target_column;
component.addColumnRegexExpression = rule.expression;
component.addColumnRegexReplacement = rule.replacement;
component.addColumnRegexGroupCount = rule.group_count;
component.addColumnRegexGroupCount = parseInt(rule.group_count);
}
let addColumnRegexType = "global";
if (component.addColumnRegexGroupCount) {
@@ -347,7 +347,7 @@ const RULES = {
},
save: (component, rule) => {
rule.target_column = component.addColumnSubstrTarget;
rule.length = parseInt(component.addColumnSubstrLength);
rule.length = parseInt(component.addColumnSubstrLength, 10);
rule.substr_type = component.addColumnSubstrType;
},
apply: (rule, data, sources, columns) => {
@@ -403,7 +403,7 @@ const RULES = {
function newRow(row) {
const newRow = [];
for (const index in row) {
if (targets.indexOf(parseInt(index)) == -1) {
if (targets.indexOf(parseInt(index, 10)) == -1) {
newRow.push(row[index]);
}
}
@@ -448,7 +448,7 @@ const RULES = {
const target = rule.target_column;
const invert = rule.invert;
const filterFunction = function(el, index) {
const row = data[parseInt(index)];
const row = data[parseInt(index, 10)];
return regExp.exec(row[target]) ? !invert : invert;
};
sources = sources.filter(filterFunction);
@@ -477,13 +477,13 @@ const RULES = {
component.addFilterCountWhich = "first";
component.addFilterCountInvert = false;
} else {
component.addFilterCountN = parseInt(rule.count);
component.addFilterCountN = parseInt(rule.count, 10);
component.addFilterCountWhich = rule.which;
component.addFilterCountInvert = rule.inverse;
}
},
save: (component, rule) => {
rule.count = parseInt(component.addFilterCountN);
rule.count = parseInt(component.addFilterCountN, 10);
rule.which = component.addFilterCountWhich;
rule.invert = component.addFilterCountInvert;
},
@@ -528,7 +528,7 @@ const RULES = {
const target = rule.target_column;
const invert = rule.invert;
const filterFunction = function(el, index) {
const row = data[parseInt(index)];
const row = data[parseInt(index, 10)];
return row[target].length ? !invert : invert;
};
sources = sources.filter(filterFunction);
@@ -562,7 +562,7 @@ const RULES = {
const invert = rule.invert;
const value = rule.value;
const filterFunction = function(el, index) {
const row = data[parseInt(index)];
const row = data[parseInt(index, 10)];
return row[target] == value ? !invert : invert;
};
sources = sources.filter(filterFunction);
@@ -598,7 +598,7 @@ const RULES = {
const compare_type = rule.compare_type;
const value = rule.value;
const filterFunction = function(el, index) {
const row = data[parseInt(index)];
const row = data[parseInt(index, 10)];
const targetValue = parseFloat(row[target]);
let matches;
if (compare_type == "less_than") {
@@ -730,7 +730,7 @@ const RULES = {
const newRow0 = [],
newRow1 = [];
for (let index in row) {
index = parseInt(index);
index = parseInt(index, 10);
if (targets0.indexOf(index) > -1) {
newRow0.push(row[index]);
} else if (targets1.indexOf(index) > -1) {
client/galaxy/scripts/mvc/tool/tools.js
+4 -8
View File
@@ -347,9 +347,7 @@ var ToolSearch = Backbone.Model.extend({
SEARCH_RESERVED_TERMS_FAVORITES: ["#favs", "#favorites", "#favourites"],
defaults: {
search_hint_string: "search tools",
min_chars_for_search: 3,
clear_btn_url: "",
visible: true,
query: "",
results: null,
@@ -635,7 +633,7 @@ var ToolSectionView = BaseView.extend({
var ToolSearchView = Backbone.View.extend({
tagName: "div",
id: "tool-search",
className: "bar",
className: "search-input",
events: {
click: "focus_and_select",
@@ -649,7 +647,6 @@ var ToolSearchView = Backbone.View.extend({
if (!this.model.is_visible()) {
this.$el.hide();
}
this.$el.find("[title]").tooltip();
return this;
},
@@ -774,10 +771,9 @@ var templates = {
// the search bar at the top of the tool panel
tool_search: _.template(
`<input id="tool-search-query" class="search-query parent-width" name="query"
placeholder="<%- search_hint_string %>" autocomplete="off" type="text" />
<a id="search-clear-btn" title="clear search (esc)"> </a>
<span id="search-spinner" class="search-spinner fa fa-spinner fa-spin"></span>
`
placeholder="search tools" autocomplete="off" type="text" />
<span id="search-clear-btn" class="search-clear fa fa-times-circle" title="clear search (esc)"/>
<span id="search-spinner" class="search-loading fa fa-spinner fa-spin"/>`
),
// the category level container in the tool panel (e.g. 'Get Data', 'Text Manipulation')
client/galaxy/scripts/mvc/workflow/workflow-view.js
+3
View File
@@ -47,6 +47,7 @@ function reset_tool_search(initValue) {
// Reset search input.
tool_menu_frame.find("#search-spinner").hide();
tool_menu_frame.find("#search-clear-btn").show();
if (initValue) {
var search_input = tool_menu_frame.find("#tool-search-query");
search_input.val("search tools");
@@ -155,6 +156,7 @@ export default Backbone.View.extend({
}
// Start a new ajax-request in X ms
$("#search-spinner").show();
$("#search-clear-btn").hide();
this.timer = window.setTimeout(() => {
$.get(
self.urls.tool_search,
@@ -209,6 +211,7 @@ export default Backbone.View.extend({
$("#search-no-results").show();
}
$("#search-spinner").hide();
$("#search-clear-btn").show();
},
"json"
);
client/galaxy/style/scss/base.scss
+37 -81
View File
@@ -735,54 +735,6 @@ button {
}
}
.search-query {
display: inline-block;
padding: 4px;
font-size: $font-size-base;
line-height: $line-height-base;
color: $text-color;
border: 1px solid $border-default-color;
padding-left: 14px !important;
padding-right: 14px;
margin-bottom: 0;
@include border-radius(14px);
background: $brand-white;
}
.search-query:focus {
border-color: darken(rgba(82, 168, 236, 0.8), 15%);
$shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6);
@include box-shadow($shadow);
outline: 0;
outline: thin dotted \9; /* IE6-8 */
}
.search-spinner {
position: absolute;
display: none;
right: 6px;
top: 5px;
font-size: 1.4em;
color: #888;
}
#tool-search {
position: relative;
@extend .mb-2;
#search-clear-btn {
position: absolute;
right: 6px;
top: 6px;
display: block;
font-size: 1.4em !important;
text-decoration: none;
color: #888;
@extend .fa-icon;
&:before {
content: "\f057";
}
}
}
// Messages
.errormessagelarge,
@@ -1477,55 +1429,59 @@ div.permissionContainer {
.toolMenuContainer {
color: $panel-text-color;
a {
color: $panel-text-color;
color: $panel-text-color;
}
background: $panel-bg-color;
min-height: 100%;
@extend .m-3;
}
div.toolSectionWrapper {
@extend .mb-1;
}
div.toolSectionTitle {
font-weight: 500;
font-size: $h4-font-size;
}
div.toolPanelLabel {
@extend .mt-3;
@extend .mb-2;
font-weight: bold;
color: $gray-600;
text-transform: uppercase;
}
div.toolTitle {
@extend .m-2;
display: block;
.labels {
float: right;
}
}
div a.tool-link {
text-decoration: none;
display: block;
span.tool-old-link {
text-decoration: underline;
}
&:hover {
background: darken($panel-bg-color, 5%);
}
}
div.toolTitleNoSection {
@extend .pb-1;
div.toolPanelLabel {
@extend .py-1;
@extend .px-3;
font-weight: bold;
font-size: $h4-font-size;
color: $gray-600;
text-transform: uppercase;
}
div.toolSectionTitle, div.toolTitle, div.toolTitleNoSection {
display: block;
.labels {
float: right;
}
a {
@extend .px-3;
@extend .py-1;
text-decoration: none;
display: block;
&:hover {
background: darken($panel-bg-color, 5%);
}
}
&.text-muted a {
&:hover {
background: inherit;
}
}
}
div.toolSectionWrapper {
div.toolTitle a, div.toolPanelLabel {
@extend .pl-4;
font-size: inherit;
}
}
// Dataset Display Styles
#loading_indicator {
position: fixed;
right: 10px;
client/galaxy/style/scss/history.scss
-15
View File
@@ -470,21 +470,6 @@
.btn {
@extend .btn-sm;
}
.search-control {
display: inline-block;
width: 40%;
.search-clear,
.search-loading {
margin-top: -22px;
}
}
input.search-query {
font-size: 90%;
height: 21px;
line-height: normal;
padding: 2px 2px 1px 2px;
}
.open-more-options {
padding: 2px 6px 2px 6px;
font-size: 100%;
client/galaxy/style/scss/theme/blue.scss
+2
View File
@@ -114,7 +114,9 @@ $layout-border: none;
// Borders
$border-radius-base: 0.1875rem;
$border-radius-large: 0.3125rem;
$border-radius-extralarge: 1rem;
$border-default-color: $gray-400;
$border-default: 1px solid $border-default-color;
// Buttons
$btn-default-color: $text-color;
client/galaxy/style/scss/ui/search-input.scss
+24 -13
View File
@@ -1,26 +1,37 @@
// search bar, see: scripts/jq-plugins/ui/search-input.js
.search-input {
.search-query {
width: 100%;
padding-right: 24px;
}
@extend .mb-2;
.search-clear,
.search-loading {
// it places the icons on the right of the bar (and puts the lotion on its skin)
@extend .mr-2;
position: relative;
display: inline-block;
float: right;
margin-top: -25px;
margin-right: 4px;
font-size: 1.4em;
line-height: 23px;
color: grey;
color: $gray-500;
}
.search-clear:hover {
color: $link-color;
color: $brand-info;
cursor: pointer;
}
.search-loading {
display: none;
}
.search-query {
@extend .px-3;
@extend .py-1;
width: 100%;
display: inline-block;
font-size: $font-size-base;
line-height: $line-height-base;
color: $text-color;
border: $border-default;
@include border-radius($border-radius-extralarge);
max-width: auto;
background: $brand-white;
}
.search-query:focus {
border-color: $brand-info;
outline: 0;
}
}
client/webpack.config.js
+1 -1
View File
@@ -19,7 +19,7 @@ let buildconfig = {
generic: ["polyfills", "bundleEntries", "entry/generic"]
},
output: {
path: path.join(__dirname, "../", "static/scripts/bundled"),
path: path.join(__dirname, "../", "lib/galaxy/web/framework/static/scripts/bundled"),
publicPath: "/static/scripts/bundled/",
filename: "[name].bundled.js",
chunkFilename: "[name].chunk.js"
config/auth_conf.xml.sample
-128
View File
@@ -1,128 +0,0 @@
<?xml version="1.0"?>
<auth>
<!--<authenticator>
<type>ldap</type>
-->
<!-- Replacement fields: instances of {email}, {username} and {password}
are replaced with the corresponding user's values inside the
<filter>, <server>, <ldap-options>, <search-fields>,
<search-filter>, <search-base>, <search-user> and <search-password>
elements. -->
<!-- Filter users for which this authenticator applies. This is a Python
expression which is evaluated after field replacement. -->
<!-- <filter>'{email}'.endswith('@example.com')</filter>
<options>
-->
<!-- Whether to allow user registration. Possible values are True,
False and Challenge (i.e. allow registration in case of
successful authentication). Default is True. -->
<!-- <allow-register>False</allow-register>
-->
<!-- Whether Galaxy should automatically register users when they
first login. Default is False. -->
<!-- <auto-register>True</auto-register>
-->
<!-- Whether users are allowed to change their password. Default is
False. -->
<!-- <allow-password-change>False</allow-password-change>
-->
<!-- Whether roles should be automatically created if
the attribute specified under auto-register-roles can be found.
Default is False. -->
<!-- <auto-create-roles>False</auto-create-roles>
-->
<!-- Whether groups should be automatically created if
the attribute specified under auto-register-roles can be found.
Can be used in combination with auto-create-roles
Default is False. -->
<!-- <auto-create-groups>False</auto-create-groups>
-->
<!-- If set, roles will be assigned to the auto generated groups,
not to the individual users. Can only be used if auto-create-roles and
auto-create-groups are True. Default is False. -->
<!-- <auto-assign-roles-to-groups-only>False</auto-assign-roles-to-groups-only>
-->
<!-- LDAP-specific options -->
<!-- <server>ldap://dc1.example.com</server>
-->
<!-- Additional options for the LDAP connection. The syntax is:
option1=value1,option2=value2,...
Options and values should match those from the python-ldap
documentation.
The following example allows connecting to ldaps:// (SSL/TLS)
when self-signed certificates are used -->
<!-- <ldap-options>OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW</ldap-options>
-->
<!-- Whether unregistered users should use their LDAP username
instead of the email at their first login when auto-register is
True. Default is False. -->
<!-- <login-use-username>False</login-use-username>
-->
<!-- Whether to continue with the following authenticators if LDAP
fails. Default is False. -->
<!-- <continue-on-failure>False</continue-on-failure>
-->
<!-- If search-fields is not specified, all other search-* elements
are ignored.
If search-user is not specified, Galaxy will bind anonymously
to the LDAP server for search. -->
<!-- For Active Directory: -->
<!-- <search-fields>sAMAccountName,mail</search-fields>
<search-base>dc=dc1,dc=example,dc=com</search-base>
-->
<!-- If login-use-username is False -->
<!-- <search-filter>(&amp;(objectClass=user)(mail={email}))</search-filter>
-->
<!-- If login-use-username is True -->
<!-- <search-filter>(&amp;(objectClass=user)(sAMAccountName={username}))</search-filter>
-->
<!-- <search-user>jsmith@dc1.example.com</search-user>
<search-password>mysecret</search-password>
-->
<!-- For OpenLDAP: -->
<!-- <search-fields>uid,mail</search-fields>
<search-base>ou=People,dc=example,dc=com</search-base>
-->
<!-- If login-use-username is False -->
<!-- <search-filter>(mail={email})</search-filter>
-->
<!-- If login-use-username is True -->
<!-- <search-filter>(uid={username})</search-filter>
-->
<!-- <search-user>cn=jsmith,ou=People,dc=domain,dc=com</search-user>
<search-password>mysecret</search-password>
-->
<!-- Replacement fields: instances of {email}, {username},
{password}, {dn} plus all fields defined in <search-fields> are
replaced with the corresponding user's values inside the
<bind-user>, <bind-password>, <auto-register-username> and
<auto-register-email> elements. -->
<!-- For Active Directory: -->
<!-- <bind-user>{sAMAccountName}@dc1.example.com</bind-user>
<bind-password>{password}</bind-password>
<auto-register-username>{sAMAccountName}</auto-register-username>
<auto-register-email>{mail}</auto-register-email>
<auto-register-roles>{gidNumber}</auto-register-roles>
-->
<!-- For OpenLDAP: -->
<!-- <bind-user>{dn}</bind-user>
<bind-password>{password}</bind-password>
<auto-register-username>{uid}</auto-register-username>
<auto-register-email>{mail}</auto-register-email>
<auto-register-roles>{gid}</auto-register-roles>
-->
<!-- </options>
</authenticator>
-->
<authenticator>
<type>localdb</type>
<options>
<!-- Whether users are allowed to change their password. Default is
False. -->
<allow-password-change>true</allow-password-change>
</options>
</authenticator>
</auth>
config/auth_conf.xml.sample
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# Build sites define the builds (dbkeys) available at sites used by display
# applications and the URL to those sites.
# The `display` attributes on the `ucsc` and `gbrowse` sites replace the
# `ucsc_display_sites` and `gbrowse_display_sites` options in galaxy.ini.
# Because these are used by "old-style" display applications, their types
# cannot change if you want the old-style display links for these sites to
# work.
- type: ucsc
file: tool-data/shared/ucsc/ucsc_build_sites.txt
display: [main,test,archaea,ucla]
- type: gbrowse
file: tool-data/shared/gbrowse/gbrowse_build_sites.txt
display: [modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225]
- type: ensembl
file: tool-data/shared/ensembl/ensembl_sites.txt
- type: ensembl_data_url
file: tool-data/shared/ensembl/ensembl_sites_data_URL.txt
- type: igv
file: tool-data/shared/igv/igv_build_sites.txt
- type: rviewer
file: tool-data/shared/rviewer/rviewer_build_sites.txt
config/build_sites.yml.sample
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<containers_resolvers>
<explicit />
<!-- explicit: resolves container URI for a job through explict container
tags in the tool XML wrapper. -->
<!-- All mulled flavors below only work if enable_beta_mulled_containers is
set to true in the galaxy.yaml config file. -->
<!-- <cached_mulled /> -->
<!-- cached_mulled: resolves container URI through bioconda to mulled
automatic mapping, preferring cached images in the accessible docker
engine. Requires docker engine. -->
<!-- <cached_mulled_singularity /> -->
<!-- cached_mulled_singularity: resolves container URI through
bioconda to mulled automatic mapping, preferring cached singularity
images to building local singularity images. Only works with
enable_beta_mulled_containers set to true in the galaxy.yaml config file.
-->
<!-- <mulled auto_install="True"/> -->
<!-- mulled: only resolves container URI through bioconda to mulled automatic
mapping. Should be the method of choice if mulled resolution is required
but the container execution is handled by a container orchestration
instead of docker directly (ie. Galaxy has no access to a docker client
binary). It works of course with direct docker engine tool executions.
Set auto_install to False if Galaxy should pull container images
through the admin interface or API, but not automatically when
a tool is run.
-->
<!-- <mulled_singularity auto_install="True"/> -->
<!-- mulled_singularity: only resolves container URI through bioconda to mulled automatic
mapping. Should be the method of choice if mulled resolution is required
but the container execution is handled by a container orchestration
instead of singularity directly (ie. Galaxy has no access to a singularity client
binary). It works of course with direct singularity tool executions.
Set auto_install to False if Galaxy should pull container images
through the admin interface or API, but not automatically when
a tool is run.
-->
<!-- <build_mulled auto_install="True"/> -->
<!-- build_mulled: builds a docker image locally for one or more bioconda
packages listed in the tools definition.
Set auto_install to False if Galaxy should build container images
through the admin interface or API, but not automatically when
a tool is run.
-->
<!-- <build_mulled_singularity auto_install="True"/> -->
<!-- build_mulled_singularity: builds a singularity image locally for one
or more package requirements listed as part of the tool's definition.
Set auto_install to False if Galaxy should build container images
through the admin interface or API, but not automatically when
a tool is run.
-->
</containers_resolvers>
config/container_resolvers_conf.xml.sample
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---
# Galaxy container interface configuration file
#
# To configure the location of this file, use the `containers_config_file` setting in galaxy.yml. Additionally, the
# containers interface is only used if `enable_beta_containers_interface` is set in galaxy.yml.
###
### Container Interfaces
###
# Define container interfaces beneath the top-level `containers` dictionary. By default, a single `_default_` interface
# of type `docker` is defined, equivalent to:
#containers:
# _default_:
# type: docker
# The interface name is arbitrary and allows multiple distinct configurations to be defined. The name can be any string,
# but `_default_` is used if a component that uses the containers interface does not specify an interface. Currently
# only Galaxy Interactive Environments use the containers interface, and do not have a way to specify which interface to
# use, so configure under the `_default_` key for now.
# Additional options can be specified are specific to the container type:
#containers:
# _default_:
# type: docker
# host: docker.example.org:2376
# force_tlsverify: yes
# Keys in `containers` are used to map container consumers to specific # container consumers. If a mapping is not
# configured, the _default_ configuration will be used. An example of multiple container configurations would be:
#containers:
# _default_:
# type: docker
# ... additional options ...
# example_swarm:
# type: docker_swarm
# ... additional options ...
#
###
### Container Types and Supported Options
###
# Command-line equivalent arguments are in [brackets] (if applicable)
containers:
#
# Supported options for all container types
#
_default_:
# [`--name` (partial)] Prepend this string to the name of containers created
#name_prefix: galaxy_
#
# Supported options for `docker` container type
#
local_docker:
type: docker
# [`-H`/`--host] Daemon socket(s) to connect to
#host: null
# [`--tlsverify`] Use TLS and verify the remote
#force_tlsverify: no
# [`--cpus`] Number of CPUs (default 0.000)
#cpus: null
# [`-m`/`--memory`] Memory limit
#memory: null
# Default image to run if one is not provided to the run method
#image: null
#
# Supported options for `docker_swarm` container type
#
swarm:
type: docker_swarm
# All of the `docker` interface type arguments are supported. Additionally:
# [`-H`/`--host] Daemon socket(s) to connect to. This can be a list, which allows failing over to another
# manager when one is down, e.g.:
# host:
# - tcp://swarm1.example.org:2376
# - tcp://swarm2.example.org:2376
#host: null
# [`--reserve-cpu` and `--limit-cpu`] Reserve the given number of CPUs when containers are run to prevent other
# containers from being scheduled on the same node once all of its CPUs are allocated. Additionally, prevent
# container from using more than the given number of CPUs.
#cpus: null
# [`--reserve-memory` and `--limit-memory`] Reserve the given amount of memory when containers are run to
# prevent other containers from being scheduled on the same node once all of its memory is allocated.
# Additionally, prevent container from using more than the given amount of memory.
#memory: null
# If set, only nodes whose names begin with this string will be visible to and managed by the swarm manager.
# Note that regardless of whether this is set, the swarm manager will not attempt to control manager nodes
#node_prefix: null
# Convert image from name[:tag] form to name@digest form when possible, to avoid dependency on the image
# registry (e.g. Docker Hub or wherever the image was pulled from) at service creation time. For details see:
# https://github.com/docker/docker/issues/31427
#resolve_image_digest: no
# If a container run request is received that defines volumes to attach, should those volumes be ignored? Swarm
# mode does not support mounting volumes.
#ignore_volumes: no
#
# For the following `service_create_*_constraint` options, if set, the swarm manager automatically sets a
# corresponding label on nodes it spawns for services with the given constraints.
#
# [`--constraint node.labels._galaxy_image=={image}`] Automatically create a constraint based on the requested
# image name when new services are created (the image name is the resolved form if `resolve_image_digest` is
# set). This is useful if your nodes do not all have all of the possible images you'll want to run. Note: It's
# currently only possible for nodes to have a single image constraint defined. If your nodes have multiple
# images available, do not use this option.
#service_create_image_constraint: no
# [`--constraint node.labels._galaxy_cpus=={cpus}`] Automatically create a constraint based on the requested
# number of CPUs (or 1, if `cpus` is unset). This is useful if you are spawning nodes with a mixture of CPU
# counts and want to prevent (for example) 1-cpu services from being scheduled on 2-cpu nodes when 2-cpu jobs
# are waiting.
#service_create_cpus_constraint: no
#
# Galaxy can manage a Docker swarm using a built-in daemon and callouts to commands to add/remove nodes from
# your swarm.
#
# Use the swarm manager to manage services on this swarm. Even if your swarm is static, using the manager is
# recommended as the manager will automatically remove services after they have terminated.
#managed: yes
# Automatically start the swarm manager when new services are created. Useful if you want to run the swarm
# manager but control it separately from Galaxy.
#manager_autostart: yes
# Configuration dictionary for the swarm manager
manager_conf:
#
# In order to use the swarm manager for more than just service cleanup, (e.g. its node spawn and destroy
# features), you'll need to configure the `cpus` option in the interface. Otherwise, there are no limits on
# the number of services that will be assigned to a given node, so the swarm manager has no way to determine
# that more nodes should be spawned.
#
# Each service consumes one "slot", and the number of slots available on a node is its number of CPUs
# divided by the value of `cpus`.
#
# When the swarm manager daemonizes, it writes a pid file so that only one manager will run at a time. This
# is the path to that pid file. {xdg_data_home} will be templated automatically and defaults to
# ~/.local/share as per the XDG specification
#pid_file: '{xdg_data_home}/galaxy_swarm_manager.pid'
# Program output will be written to the log
#log_file: '{xdg_data_home}/galaxy_swarm_manager.log'
# Level of log messages (levels are Python logging module level names (case insensitive))
#log_level: INFO
# Log message format
#log_format: %(name)s %(levelname)s %(asctime)s %(message)s
# List of services' environment variables that should be logged when performing periodic service logging. By
# default, none are logged, but `USER_EMAIL` is useful for GIE containers to log the user who is running the
# container.
#log_environment_variables:
# - USER_EMAIL
# Command to run to spawn new nodes. This command should join the node to the swarm. It is run once per
# unique set of constraints of waiting services. Can include template variables:
#
# - {cpus}: Number of CPUs needed by the requested service(s) or minimum limits
# - {slots}: Number of "slots" needed by the requested service(s) or minimum limits, where slots are CPU
# fractions determined by use of the "cpus" option in the `docker_swarm` section.
# - {image}: Image requested by service
# - {service_ids}: Comma-separated list of service ids with these constraints currently waiting
# - {service_count}: Number of services with these constraints currently waiting
#
# If this command does not block until the node is joined to the swarm, make sure it at least completes that
# step in `spawn_wait_time` once it returns control. How the `spawn_command` exits controls the swarm
# manager's behavior:
#
# - return code: 0, output: space-separated list of spawned nodes:
# Swarm manager will wait for the nodes to appear in the swarm and manage them. You are responsible for ensuring
# the names returned match the name as it will appear in the output of `docker node ls`.
# - return code: 0, output: empty:
# Refusing to allocate nodes and the swarm manager should not attempt to spawn nodes for the given service(s)
# again. This is useful for controlling the maximum number of nodes that will be spawned.
# - return code: 2, output: anything (it will be logged as a message)
# Refusing/failed to allocate nodes but the swarm manager should attempt to spawn nodes for the given
# service(s) again.
#
#spawn_command: /bin/true
# Command to run to destroy idle nodes. Can include template variables:
#
# - {nodes}: Space-separated list of node names to destroy
#
# This command should block until at least the point at which any nodes being destroyed no longer appear in
# the swarm. It should return the names of nodes destroyed, separated by spaces.
#
#destroy_command: /bin/true
# Command to run if either of the above commands failed (e.g. to notify an administrator). Can include
# template variables:
#
# - {failed_command}: Command line of the command that failed
#
#command_failure_command: /bin/true
# Number of times to retry spawn/destroy commands before considering them to have failed, and seconds to
# wait between retries.
#command_retries: 0
#command_retry_wait: 10
# Amount of time to wait for a spawning node to appear in the swarm before considering it failed
#spawn_wait_time: 30
# Stop the swarm manager daemon when there are no services or nodes to manage
#terminate_when_idle: yes
#
# Limits control when the swarm manager will spawn and terminate nodes.
#
# Number of services that must be waiting to run before attempting to spawn a node. If using constraints,
# then waiting services are grouped by constraint.
#service_wait_count_limit: 0
# Number of seconds a service must be waiting before attempting to spawn a node.
#service_wait_time_limit: 5
# Number of seconds a node must be idle before terminating it.
#node_idle_limit: 120
# Minimum number of worker slots that should be started and active.
#slots_min_limit: 0
# Number of spare (unused) worker slots that should be started and active
#slots_min_spare: 0
#
# Each set of limits can also be set on a per-constraint basis under the `limits` list. Each member of
# `limits` is a dictionary dictionary with at least the key `constraints`, whose value is a list of
# constraint strings matching constraint strings that jobs will be created with, either by the use of
# `service_create_*_constraint` or manually setting constraints. Other keys match the `node_*` and `slots_*`
# limits above. Any limits unset will default to the "global" limits as set above, or their defaults.
#
# If you are using constraints, you should at least define them in the limits section, even if using all
# "global" values for the limits. This allows the swarm manager to know what node types to keep around if
# you're using `slots_min_limit`.
#
# Limits section example:
#limits:
# constraints:
# - node.labels._galaxy_image==bgruening/docker-jupyter-notebook:16.01.1
# - node.labels._galaxy_cpus==1
# slots_min_limit: 2
# slots_min_spare: 1
config/containers_conf.yml.sample
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<?xml version="1.0"?>
<data_managers>
</data_managers>
config/datatypes_conf.xml.sample
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<?xml version="1.0"?>
<datatypes>
<registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
<datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/>
<datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/>
<datatype extension="anvio_cog_profile" type="galaxy.datatypes.anvio:AnvioComposite" display_in_upload="false" subclass="true" />
<datatype extension="anvio_composite" type="galaxy.datatypes.anvio:AnvioComposite" display_in_upload="false" />
<datatype extension="anvio_classifier" type="galaxy.datatypes.data:Data" display_in_upload="false" subclass="true" />
<datatype extension="anvio_contigs_db" type="galaxy.datatypes.anvio:AnvioContigsDB" display_in_upload="false" />
<datatype extension="anvio_db" type="galaxy.datatypes.anvio:AnvioDB" display_in_upload="false" />
<datatype extension="anvio_genomes_db" type="galaxy.datatypes.anvio:AnvioGenomesDB" display_in_upload="false" />
<datatype extension="anvio_pan_db" type="galaxy.datatypes.anvio:AnvioPanDB" display_in_upload="false" />
<datatype extension="anvio_pfam_profile" type="galaxy.datatypes.anvio:AnvioComposite" display_in_upload="false" subclass="true" />
<datatype extension="anvio_profile_db" type="galaxy.datatypes.anvio:AnvioProfileDB" display_in_upload="false" />
<datatype extension="anvio_samples_db" type="galaxy.datatypes.anvio:AnvioSamplesDB" display_in_upload="false" />
<datatype extension="anvio_state" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false" />
<datatype extension="anvio_structure_db" type="galaxy.datatypes.anvio:AnvioStructureDB" display_in_upload="false" />
<datatype extension="anvio_variability" type="galaxy.datatypes.tabular:TSV" display_in_upload="false" subclass="true" />
<datatype extension="arff" type="galaxy.datatypes.text:Arff" mimetype="text/plain" display_in_upload="true"/>
<datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
<datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
<datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bai.xml" target_datatype="bai"/>
<converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
<display file="ucsc/bam.xml"/>
<display file="ensembl/ensembl_bam.xml"/>
<display file="igv/bam.xml"/>
<display file="igb/bam.xml"/>
<display file="iobio/bam.xml"/>
</datatype>
<datatype extension="bai" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="false"/>
<datatype extension="qname_input_sorted.bam" type="galaxy.datatypes.binary:BamInputSorted" mimetype="application/octet-stream" display_in_upload="false" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted based on the aligner output." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
</datatype>
<datatype extension="qname_sorted.bam" type="galaxy.datatypes.binary:BamQuerynameSorted" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted by queryname." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
</datatype>
<datatype extension="unsorted.bam" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
</datatype>
<datatype extension="probam" type="galaxy.datatypes.binary:ProBam" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="cram" type="galaxy.datatypes.binary:CRAM" mimetype="application/octet-stream" display_in_upload="true" description="CRAM is a file format for highly efficient and tunable reference-based compression of alignment data." description_url="http://www.ebi.ac.uk/ena/software/cram-usage">
<converter file="cram_to_bam_converter.xml" target_datatype="bam"/>
</datatype>
<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed">
<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
<converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="bed_to_fli_converter.xml" target_datatype="fli"/>
<!-- <display file="ucsc/interval_as_bed.xml" /> -->
<display file="igb/bed.xml"/>
</datatype>
<datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true">
<converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/>
<display file="igb/bedgraph.xml"/>
</datatype>
<datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" display_in_upload="true"/>
<datatype extension="bed6" type="galaxy.datatypes.interval:Bed6" display_in_upload="true">
</datatype>
<datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" display_in_upload="true"/>
<datatype extension="probed" type="galaxy.datatypes.interval:ProBed" display_in_upload="true"/>
<datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
<converter file="len_to_linecount.xml" target_datatype="linecount"/>
</datatype>
<datatype extension="daa" type="galaxy.datatypes.binary:DAA" display_in_upload="true"/>
<datatype extension="rma6" type="galaxy.datatypes.binary:RMA6" display_in_upload="true"/>
<datatype extension="dmnd" type="galaxy.datatypes.binary:DMND" display_in_upload="false"/>
<datatype extension="idat" type="galaxy.datatypes.binary:Idat" display_in_upload="true"/>
<datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
<display file="ucsc/bigbed.xml"/>
<display file="igb/bb.xml"/>
</datatype>
<datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true">
<display file="ucsc/bigwig.xml"/>
<display file="igb/bigwig.xml"/>
<display file="igv/bigwig.xml"/>
</datatype>
<datatype extension="cxb" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" description="Cuffquant output format"/>
<datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="true">
<converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
</datatype>
<datatype extension="csv" type="galaxy.datatypes.tabular:CSV" display_in_upload="true">
<converter file="csv_to_tabular.xml" target_datatype="tabular"/>
</datatype>
<datatype extension="tsv" type="galaxy.datatypes.tabular:TSV" display_in_upload="true">
<converter file="tabular_to_csv.xml" target_datatype="csv"/>
</datatype>
<datatype extension="intermine_tabular" type="galaxy.datatypes.tabular:TSV" subclass="true" display_in_upload="true">
<display file="intermine/intermine_simple.xml"/>
</datatype>
<datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
<datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="false"/>
<datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="false"/>
<datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
<datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
<datatype extension="d3_hierarchy" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="true"/>
<datatype extension="imgt.json" type="galaxy.datatypes.text:ImgtJson" mimetype="application/json" display_in_upload="True"/>
<datatype extension="geojson" type="galaxy.datatypes.text:GeoJson" mimetype="application/json" display_in_upload="True"/>
<datatype extension="data_manager_json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="dbn" type="galaxy.datatypes.sequence:DotBracket" display_in_upload="true" description="Dot-Bracket format is a text-based format for storing both an RNA sequence and its corresponding 2D structure." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Dbn"/>
<datatype extension="fai" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true" description="A Fasta Index File is a text file consisting of lines each with five TAB-delimited columns : Name, Length, offset, linebases, Linewidth" description_url="http://www.htslib.org/doc/faidx.html"/>
<datatype extension="fasta" auto_compressed_types="gz" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('&gt;') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta">
<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
<converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
<converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>
<converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
<converter file="fasta_to_len.xml" target_datatype="len"/>
<converter file="fasta_to_fai.xml" target_datatype="fai"/>
<display file="igv/genome_fasta.xml" inherit="true"/>
</datatype>
<datatype extension="fastg" type="galaxy.datatypes.sequence:Fastg" display_in_upload="true" description="fastg format faithfully represents genome assemblies in the face of allelic polymorphism and assembly uncertainty" description_url="http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"/>
<datatype extension="fastq" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqsanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqsolexa" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqcssanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqillumina" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
<datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
<datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
<datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">
<!-- <display file="genetrack.xml" /> -->
</datatype>
<datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true" description="GFF lines have nine required fields that must be tab-separated." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF">
<converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
<converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="gff_to_fli_converter.xml" target_datatype="fli"/>
<display file="ensembl/ensembl_gff.xml" inherit="true"/>
<display file="igv/gff.xml" inherit="true"/>
<!-- <display file="gbrowse/gbrowse_gff.xml" inherit="true" /> -->
</datatype>
<datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/>
<datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
<datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
<datatype extension="graph_dot" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
<converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<display file="igb/gtf.xml"/>
</datatype>
<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="true"/>
<datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="cool" type="galaxy.datatypes.binary:Cool" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="mcool" type="galaxy.datatypes.binary:MCool" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
<datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order).">
<converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
<converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/>
<converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/>
<converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
<converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/>
<!-- <display file="ucsc/interval_as_bed.xml" inherit="true" /> -->
<display file="ensembl/ensembl_interval_as_bed.xml" inherit="true"/>
<display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="true"/>
<display file="rviewer/bed.xml" inherit="true"/>
<display file="igv/interval_as_bed.xml" inherit="true"/>
</datatype>
<!-- ISA data types -->
<datatype extension="isa-tab" type="galaxy.datatypes.isa:IsaTab" mimetype="application/isa-tools" display_in_upload="true" description="ISA-Tab data type." description_url="https://isa-tools.org"/>
<datatype extension="isa-json" type="galaxy.datatypes.isa:IsaJson" mimetype="application/isa-tools" display_in_upload="true" description="ISA-JSON data type." description_url="https://isa-tools.org"/>
<datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true">
<converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/>
</datatype>
<datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
<datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff" display_in_upload="true"/>
<datatype extension="tf2" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="tf8" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="btf" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="tif" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="svs" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="scn" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="bif" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="vms" type="galaxy.datatypes.images:Hamamatsu" mimetype="image/hamamatsu"/>
<datatype extension="vmu" type="galaxy.datatypes.images:Hamamatsu" subclass="true" display_in_upload="false"/>
<datatype extension="ndpi" type="galaxy.datatypes.images:Hamamatsu" subclass="true" display_in_upload="false"/>
<datatype extension="mrxs" type="galaxy.datatypes.images:Mirax" mimetype="image/mirax"/>
<datatype extension="svslide" type="galaxy.datatypes.images:Sakura" mimetype="image/sakura"/>
<datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/>
<datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/>
<datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/>
<datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/>
<datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/>
<datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/>
<datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/>
<datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/>
<datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
<datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
<datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
<datatype extension="nrrd" type="galaxy.datatypes.images:Nrrd" mimetype="image/nrrd"/>
<datatype extension="nhdr" type="galaxy.datatypes.images:Nrrd" subclass="true"/>
<datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="true"/>
<datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true"/>
<datatype extension="tar" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
<converter file="tar_to_directory.xml" target_datatype="directory"/>
</datatype>
<datatype extension="directory" type="galaxy.datatypes.data:Directory">
</datatype>
<!-- Proteomics Datatypes -->
<datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="raw_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
<datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
<datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
<datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Transformation of retention times"/>
<datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
<datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
<datatype extension="protxml.tsv" type="galaxy.datatypes.proteomics:ProtXmlReport" display_in_upload="true"/>
<datatype extension="mascotdat" type="galaxy.datatypes.proteomics:MascotDat" display_in_upload="false"/>
<datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="tandem" type="galaxy.datatypes.proteomics:TandemXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="thermo.raw" type="galaxy.datatypes.proteomics:ThermoRAW" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="brukerbaf.d.tar" type="galaxy.datatypes.binary:BafTar" display_in_upload="true"/>
<datatype extension="agilentbrukeryep.d.tar" type="galaxy.datatypes.binary:YepTar" display_in_upload="true"/>
<datatype extension="brukertdf.d.tar" type="galaxy.datatypes.binary:TdfTar" display_in_upload="true"/>
<datatype extension="agilentmasshunter.d.tar" type="galaxy.datatypes.binary:MassHunterTar" display_in_upload="true"/>
<datatype extension="watersmasslynx.raw.tar" type="galaxy.datatypes.binary:MassLynxTar" display_in_upload="true"/>
<datatype extension="wiff.tar" type="galaxy.datatypes.binary:WiffTar" display_in_upload="true"/>
<datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
<datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
<datatype extension="wiff" type="galaxy.datatypes.proteomics:Wiff" display_in_upload="true"/>
<datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="mzdata" type="galaxy.datatypes.proteomics:MzData" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true"/>
<datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true"/>
<datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true"/>
<datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true"/>
<datatype extension="blib" type="galaxy.datatypes.binary:BlibSQlite" display_in_upload="true"/>
<datatype extension="hlf" type="galaxy.datatypes.proteomics:XHunterAslFormat" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="idpdb" type="galaxy.datatypes.binary:IdpDB" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="sf3" type="galaxy.datatypes.proteomics:Sf3" display_in_upload="true"/>
<datatype extension="cps" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true"/>
<datatype extension="ct" type="galaxy.datatypes.tabular:ConnectivityTable" display_in_upload="true"/>
<datatype extension="postgresql" type="galaxy.datatypes.binary:PostgresqlArchive" display_in_upload="True"/>
<datatype extension="searchgui_archive" type="galaxy.datatypes.binary:SearchGuiArchive" display_in_upload="true"/>
<datatype extension="fast5.tar" type="galaxy.datatypes.binary:Fast5Archive" display_in_upload="true"/>
<datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>
<datatype extension="fast5.tar.bz2" type="galaxy.datatypes.binary:Fast5ArchiveBz2" display_in_upload="true"/>
<datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<datatype extension="percin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true"/>
<datatype extension="hardklor" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="imzml" type="galaxy.datatypes.proteomics:ImzML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="analyze75" type="galaxy.datatypes.proteomics:Analyze75" mimetype="application/xml" display_in_upload="true"/>
<!-- End Proteomics Datatypes -->
<datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<datatype extension="netcdf" type="galaxy.datatypes.binary:NetCDF" mimetype="application/octet-stream" display_in_upload="true" description="Format used by netCDF software library for writing and reading chromatography-MS data files."/>
<datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
<datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
<datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
<datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true" description="Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.."/>
<datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true" description="TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated 'variable=value' pairs. There should be no white space surrounding the '='." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#MAF">
<converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
</datatype>
<datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
<display file="ucsc/maf_customtrack.xml"/>
</datatype>
<datatype extension="mtx" type="galaxy.datatypes.tabular:MatrixMarket" display_in_upload="true"/>
<datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="true">
<converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
</datatype>
<datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf" display_in_upload="true"/>
<datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true">
<converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
</datatype>
<datatype extension="obo" type="galaxy.datatypes.text:Obo" mimetype="text/html" display_in_upload="true"/>
<datatype extension="owl" type="galaxy.datatypes.xml:Owl" mimetype="text/html" display_in_upload="true"/>
<datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
<datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore"/>
<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
<datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/>
<datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
<datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
<datatype extension="roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
<datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
<converter file="sam_to_unsorted_bam.xml" target_datatype="unsorted.bam"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
<converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
</datatype>
<datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/>
<datatype extension="sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
<datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="true"/>
<datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="true"/>
<datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true">
<converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/>
</datatype>
<datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/>
<datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true" description="A binary file archive format from the NCBI Sequence Read Archive with a '.sra' file extension." description_url="http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure"/>
<datatype extension="svg" type="galaxy.datatypes.xml:GenericXml" mimetype="image/svg+xml" subclass="true"/>
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29">
<converter file="tabular_to_csv.xml" target_datatype="csv"/>
</datatype>
<datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>
<datatype extension="gafa.sqlite" type="galaxy.datatypes.binary:GAFASQLite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/>
<datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/>
<datatype extension="memepsp" type="galaxy.datatypes.sequence:MemePsp" display_in_upload="true" description="The MEME Position Specific Priors (PSP) format includes the name of the sequence for which a prior distribution corresponds." description_url="http://meme-suite.org/doc/psp-format.html"/>
<datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
<converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/>
<converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<display file="ucsc/vcf.xml"/>
<display file="igv/vcf.xml"/>
<display file="rviewer/vcf.xml" inherit="true"/>
<display file="iobio/vcf.xml"/>
</datatype>
<datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="true">
<converter file="bcf_to_bcf_uncompressed_converter.xml" target_datatype="bcf_uncompressed"/>
</datatype>
<!-- bcf_bgzip is just an alias for bcf for backward-compatibility -->
<datatype extension="bcf_bgzip" type="galaxy.datatypes.binary:Bcf" subclass="true"/>
<datatype extension="bcf_uncompressed" type="galaxy.datatypes.binary:BcfUncompressed" mimetype="application/octet-stream">
<converter file="bcf_uncompressed_to_bcf_converter.xml" target_datatype="bcf"/>
</datatype>
<datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="true"/>
<datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig">
<converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
<!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
<display file="igb/wig.xml"/>
</datatype>
<datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
<datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
<datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
<datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
<display file="igv/vcf.xml"/>
<converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>
</datatype>
<datatype extension="kallisto.ec" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
<datatype extension="kallisto.idx" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
<!-- Phylogenetic tree datatypes -->
<datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true"/>
<datatype extension="newick" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
<datatype extension="nhx" type="galaxy.datatypes.data:Newick" subclass="true" display_in_upload="true"/>
<datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true"/>
<datatype extension="iqtree" type="galaxy.datatypes.text:IQTree"/>
<datatype extension="mldist" type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
<!-- Start RGenetics Datatypes -->
<datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
<!-- eigenstrat pedigree input file -->
<datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
<!-- eigenstrat pca output file for adjusted eigenQTL eg -->
<datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
<datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true"/>
<!-- fbat/pbat format pedigree (header row of marker names) -->
<datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
<!-- phenotype file - fbat format -->
<datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
<!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
<datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
<!-- part of linkage format pedigree -->
<!-- information redundancy (LD) filtered plink pbed -->
<datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true">
</datatype>
<datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
<!-- linkage format pedigree (separate .map file) -->
<datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
<converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
<converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
</datatype>
<!-- plink compressed file - has bed extension unfortunately -->
<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
<converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
<converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/>
</datatype>
<datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
<!-- phenotype file - plink format -->
<datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/>
<datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
<datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
<datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
<!-- deprecated, should use excel.xls -->
<datatype extension="xls" type="galaxy.datatypes.binary:ExcelXls"/>
<!-- End RGenetics Datatypes -->
<datatype extension="ipynb" type="galaxy.datatypes.text:Ipynb" display_in_upload="true"/>
<datatype extension="json" type="galaxy.datatypes.text:Json" display_in_upload="true"/>
<datatype extension="expression.json" type="galaxy.datatypes.text:ExpressionJson" display_in_upload="true"/>
<!-- graph datatypes -->
<datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/>
<datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/>
<!-- datatypes storing triples -->
<datatype extension="triples" type="galaxy.datatypes.triples:Triples" display_in_upload="false"/>
<datatype extension="hdt" type="galaxy.datatypes.triples:HDT" display_in_upload="true"/>
<datatype extension="nt" type="galaxy.datatypes.triples:NTriples" display_in_upload="true"/>
<datatype extension="n3" type="galaxy.datatypes.triples:N3" display_in_upload="true"/>
<datatype extension="ttl" type="galaxy.datatypes.triples:Turtle" display_in_upload="true"/>
<datatype extension="rdf" type="galaxy.datatypes.triples:Rdf" display_in_upload="true"/>
<datatype extension="jsonld" type="galaxy.datatypes.triples:Jsonld" display_in_upload="true"/>
<!-- Excel datatypes -->
<datatype extension="excel.xls" type="galaxy.datatypes.binary:ExcelXls" display_in_upload="true"/>
<datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true"/>
<datatype extension="btwisted" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cai" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="charge" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="checktrans" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="chips" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="codcmp" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="coderet" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="compseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cpgplot" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cpgreport" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cusp" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cut" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="dan" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="digest" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="dreg" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="einverted" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="epestfind" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="equicktandem" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="est2genome" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="etandem" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="freak" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="hmoment" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="isochore" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="match" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="nametable" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="needle" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="newcpgreport" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="newcpgseek" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="noreturn" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="palindrome" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pepcoil" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pepinfo" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pepstats" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="polydot" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="preg" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="prettyseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="primersearch" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="showfeat" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="showorf" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="sixpack" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="strider" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="supermatcher" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="syco" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="textsearch" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="vectorstrip" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="wobble" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="wordcount" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Report formats http://emboss.sourceforge.net/docs/themes/ReportFormats.html -->
<datatype extension="dbmotif" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="diffseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="excel" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="feattable" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="motif" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="regions" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="seqtable" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="simple" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="table" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="tagseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Sequence formats http://emboss.sourceforge.net/docs/themes/SequenceFormats.html -->
<datatype extension="acedb" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="clustal" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="codata" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="genbank" auto_compressed_types="gz" sniff_compressed_types="true" type="galaxy.datatypes.sequence:Genbank" display_in_upload="True"/>
<datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="jackknifernon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="mega" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="meganon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="ncbi" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="nexus" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="nexusnon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="phylip" type="galaxy.datatypes.phylip:Phylip" display_in_upload="true"/>
<datatype extension="phylipnon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pir" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="staden" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="swiss" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Alignment Formats http://emboss.sourceforge.net/docs/themes/AlignFormats.html -->
<datatype extension="markx0" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx1" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx10" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx2" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx3" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pair" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="score" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="srs" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="srspair" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Annotation Datatypes -->
<datatype extension="snaphmm" type="galaxy.datatypes.annotation:SnapHmm" display_in_upload="true"/>
<datatype extension="augustus" type="galaxy.datatypes.annotation:Augustus" display_in_upload="true"/>
<datatype extension="icm" type="galaxy.datatypes.binary:ICM" display_in_upload="true"/>
<!-- MSA Datatypes -->
<datatype extension="cm" type="galaxy.datatypes.msa:InfernalCM" display_in_upload="False"/>
<datatype extension="hmm2" type="galaxy.datatypes.msa:Hmmer2" display_in_upload="true"/>
<datatype extension="hmm3" type="galaxy.datatypes.msa:Hmmer3" display_in_upload="true"/>
<datatype extension="stockholm" type="galaxy.datatypes.msa:Stockholm_1_0" display_in_upload="true"/>
<datatype extension="xmfa" type="galaxy.datatypes.msa:MauveXmfa" display_in_upload="true"/>
<datatype extension="cel" type="galaxy.datatypes.microarrays:Cel" display_in_upload="true"/>
<datatype extension="gpr" type="galaxy.datatypes.microarrays:Gpr" display_in_upload="true"/>
<datatype extension="gal" type="galaxy.datatypes.microarrays:Gal" display_in_upload="true"/>
<datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
<datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" display_in_upload="true"/>
<datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxlits" type="galaxy.datatypes.binary:OxliTagSet" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxlist" type="galaxy.datatypes.binary:OxliStopTags" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxliss" type="galaxy.datatypes.binary:OxliSubset" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxligl" type="galaxy.datatypes.binary:OxliGraphLabels" mimetype="application/octet-stream" display_in_upload="true"/>
<!-- Constructive solid geometry datatypes -->
<datatype extension="stl" type="galaxy.datatypes.constructive_solid_geometry:STL" display_in_upload="true"/>
<datatype extension="plyascii" type="galaxy.datatypes.constructive_solid_geometry:PlyAscii" display_in_upload="true"/>
<datatype extension="plybinary" type="galaxy.datatypes.constructive_solid_geometry:PlyBinary" display_in_upload="true"/>
<datatype extension="vtkascii" type="galaxy.datatypes.constructive_solid_geometry:VtkAscii" display_in_upload="true"/>
<datatype extension="vtkbinary" type="galaxy.datatypes.constructive_solid_geometry:VtkBinary" display_in_upload="true"/>
<!-- Metagenomic Datatypes -->
<datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="true" mimetype="application/json">
<display file="biom/biom_simple.xml"/>
<converter file="biom1_to_biom2.xml" target_datatype="biom2"/>
</datatype>
<datatype extension="biom2" type="galaxy.datatypes.binary:Biom2" mimetype="application/octet-stream" display_in_upload="true">
<converter file="biom2_to_biom1.xml" target_datatype="biom1"/>
</datatype>
<datatype extension="msh" type="galaxy.datatypes.binary:MashSketch" display_in_upload="True" />
<!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
<datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true"/>
<!--Cheminformatics Datatypes -->
<datatype extension="smi" type="galaxy.datatypes.molecules:SMILES" display_in_upload="true">
<!-- The ordering is important. The first one is considered as default converter in the build-in conversion function -> (as sdf)-->
<converter file="smi_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="smi_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="smi_to_cml_converter.xml" target_datatype="cml"/>
<converter file="smi_to_mol_converter.xml" target_datatype="mol"/>
<converter file="smi_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="smi_to_smi_converter.xml" target_datatype="smi"/>
</datatype>
<datatype extension="sdf" type="galaxy.datatypes.molecules:SDF" display_in_upload="true">
<converter file="sdf_to_smi_converter.xml" target_datatype="smi"/>
<converter file="sdf_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="sdf_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="sdf_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="inchi" type="galaxy.datatypes.molecules:InChI" display_in_upload="true">
<converter file="inchi_to_smi_converter.xml" target_datatype="smi"/>
<converter file="inchi_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="inchi_to_mol_converter.xml" target_datatype="mol"/>
<converter file="inchi_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="inchi_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="mol" type="galaxy.datatypes.molecules:MOL" display_in_upload="true">
<converter file="mol_to_smi_converter.xml" target_datatype="smi"/>
<converter file="mol_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="mol_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="mol_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="mol2" type="galaxy.datatypes.molecules:MOL2" display_in_upload="false">
<converter file="mol2_to_smi_converter.xml" target_datatype="smi"/>
<converter file="mol2_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="mol2_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="mol2_to_mol_converter.xml" target_datatype="mol"/>
<converter file="mol2_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="cml" type="galaxy.datatypes.molecules:CML" display_in_upload="true">
<converter file="cml_to_smi_converter.xml" target_datatype="smi"/>
<converter file="cml_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="cml_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="cml_to_mol2_converter.xml" target_datatype="mol2"/>
</datatype>
<datatype extension="fps" type="galaxy.datatypes.molecules:FPS" mimetype="text/html" display_in_upload="true"/>
<datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="true"/>
<datatype extension="drf" type="galaxy.datatypes.molecules:DRF" display_in_upload="true"/>
<datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="false"/>
<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="true"/>
<datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
<datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
<datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true"/>
<datatype extension="dcd" type="galaxy.datatypes.binary:Dcd" display_in_upload="true"/>
<datatype extension="top" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="itp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="mdp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="xtc" type="galaxy.datatypes.binary:Xtc" display_in_upload="true"/>
<datatype extension="cpt" type="galaxy.datatypes.binary:Cpt" display_in_upload="true"/>
<datatype extension="gro" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="vel" type="galaxy.datatypes.binary:Vel" display_in_upload="true"/>
<datatype extension="grd" type="galaxy.datatypes.molecules:grd" display_in_upload="true"/>
<datatype extension="grd.tgz" type="galaxy.datatypes.molecules:grdtgz" display_in_upload="true"/>
<!-- mothur formats -->
<datatype extension="mothur.otu" type="galaxy.datatypes.mothur:Otu" display_in_upload="true"/>
<datatype extension="mothur.list" type="galaxy.datatypes.mothur:Otu" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.sabund" type="galaxy.datatypes.mothur:Sabund" display_in_upload="true"/>
<datatype extension="mothur.rabund" type="galaxy.datatypes.mothur:Sabund" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.shared" type="galaxy.datatypes.mothur:GroupAbund" display_in_upload="true"/>
<datatype extension="mothur.relabund" type="galaxy.datatypes.mothur:GroupAbund" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.names" type="galaxy.datatypes.mothur:Names" display_in_upload="true"/>
<datatype extension="mothur.design" type="galaxy.datatypes.mothur:Group" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.summary" type="galaxy.datatypes.mothur:Summary" display_in_upload="true"/>
<datatype extension="mothur.groups" type="galaxy.datatypes.mothur:Group" display_in_upload="true"/>
<datatype extension="mothur.oligos" type="galaxy.datatypes.mothur:Oligos" display_in_upload="true"/>
<datatype extension="mothur.align" type="galaxy.datatypes.sequence:Fasta" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.accnos" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="mothur.otulabels" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="mothur.otu.corr" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.map" type="galaxy.datatypes.mothur:SecondaryStructureMap" display_in_upload="true"/>
<datatype extension="mothur.align.check" type="galaxy.datatypes.mothur:AlignCheck" display_in_upload="true"/>
<datatype extension="mothur.align.report" type="galaxy.datatypes.mothur:AlignReport" display_in_upload="true"/>
<datatype extension="mothur.filter" type="galaxy.datatypes.mothur:LaneMask" display_in_upload="true"/>
<datatype extension="mothur.dist" type="galaxy.datatypes.mothur:DistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.tre" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.pair.dist" type="galaxy.datatypes.mothur:PairwiseDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.square.dist" type="galaxy.datatypes.mothur:SquareDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.lower.dist" type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.ref.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" display_in_upload="true">
<converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="mothur.seq.taxonomy"/>
</datatype>
<datatype extension="mothur.seq.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.rdp.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.cons.taxonomy" type="galaxy.datatypes.mothur:ConsensusTaxonomy" display_in_upload="true"/>
<datatype extension="mothur.tax.summary" type="galaxy.datatypes.mothur:TaxonomySummary" display_in_upload="true"/>
<datatype extension="mothur.freq" type="galaxy.datatypes.mothur:Frequency" display_in_upload="true"/>
<datatype extension="mothur.quan" type="galaxy.datatypes.mothur:Quantile" display_in_upload="true"/>
<datatype extension="mothur.filtered.quan" type="galaxy.datatypes.mothur:Quantile" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.filtered.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.axes" type="galaxy.datatypes.mothur:Axes" display_in_upload="true"/>
<datatype extension="mothur.sff.flow" type="galaxy.datatypes.mothur:SffFlow" display_in_upload="true"/>
<datatype extension="mothur.count_table" type="galaxy.datatypes.mothur:CountTable" display_in_upload="true"/>
<datatype extension="neostore" type="galaxy.datatypes.neo4j:Neo4jDB" mimetype="text/html" display_in_upload="false"/>
<datatype extension="neostore.zip" type="galaxy.datatypes.neo4j:Neo4jDBzip" display_in_upload="true">
<converter file="neostorezip_to_neostore_converter.xml" target_datatype="neostore"/>
</datatype>
<datatype extension="trackhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
<display file="ucsc/trackhub.xml"/>
</datatype>
<datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
<datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
<datatype extension="blastdbd" type="galaxy.datatypes.blast:BlastDomainDb" mimetype="text/html" display_in_upload="false"/>
<datatype extension="maskinfo-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true"/>
<datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true"/>
<datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true"/>
<!-- PlantTribes datatypes -->
<!--
The commented entries in this section are required by versions 1.0.0, 1.0.1 and 1.0.2 of the
PlantTribes tools in the MTS Phylogenetics category, and are not required by version 1.0.3 of
later. These datatypes will be removed in a future Galaxy release.
-->
<!--
<datatype extension="ptalign" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment" />
<datatype extension="ptalignca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment" />
<datatype extension="ptaligntrimmed" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed" />
<datatype extension="ptaligntrimmedca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment" />
<datatype extension="ptalignfiltered" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered" />
<datatype extension="ptalignfilteredca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment" />
-->
<datatype extension="ptkscmp" type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents" display_in_upload="true"/>
<!--
<datatype extension="ptortho" type="galaxy.datatypes.plant_tribes:PlantTribesOrtho" />
<datatype extension="ptorthocs" type="galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence" />
<datatype extension="ptphylip" type="galaxy.datatypes.plant_tribes:PlantTribesPhylip" />
<datatype extension="pttgf" type="galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies" />
<datatype extension="pttree" type="galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree" />
-->
<datatype extension="smat" type="galaxy.datatypes.plant_tribes:Smat" display_in_upload="true"/>
<!-- Start Haplotype / LOD Datatypes -->
<datatype extension="alohomora_gts" type="galaxy.datatypes.genetics:GenotypeMatrix"/>
<datatype extension="alohomora_map" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="alohomora_maf" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="alohomora_ped" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<!-- Common input formats: Generated by alohomora, but user may also upload these manually -->
<datatype extension="linkage_pedin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="linkage_datain" type="galaxy.datatypes.genetics:DataIn"/>
<datatype extension="linkage_map" type="galaxy.datatypes.genetics:MarkerMap"/>
<!-- All output linkage is converted into the Allegro output format -->
<datatype extension="allegro_ihaplo" type="galaxy.datatypes.tabular:Tabular"/>
<datatype extension="allegro_descent" type="galaxy.datatypes.tabular:Tabular"/>
<datatype extension="allegro_fparam" type="galaxy.datatypes.genetics:AllegroLOD"/>
<!-- IDEAS datatypes -->
<datatype extension="ideaspre" type="galaxy.datatypes.genetics:IdeasPre" display_in_upload="true"/>
<!-- End IDEAS datatypes -->
<datatype extension="sbml" type="galaxy.datatypes.xml:Sbml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="spalndbnp" type="galaxy.datatypes.spaln:SpalnNuclDb" display_in_upload="true" />
<datatype extension="spalndba" type="galaxy.datatypes.spaln:SpalnProtDb" display_in_upload="true" />
<datatype extension="dada2_derep" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
<datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
<datatype extension="ckpt" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
</registration>
<sniffers>
<!--
The order in which Galaxy attempts to determine data types is
important because some formats are much more loosely defined
than others. The following list should be the most rigidly
defined format first, followed by next-most rigidly defined,
and so on.
-->
<sniffer type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents"/>
<sniffer type="galaxy.datatypes.plant_tribes:Smat"/>
<sniffer type="galaxy.datatypes.mothur:Sabund"/>
<sniffer type="galaxy.datatypes.mothur:Otu"/>
<sniffer type="galaxy.datatypes.mothur:GroupAbund"/>
<sniffer type="galaxy.datatypes.mothur:SecondaryStructureMap"/>
<sniffer type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix"/>
<sniffer type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
<sniffer type="galaxy.datatypes.mothur:PairwiseDistanceMatrix"/>
<sniffer type="galaxy.datatypes.mothur:Oligos"/>
<sniffer type="galaxy.datatypes.mothur:Quantile"/>
<sniffer type="galaxy.datatypes.mothur:Frequency"/>
<sniffer type="galaxy.datatypes.mothur:LaneMask"/>
<sniffer type="galaxy.datatypes.mothur:RefTaxonomy"/>
<sniffer type="galaxy.datatypes.mothur:Axes"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
<sniffer type="galaxy.datatypes.interval:ScIdx"/>
<sniffer type="galaxy.datatypes.tabular:Vcf"/>
<sniffer type="galaxy.datatypes.binary:TwoBit"/>
<sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
<sniffer type="galaxy.datatypes.binary:MzSQlite"/>
<sniffer type="galaxy.datatypes.binary:IdpDB"/>
<sniffer type="galaxy.datatypes.binary:BlibSQlite"/>
<sniffer type="galaxy.datatypes.binary:CuffDiffSQlite"/>
<sniffer type="galaxy.datatypes.binary:GAFASQLite"/>
<sniffer type="galaxy.datatypes.binary:SQlite"/>
<sniffer type="galaxy.datatypes.binary:Cool"/>
<sniffer type="galaxy.datatypes.binary:MCool"/>
<sniffer type="galaxy.datatypes.binary:Loom"/>
<sniffer type="galaxy.datatypes.binary:Anndata"/>
<sniffer type="galaxy.datatypes.binary:Biom2"/>
<sniffer type="galaxy.datatypes.binary:H5"/>
<sniffer type="galaxy.datatypes.binary:Bam"/>
<sniffer type="galaxy.datatypes.binary:BamQuerynameSorted"/>
<sniffer type="galaxy.datatypes.binary:BamNative"/>
<sniffer type="galaxy.datatypes.binary:CRAM"/>
<sniffer type="galaxy.datatypes.binary:Sff"/>
<sniffer type="galaxy.datatypes.binary:Sra"/>
<sniffer type="galaxy.datatypes.binary:NetCDF"/>
<sniffer type="galaxy.datatypes.binary:DAA"/>
<sniffer type="galaxy.datatypes.binary:RMA6"/>
<sniffer type="galaxy.datatypes.binary:DMND"/>
<sniffer type="galaxy.datatypes.binary:BafTar"/>
<sniffer type="galaxy.datatypes.binary:TdfTar"/>
<sniffer type="galaxy.datatypes.binary:MassHunterTar"/>
<sniffer type="galaxy.datatypes.binary:MassLynxTar"/>
<sniffer type="galaxy.datatypes.binary:YepTar"/>
<sniffer type="galaxy.datatypes.binary:WiffTar"/>
<sniffer type="galaxy.datatypes.binary:Fast5ArchiveGz"/>
<sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>
<sniffer type="galaxy.datatypes.binary:Fast5Archive"/>
<sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>
<sniffer type="galaxy.datatypes.binary:ICM"/>
<sniffer type="galaxy.datatypes.binary:Idat"/>
<sniffer type="galaxy.datatypes.binary:Trr"/>
<sniffer type="galaxy.datatypes.binary:Dcd"/>
<sniffer type="galaxy.datatypes.binary:Xtc"/>
<sniffer type="galaxy.datatypes.binary:Cpt"/>
<sniffer type="galaxy.datatypes.binary:Vel"/>
<sniffer type="galaxy.datatypes.annotation:Augustus"/>
<sniffer type="galaxy.datatypes.triples:Rdf"/>
<sniffer type="galaxy.datatypes.blast:BlastXml"/>
<sniffer type="galaxy.datatypes.xml:Phyloxml"/>
<sniffer type="galaxy.datatypes.xml:Owl"/>
<sniffer type="galaxy.datatypes.xml:Sbml"/>
<sniffer type="galaxy.datatypes.proteomics:MzML"/>
<sniffer type="galaxy.datatypes.proteomics:NmrML"/>
<sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
<sniffer type="galaxy.datatypes.proteomics:PepXml"/>
<sniffer type="galaxy.datatypes.proteomics:Mgf"/>
<sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
<sniffer type="galaxy.datatypes.proteomics:MzXML"/>
<sniffer type="galaxy.datatypes.proteomics:MzData"/>
<sniffer type="galaxy.datatypes.proteomics:TraML"/>
<sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
<sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
<sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
<sniffer type="galaxy.datatypes.proteomics:Msp"/>
<sniffer type="galaxy.datatypes.proteomics:SPLib"/>
<sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
<sniffer type="galaxy.datatypes.molecules:CML"/>
<sniffer type="galaxy.datatypes.xml:GenericXml"/>
<sniffer type="galaxy.datatypes.triples:HDT"/>
<sniffer type="galaxy.datatypes.triples:Turtle"/>
<sniffer type="galaxy.datatypes.triples:NTriples"/>
<sniffer type="galaxy.datatypes.triples:Jsonld"/>
<sniffer type="galaxy.datatypes.sequence:Maf"/>
<sniffer type="galaxy.datatypes.sequence:Lav"/>
<sniffer type="galaxy.datatypes.sequence:MemePsp"/>
<sniffer type="galaxy.datatypes.sequence:Fastg"/>
<sniffer type="galaxy.datatypes.sequence:csFasta"/>
<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
<sniffer type="galaxy.datatypes.molecules:SDF"/>
<sniffer type="galaxy.datatypes.molecules:PDB"/>
<sniffer type="galaxy.datatypes.molecules:MOL2"/>
<sniffer type="galaxy.datatypes.molecules:InChI"/>
<sniffer type="galaxy.datatypes.molecules:FPS"/>
<sniffer type="galaxy.datatypes.molecules:PQR"/>
<!-- TODO: see molecules.py <sniffer type="galaxy.datatypes.molecules:SMILES"/>-->
<sniffer type="galaxy.datatypes.phylip:Phylip"/>
<sniffer type="galaxy.datatypes.sequence:Fasta"/>
<sniffer type="galaxy.datatypes.sequence:FastqCSSanger"/>
<sniffer type="galaxy.datatypes.sequence:FastqSanger"/>
<sniffer type="galaxy.datatypes.sequence:Fastq"/>
<sniffer type="galaxy.datatypes.interval:Wiggle"/>
<sniffer type="galaxy.datatypes.text:Html"/>
<sniffer type="galaxy.datatypes.images:Pdf"/>
<sniffer type="galaxy.datatypes.sequence:Axt"/>
<sniffer type="galaxy.datatypes.sequence:Genbank"/>
<sniffer type="galaxy.datatypes.interval:Bed"/>
<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
<sniffer type="galaxy.datatypes.interval:Gtf"/>
<sniffer type="galaxy.datatypes.interval:Gff"/>
<sniffer type="galaxy.datatypes.interval:Gff3"/>
<sniffer type="galaxy.datatypes.tabular:Pileup"/>
<sniffer type="galaxy.datatypes.interval:Interval"/>
<sniffer type="galaxy.datatypes.tabular:Sam"/>
<sniffer type="galaxy.datatypes.data:Newick"/>
<sniffer type="galaxy.datatypes.data:Nexus"/>
<sniffer type="galaxy.datatypes.text:IQTree"/>
<sniffer type="galaxy.datatypes.text:Obo"/>
<sniffer type="galaxy.datatypes.text:Arff"/>
<sniffer type="galaxy.datatypes.text:Ipynb"/>
<sniffer type="galaxy.datatypes.text:Biom1"/>
<sniffer type="galaxy.datatypes.text:ImgtJson"/>
<sniffer type="galaxy.datatypes.text:GeoJson"/>
<sniffer type="galaxy.datatypes.text:Json"/>
<sniffer type="galaxy.datatypes.genetics:GenotypeMatrix"/>
<sniffer type="galaxy.datatypes.genetics:DataIn"/>
<sniffer type="galaxy.datatypes.genetics:MarkerMap"/>
<sniffer type="galaxy.datatypes.genetics:AllegroLOD"/>
<sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/>
<sniffer type="galaxy.datatypes.sequence:DotBracket"/>
<sniffer type="galaxy.datatypes.tabular:ConnectivityTable"/>
<sniffer type="galaxy.datatypes.tabular:CSV"/>
<sniffer type="galaxy.datatypes.tabular:TSV"/>
<sniffer type="galaxy.datatypes.tabular:MatrixMarket"/>
<sniffer type="galaxy.datatypes.msa:Hmmer2"/>
<sniffer type="galaxy.datatypes.msa:Hmmer3"/>
<sniffer type="galaxy.datatypes.msa:Stockholm_1_0"/>
<sniffer type="galaxy.datatypes.msa:MauveXmfa"/>
<sniffer type="galaxy.datatypes.msa:InfernalCM"/>
<sniffer type="galaxy.datatypes.annotation:SnapHmm"/>
<sniffer type="galaxy.datatypes.microarrays:Cel"/>
<sniffer type="galaxy.datatypes.microarrays:Gpr"/>
<sniffer type="galaxy.datatypes.microarrays:Gal"/>
<sniffer type="galaxy.datatypes.binary:RData"/>
<sniffer type="galaxy.datatypes.images:Jpg"/>
<sniffer type="galaxy.datatypes.images:Png"/>
<sniffer type="galaxy.datatypes.images:Tiff"/>
<sniffer type="galaxy.datatypes.images:Bmp"/>
<sniffer type="galaxy.datatypes.images:Gif"/>
<sniffer type="galaxy.datatypes.images:Im"/>
<sniffer type="galaxy.datatypes.images:Pcd"/>
<sniffer type="galaxy.datatypes.images:Pcx"/>
<sniffer type="galaxy.datatypes.images:Ppm"/>
<sniffer type="galaxy.datatypes.images:Psd"/>
<sniffer type="galaxy.datatypes.images:Xbm"/>
<sniffer type="galaxy.datatypes.images:Rgb"/>
<sniffer type="galaxy.datatypes.images:Pbm"/>
<sniffer type="galaxy.datatypes.images:Pgm"/>
<sniffer type="galaxy.datatypes.images:Xpm"/>
<sniffer type="galaxy.datatypes.images:Eps"/>
<sniffer type="galaxy.datatypes.images:Rast"/>
<!--
Keep this commented until the sniff method in the assembly.py
module is fixed to not read the entire file.
<sniffer type="galaxy.datatypes.assembly:Amos"/>
-->
<sniffer type="galaxy.datatypes.binary:OxliCountGraph"/>
<sniffer type="galaxy.datatypes.binary:OxliNodeGraph"/>
<sniffer type="galaxy.datatypes.binary:OxliTagSet"/>
<sniffer type="galaxy.datatypes.binary:OxliStopTags"/>
<sniffer type="galaxy.datatypes.binary:OxliSubset"/>
<sniffer type="galaxy.datatypes.binary:OxliGraphLabels"/>
<sniffer type="galaxy.datatypes.neo4j:Neo4jDBzip"/>
</sniffers>
</datatypes>
config/datatypes_conf.xml.sample
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<dependency_resolvers>
<!-- the default configuration, first look for dependencies installed from the toolshed -->
<tool_shed_packages />
<!-- then look for env.sh files in directories according to the "galaxy packages" schema.
These resolvers can take a base_path attribute to specify where to look for
package definitions, but by default look in the directory specified by tool_dependency_dir
in Galaxy's config/galaxy.ini -->
<galaxy_packages />
<!-- check whether the correct version has been installed via conda -->
<conda />
<!-- look for a "default" symlink pointing to a directory containing an
env.sh file for the package in the "galaxy packages" schema -->
<galaxy_packages versionless="true" />
<!-- look for any version of the dependency installed via conda -->
<conda versionless="true" />
<!-- LMOD dependency resolver (For the LMOD environment modules system - https://github.com/TACC/Lmod) -->
<!--
The LMOD dependency resolver attributes are:
* lmodexec - Path to the lmod executable on your system - Default: value of the "LMOD_CMD" environment variable
* settargexec - Path to the settarg executable on your system - Default: value of the "LMOD_SETTARG_CMD" environment variable
* modulepath - Path to the folder that contains the LMOD module files on your system - Default: value of the "MODULEPATH" environment variable
* versionless - Set it to true to resolve a dependency based on its name only (the version number is ignored) - Default: false
* mapping_files - Path to a Yaml configuration file that can be used to link tools requirements with existing LMOD modules - Default: config/lmod_modules_mapping.yml
Important notes:
- All the above attributes are optional
- The value of the lmodexec attribute can't just be "module" because module is actually a bash function and not the real LMOD binary (see the result of the "type module" command)
- The value of the modulepath attribute can also be a semicolon separated list of path
- In versionless mode, only modules marked as Default will be listed by the "avail" command (The -d option is used)
- If the config folder of your Galaxy instance contains a file called "lmod_modules_mapping.yml" (based on the lmod_modules_mapping.yml.sample file) it will be taken into consideration automatically
-->
<!--
<lmod />
<lmod versionless="true" />
-->
<!-- Example configuration of modules dependency resolver, uses Environment Modules -->
<!--
<modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd" />
<modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd" versionless="true" default_indicator="default" />
Attributes are:
* modulecmd - path to modulecmd
* versionless - default: false - whether to resolve tools using a version number or not
* find_by - directory or avail - use the DirectoryModuleChecker or AvailModuleChecker
* prefetch - default: true - in the AvailModuleChecker prefetch module info with 'module avail'
* default_indicator - default: '(default)' - what indicate to the AvailModuleChecker that a module is the default version
-->
<!-- other resolvers
<tool_shed_tap />
<homebrew />
-->
</dependency_resolvers>
config/dependency_resolvers_conf.xml.sample
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If you want to disable registration for users that are using disposable email address
rename this file to disposable_email_blacklist.conf and fill it with the disposable domains
that you want to have blacklisted. Each on its own line without the '@' character as shown below.
Users using emails from these domains will get an error during the registration.
mailinator.com
sogetthis.com
spamgourmet.com
trashmail.net
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# This is an example mapping file for the module (http://modules.sourceforge.net/) Dependency resolver (in YAML format)
#
# The goal of this file is to map tool's requirements to existing modules available on your system
# Of course, if the name of a requirement and the name of a module match perfectly, there is no need to map them together through this mapping file.
#
# This is a sample file so the first thing to do to activate the mapping system is to create a copy of this file called "environment_modules_mapping.yml".
# The module dependency resolver is programmed to search and use this YAML file automatically if it exists in the "config" folder of your Galaxy instance.
# Alternatively, you can also use the "mapping_files" attribute of the <modules /> resolver in the dependency_resolvers_conf.xml file to specify a custom mapping file
#
# Example 1:
#
# Let's say that one of the wrapper installed on your Galaxy instance has the following requirement:
#
# <requirements>
# <requirement type="package" version="1.5.0">PIPITS</requirement>
# </requirements>
#
# But unfortunately, the name of the corresponding module file on your system is "pipits_pipeline/1.5.0"
#
# Then, to make Galaxy load/unload the appropriate module, you just have to add the following lines (without the #) to the "environment_modules_mapping.yml" file:
#
#- from:
# name: PIPITS
# version: 1.5.0
# to:
# name: pipits_pipeline
# version: 1.5.0.6
#
#
# Example 2:
#
# The requirements section specify a requirement on the PIPITS tool but do not ask for a specific version of it:
#
# <requirements>
# <requirement type="package">PIPITS</requirement>
# </requirements>
#
# Although, there is no version required you may want to force the loading of a version that is known to run well on your system.
#
# In that case you can add the following lines to the "environment_modules_mapping.yml" file:
#
#- from:
# name: PIPITS
# unversioned: true
# to:
# name: pipits_pipeline
# version: 1.4.0
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config/error_report.yml.sample
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# Each element in this file corresponds to a destination for an error
# report.
# If you supply the parameter ``user_submission``, and set it to True,
# this error plugin will only be activated when the user uses the bug
# report submission interface. Otherwise, it will be triggered without
# any user interaction (e.g. historical behaviour of sentry plugin)
# If your plugin is ``user_submission=True``, then supplying
# ``verbose=True`` will cause the plugin to display a message to the end
# user. E.g. the email plugin simply states "Your error report has been
# sent", or the JSON plugin informs the user "Wrote error report to ..."
# The plugins below are listed with their default values of
# verbose/user_submission, but those are not necessary to provide.
# The default Email bug reporter. By default, the standard
# configuration is taken from your galaxy.ini
- type: email
verbose: true
user_submission: true
# Example JSON bug reporter implementation. This just writes the bug
# report as a JSON file to a specified directory and serves as an
# example for others to extend.
# - type: json
# verbose: true
# user_submission: true
# directory: /tmp/reports/
# Submit error reports to sentry. If a sentry_dsn is configured in your
# galaxy.ini, then Galaxy will submit the job error to Sentry. You may supply a
# separate DSN for tool reports by supplying a ``custom_dsn`` parameter.
- type: sentry
user_submission: false
# InfluxDB error reporting backend. You will need to `pip install
# influxdb` in the galaxy virtualenv yourself. This sends well tagged
# errors InfluxDB allowing you to notice relationships between tool errors and
# other infrastructure issues.
# - type: influxdb
# # All arguments prefixed with `influxdb_` are per https://influxdb-python.readthedocs.io/en/latest/api-documentation.html#influxdbclient
# influxdb_host: 127.0.0.1
# influxdb_port: 8086
# influxdb_database: galaxy
# influxdb_timeout: 2
# Github error reporting backend. You will need to `pip install pygithub` in
# the galaxy virtualenv. This will create a new issue if none exists, and
# comment on existing, open issues. The issues are labelled based on tool ID /
# version and include all of the information the normal emailed bug reports
# include. If you use a private Github Enterprise deployment, you can set
# github_base_url='https://...' and github_api_url='https://api.....' as shown below.
# The 'github_default_repo_only' flag restores the previous behaviour. When this is set
# to true it will automatically only submit to the default git repository.
# - type: github
# verbose: false
# user_submission: true
# github_oauth_token: 00000000000
# github_base_url: https://github.com
# github_api_url: https://api.github.com
# github_default_repo_owner: galaxyproject
# github_default_repo_name: galaxy
# github_default_repo_only: true
# GitLab error reporting backend. You will need to `pip install python-gitlab`
# in the galaxy virtualenv. This will create a new issue if none exists, and
# comment on existing, open issues. The issues are labelled based on tool ID /
# version and include all of the information the normal emailed bug reports
# include. If you use a private GitLab deployment, you can set
# gitlab_base_url='https://...'. It supports creating an issue on the git
# repository of the tool by querying the ToolShed where the tool comes from
# (if applicable). Set verbose to true if you want the message to be displayed
# to the user. The 'gitlab_default_repo_only' flags ensures all errors are
# submitted to the default repository only.
# - type: gitlab
# verbose: false
# user_submission: true
# gitlab_base_url: https://gitlab.com
# gitlab_private_token: 00000000000
# gitlab_default_repo_owner: galaxyproject
# gitlab_default_repo_name: galaxy
# gitlab_default_repo_only: true
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<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
</plugins>
<destinations>
<destination id="local" runner="local"/>
</destinations>
</job_conf>
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<?xml version="1.0"?>
<!-- If job_metrics.xml exists, this file will define the default job metric
plugin used for all jobs. Individual job_conf.xml destinations can
disable metric collection by setting metrics="off" on that destination.
The metrics attribute on destination definition elements can also be
a path - in which case that XML metrics file will be loaded and used for
that destination. Finally, the destination element may contain a job_metrics
child element (with all options defined below) to define job metrics in an
embedded manner directly in the job_conf.xml file.
-->
<job_metrics>
<!-- Each element in this file corresponds to a job instrumentation plugin
used to generate metrics in lib/galaxy/jobs/metrics/instrumenters. -->
<!-- Core plugin captures Galaxy slots, start and end of job (in seconds
since epoch) and computes runtime in seconds. -->
<core />
<!-- Uncomment to dump processor count for each job - linux only. -->
<!-- <cpuinfo /> -->
<!-- Uncomment to dump information about all processors for for each
job - this is likely too much data. Linux only. -->
<!-- <cpuinfo verbose="true" /> -->
<!-- Uncomment to dump system memory information for each job - linux
only. -->
<!-- <meminfo /> -->
<!-- Uncomment to record operating system each job is executed on - linux
only. -->
<!-- <uname /> -->
<!-- Uncomment following to enable plugin dumping complete environment
for each job, potentially useful for debuging -->
<!-- <env /> -->
<!-- env plugin can also record more targetted, obviously useful variables
as well. -->
<!-- <env variables="HOSTNAME,SLURM_CPUS_ON_NODE,SLURM_JOBID" /> -->
<!-- If galaxy jobs are run in cgroups, like slurm does if memory limits
are enforced, we can try to grep some information from this. By default,
only a small set of cgroup parameters will be recorded, the list of which
can be found in lib/galaxy/jobs/metrics/instrumenters/cgroup.py. -->
<!-- <cgroup /> -->
<!-- All params from the `cpuacct,cpu` and `memory` controllers can be
recorded. -->
<!-- <cgroup verbose="true" /> -->
<!-- Or, specific params can be recorded. -->
<!-- <cgroup params="cpuacct.usage,memory.max_usage_in_bytes,memory.memsw.max_usage_in_bytes" /> -->
<!-- Uncomment to record hostname - *nix only -->
<!-- <hostname /> -->
<!-- <collectl /> -->
<!-- Collectl (http://collectl.sourceforge.net/) is a powerful monitoring
utility capable of gathering numerous system and process level
statistics of running applications. The Galaxy collectl job metrics
plugin by default will grab a variety of process level metrics
aggregated across all processes corresponding to a job, this behavior
is highly customiziable - both using the attributes documented below
or simply hacking up the code in lib/galaxy/jobs/metrics.
Warning: In order to use this plugin collectl must be available on the
compute server the job runs on and on the local Galaxy server as well
(unless in this latter case summarize_process_data is set to False).
Attributes (the follow describes attributes that can be used with
the collectl job metrics element above to modify its behavior).
'summarize_process_data': Boolean indicating whether to run collectl
in playback mode after jobs complete and gather process level
statistics for the job run. These statistics can be customized
with the 'process_statistics' attribute. (defaults to True)
'saved_logs_path': If set (it is off by default), all collectl logs
will be saved to the specified path after jobs complete. These
logs can later be replayed using collectl offline to generate
full time-series data corresponding to a job run.
'subsystems': Comma separated list of collectl subystems to collect
data for. Plugin doesn't currently expose all of them or offer
summary data for any of them except 'process' but extensions
would be welcome. May seem pointless to include subsystems
beside process since they won't be processed online by Galaxy -
but if 'saved_logs_path' these files can be played back at anytime.
Available subsystems - 'process', 'cpu', 'memory', 'network',
'disk', 'network'. (Default 'process').
Warning: If you override this - be sure to include 'process'
unless 'summarize_process_data' is set to false.
'process_statistics': If 'summarize_process_data' this attribute can be
specified as a comma separated list to override the statistics
that are gathered. Each statistics is of the for X_Y where X
if one of 'min', 'max', 'count', 'avg', or 'sum' and Y is a
value from 'S', 'VmSize', 'VmLck', 'VmRSS', 'VmData', 'VmStk',
'VmExe', 'VmLib', 'CPU', 'SysT', 'UsrT', 'PCT', 'AccumT' 'WKB',
'RKBC', 'WKBC', 'RSYS', 'WSYS', 'CNCL', 'MajF', 'MinF'. Consult
lib/galaxy/jobs/metrics/collectl/processes.py for more details
on what each of these resource types means.
Defaults to 'max_VmSize,avg_VmSize,max_VmRSS,avg_VmRSS,sum_SysT,sum_UsrT,max_PCT avg_PCT,max_AccumT,sum_RSYS,sum_WSYS'
as variety of statistics roughly describing CPU and memory
usage of the program and VERY ROUGHLY describing I/O consumption.
'procfilt_on': By default Galaxy will tell collectl to only collect
'process' level data for the current user (as identified)
by 'username' (default) - this can be disabled by settting this
to 'none' - the plugin will still only aggregate process level
statistics for the jobs process tree - but the additional
information can still be used offline with 'saved_logs_path'
if set. Obsecurely, this can also be set 'uid' to identify
the current user to filter on by UID instead of username -
this may needed on some clusters(?).
'interval': The time (in seconds) between data collection points.
Collectl uses a variety of different defaults for different
subsystems if this is not set, but process information (likely
the most pertinent for Galaxy jobs will collect data every
60 seconds).
'flush': Interval (in seconds I think) between when collectl will
flush its buffer to disk. Galaxy overrides this to disable
flushing by default if not set.
'local_collectl_path', 'remote_collectl_path', 'collectl_path':
By default, jobs will just assume collectl is on the PATH, but
it can be overridden with 'local_collectl_path' and
'remote_collectl_path' (or simply 'collectl_path' if it is not
on the path but installed in the same location both locally and
remotely).
There are more and more increasingly obsecure options including -
log_collectl_program_output, interval2, and interval3. Consult
source code for more details.
-->
</job_metrics>
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<parameters>
<param label="Processors" name="processors" type="integer" min="1" max="64" value="" help="Number of processing cores, 'ppn' value (1-64). Leave blank to use default value." />
<param label="Memory" name="memory" type="integer" min="1" max="256" value="" help="Memory size in gigabytes, 'pmem' value (1-256). Leave blank to use default value." />
<param label="Time" name="time" type="integer" min="1" max="744" value="" help="Maximum job time in hours, 'walltime' value (1-744). Leave blank to use default value." />
<param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value." />
</parameters>
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# This is an example mapping file for the LMOD Dependency resolver (in YAML format)
#
# The goal of this file is to map tool's requirements to existing LMOD modules available on your system
# Of course, if the name of a requirement and the name of a module match perfectly, there is no need to map them together through this mapping file.
#
# This is a sample file so the first thing to do to activate the mapping system is to create a copy of this file called "lmod_modules_mapping.yml".
# The Lmod dependency resolver is programmed to search and use this YAML file automatically if it exists in the "config" folder of your Galaxy instance.
# Alternatively, you can also use the "mapping_files" attribute of the <lmod /> resolver in the dependency_resolvers_conf.xml file to specify a custom mapping file
#
# Example 1:
#
# Let's say that one of the wrapper installed on your Galaxy instance has the following requirement:
#
# <requirements>
# <requirement type="package" version="1.5.0">PIPITS</requirement>
# </requirements>
#
# But unfortunately, the name of the corresponding module file on your system is "pipits_pipeline/1.5.0"
#
# Then, to make Galaxy load/unload the appropriate module, you just have to add the following lines (without to the #) to the "lmod_modules_mapping.yml" file:
#
#- from:
# name: PIPITS
# version: 1.5.0
# to:
# name: pipits_pipeline
# version: 1.5.0.6
#
#
# Example 2:
#
# The requirements section specify a requirement on the PIPITS tool but do not ask for a specific version of it:
#
# <requirements>
# <requirement type="package">PIPITS</requirement>
# </requirements>
#
# Although, there is no version required you may want to force the loading of a version that is known to run well on your system.
#
# In that case you can add the following lines to the "lmod_modules_mapping.yml" file:
#
#- from:
# name: PIPITS
# unversioned: true
# to:
# name: pipits_pipeline
# version: 1.4.0
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# See $GALAXY_ROOT/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml for example mapping -
# additional site-specific mappings can be added to config/local_conda_mapping.yml.
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<?xml version="1.0"?>
<toolbox tool_path="database/shed_tools">
</toolbox>
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<?xml version="1.0"?>
<object_store type="hierarchical">
<backends>
<object_store type="distributed" id="primary" order="0">
<backends>
<backend id="files1" type="disk" weight="1">
<files_dir path="database/files1"/>
<extra_dir type="temp" path="database/tmp1"/>
<extra_dir type="job_work" path="database/job_working_directory1"/>
</backend>
<backend id="files2" type="disk" weight="1">
<files_dir path="database/files2"/>
<extra_dir type="temp" path="database/tmp2"/>
<extra_dir type="job_work" path="database/job_working_directory2"/>
</backend>
</backends>
</object_store>
<object_store type="disk" id="secondary" order="1">
<files_dir path="database/files3"/>
<extra_dir type="temp" path="database/tmp3"/>
<extra_dir type="job_work" path="database/job_working_directory3"/>
</object_store>
<!-- Sample S3 Object Store
The "size" attribute of <cache> is in gigabytes.
-->
<!--
<object_store type="s3">
<auth access_key="...." secret_key="....." />
<bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" />
<cache path="database/object_store_cache" size="1000" />
<extra_dir type="job_work" path="database/job_working_directory_s3"/>
<extra_dir type="temp" path="database/tmp_s3"/>
</object_store>
-->
<!-- Sample Swift Object Store
The "size" attribute of <cache> is in gigabytes.
-->
<!--
<object_store type="swift">
<auth access_key="...." secret_key="....." />
<bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/>
<connection host="" port="" is_secure="" conn_path="" multipart="True"/>
<cache path="database/object_store_cache" size="1000" />
<extra_dir type="job_work" path="database/job_working_directory_swift"/>
<extra_dir type="temp" path="database/tmp_swift"/>
</object_store>
-->
<!-- Sample Azure Object Store
The "size" attribute of <cache> is in gigabytes.
-->
<!--
<object_store type="azure_blob">
<auth account_name="..." account_key="...." />
<container name="unique_container_name" max_chunk_size="250"/>
<cache path="database/object_store_cache" size="100" />
<extra_dir type="job_work" path="database/job_working_directory_azure"/>
<extra_dir type="temp" path="database/tmp_azure"/>
</object_store>
-->
<!-- Cloud ObjectStore: Amazon Simple Storage Service (S3)
The "size" attribute of <cache> is in gigabytes.
-->
<!--
<object_store type="cloud" provider="aws" order="0">
<auth access_key="..." secret_key="..." />
<bucket name="..." use_reduced_redundancy="False" />
<cache path="database/object_store_cache" size="100" />
<extra_dir type="job_work" path="database/job_working_directory_s3"/>
<extra_dir type="temp" path="database/tmp_s3"/>
</object_store>
-->
<!-- Cloud ObjectStore: Microsoft Azure Blob Storage
The "size" attribute of <cache> is in gigabytes.
-->
<!--
<object_store type="cloud" provider="azure" order="0">
<auth subscription_id="..." client_id="..." secret="..." tenant="..." />
<bucket name="..." use_reduced_redundancy="False" />
<cache path="database/object_store_cache" size="100" />
<extra_dir type="job_work" path="database/job_working_directory_azure"/>
<extra_dir type="temp" path="database/tmp_azure"/>
</object_store>
-->
<!-- Cloud ObjectStore: Google Compute Platform (GCP)
The "size" attribute of <cache> is in gigabytes.
-->
<!--
<object_store type="cloud" provider="google" order="0">
<auth credentials_file="..." />
<bucket name="..." use_reduced_redundancy="False" />
<cache path="database/object_store_cache" size="1000" />
<extra_dir type="job_work" path="database/job_working_directory_gcp"/>
<extra_dir type="temp" path="database/tmp_gcp"/>
</object_store>
-->
</backends>
</object_store>
config/object_store_conf.xml.sample
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config/oidc_backends_config.xml.sample
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<?xml version="1.0"?>
<!--
This file shall be properly set for user authentication and authorization leveraging the OpenID Connect protocol.
Here we provide a quick reference for configuration setters, and we provide a complete documentation
at the following page:
https://galaxyproject.org/authnz/config/oidc/
Quick Reference
_______________
- provider: Sets the name of OpenID Connect (OIDC) Identity Provider (IdP).
The following IdPs are currently supported:
{ "Google", "Globus" }
- client id: Sets the id of this client (i.e., your Galaxy instance) with the IdP, which is
obtained from the IdP at client registration.
See: https://tools.ietf.org/html/rfc6749#section-2.2
- client secret: A secret generated by IdP for your client upon its registration.
See https://tools.ietf.org/html/rfc6749#section-2.3.1
IMPORTANT NOTES
_______________
While registering your client (i.e., your Galaxy instance), you would need to provide the IdP with a
`redirect_uri`: a URL at which the IdP will callback your Galaxy instance upon a successful user authentication.
This URL for your Galaxy instance is composed as:
<host_url>/authnz/<provider>/callback
Some examples:
- using localhost to authenticate with Google:
http://localhost:8080/authnz/google/callback
- using localhost to authenticat with Globus:
http://localhost:8080/authnz/globus/callback
- using an instance hosted at `https://usegalaxy.org` with Google:
https://usegalaxy.org/authnz/google/callback
Please mind `http` and `https`.
-->
<OIDC>
<provider name="Google">
<client_id> ... </client_id>
<client_secret> ... </client_secret>
<redirect_uri>http://localhost:8080/authnz/google/callback</redirect_uri>
<prompt>consent</prompt>
<!--The value of this parameter (i.e., prompt) specifies whether the Google authorization server should prompt
a galaxy user for (re)authorization and consent. The possible values are: `none`, `consent`, and
`select_account`. HOWEVER, DO NOT USE `none`, because it will cause authentication failure for new users.
see the following page for more information:
https://developers.google.com/identity/protocols/OpenIDConnect#prompt
If you want the consent screen to be shown to the new users only, and re-authorization happen without
asking for user's consent, then remove this attribute.
NOTE: Galaxy sets OIDC 'scope' (requested scope of access to user's account) to `openid`. This is the
minimum scope value that request only user's email address and profile name. For login process Galaxy
does not need any more information, hence we request minimum possible information. By design, Google
does NOT show consent screen for this scope, hence user will only see a login page when they try to
login to Galaxy using their Google account.
-->
</provider>
<!-- Documentation: http://globus-integration-examples.readthedocs.io -->
<provider name="Globus">
<client_id> ... </client_id>
<client_secret> ... </client_secret>
<redirect_uri>http://localhost:8080/authnz/globus/callback</redirect_uri>
<prompt>consent</prompt>
</provider>
<provider name="Custos">
<url> ... </url>
<client_id> ... </client_id>
<client_secret> ... </client_secret>
<redirect_uri>http://localhost:8000/authnz/custos/callback</redirect_uri>
<realm> ... </realm>
<!-- (Optional) Trusted CA certificate file or directory to use when verify Custos authorization server.
See http://docs.python-requests.org/en/master/user/advanced/#ssl-cert-verification for more information. -->
<!-- <ca_bundle>/path/to/ca_bundle</ca_bundle> -->
<!-- (Optional) Override the default Custos well-known URL to point to a different instance -->
<!-- <well_known_oidc_config_uri>https://.../.well-known/openid-configuration</well_known_oidc_config_uri> -->
<!-- (Optional) Override the default idp hint -->
<!-- <idphint>cilogon</idphint> -->
</provider>
<!-- Documentation: https://galaxyproject.org/authnz/config/oidc/idps/elixir-aai -->
<provider name="Elixir">
<client_id>...</client_id>
<client_secret>...</client_secret>
<redirect_uri>http://localhost:8080/authnz/elixir/callback</redirect_uri>
<prompt>consent</prompt>
</provider>
</OIDC>
config/oidc_backends_config.xml.sample
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<?xml version="1.0"?>
<!--
Each Setter must have three attributes: Property, Value, and Type.
- Property: sets the name of a Python Social Auth (PSA) configuration attribute that its value is set by the setter.
- Value: sets a value for the property.
- Type: sets the type of the value. Galaxy uses the specified type to cast the values of string type to their actual
type. For instance, casts "False" -> False (string -> boolean). The value of the `Type` attribute should be a Python
built-in type, which could be any of the following types: int; long; float; str; tuple; list; and dict.
Note that the values of these attributes are case-sensitive.
-->
<OIDC>
<Setter Property="VERIFY_SSL" Value="False" Type="bool"/>
<Setter Property="REQUESTS_TIMEOUT" Value="3600" Type="float"/>
<!-- The unit of value is seconds -->
<Setter Property="ID_TOKEN_MAX_AGE" Value="3600" Type="float"/>
<!-- The unit of value is seconds -->
</OIDC>
config/oidc_config.xml.sample
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config/reports.yml.sample
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uwsgi:
# The address and port on which to listen. By default, only listen to
# localhost (reports will not be accessible over the network). Use
# ':9001' to listen on all available network interfaces.
http: 127.0.0.1:9001
# By default uWSGI allocates a very small buffer (4096 bytes) for the
# headers of each request. If you start receiving "invalid request
# block size" in your logs, it could mean you need a bigger buffer. We
# recommend at least 16384.
buffer-size: 16384
# Number of web server (worker) processes to fork after the
# application has loaded. If this is set to greater than 1, thunder-
# lock likely should be enabled below.
processes: 1
# Number of threads for each web server process.
threads: 4
# Number of threads for serving static content and handling internal
# routing requests.
offload-threads: 2
# Mapping to serve style content.
static-map: /static/style=static/style/blue
# Mapping to serve the remainder of the static content.
static-map: /static=static
# Mapping to serve the favicon.
static-map: /favicon.ico=static/favicon.ico
# Enable the master process manager. Disabled by default for maximum
# compatibility with CTRL+C, but should be enabled for use with
# --daemon and/or production deployments.
master: false
# Path to the application's Python virtual environment. If using Conda
# for Galaxy's framework dependencies (not tools!), do not set this.
virtualenv: .venv
# Path to the application's Python library.
pythonpath: lib
# The entry point which returns the web application (e.g. Galaxy,
# Reports, etc.) that you are loading.
module: galaxy.webapps.reports.buildapp:uwsgi_app()
# Mount the web application (e.g. Galaxy, Reports, etc.) at the given
# URL prefix. Cannot be used together with 'module:' above.
#mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-
# points. Set this to true if a URL prefix is used.
manage-script-name: false
# It is usually a good idea to set this to ``true`` if processes is
# greater than 1.
thunder-lock: false
# Cause uWSGI to respect the traditional behavior of dying on SIGTERM
# (its default is to brutally reload workers)
die-on-term: true
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGINT (its default is to brutally kill workers)
hook-master-start: unix_signal:2 gracefully_kill_them_all
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGTERM (its default is to brutally kill workers)
hook-master-start: unix_signal:15 gracefully_kill_them_all
# Feature necessary for proper mule signal handling
py-call-osafterfork: true
# Ensure application threads will run if `threads` is unset.
enable-threads: true
reports:
# Verbosity of console log messages. Acceptable values can be found
# here: https://docs.python.org/2/library/logging.html#logging-levels
#log_level: DEBUG
# Database connection. Galaxy Reports are intended for production
# Galaxy instances, so sqlite (and the default value below) is not
# supported. An SQLAlchemy connection string should be used specify an
# external database.
#database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
# Where dataset files are stored.
#file_path: database/files
# Where temporary files are stored.
#new_file_path: database/tmp
# Mako templates are compiled as needed and cached for reuse, this
# directory is used for the cache
#template_cache_path: database/compiled_templates/reports
# Configuration for debugging middleware
#debug: false
# Check for WSGI compliance.
#use_lint: false
# NEVER enable this on a public site (even test or QA)
#use_interactive: false
# Write thread status periodically to 'heartbeat.log' (careful, uses
# disk space rapidly!)
#use_heartbeat: true
# Profiling middleware (cProfile based)
#use_profile: true
# Mail
#smtp_server: yourserver@yourfacility.edu
# Mail
#error_email_to: your_bugs@bx.psu.edu
# Enables GDPR Compliance mode. This makes several changes to the way
# Galaxy logs and exposes data externally such as removing
# emails/usernames from logs and bug reports. You are responsible for
# removing personal data from backups. Please read the GDPR section
# under the special topics area of the admin documentation.
#enable_beta_gdpr: false
config/reports.yml.sample
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config/shed_data_manager_conf.xml.sample
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<?xml version="1.0"?>
<data_managers>
</data_managers>
config/shed_tool_conf.xml.sample
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<?xml version="1.0"?>
<toolbox tool_path="database/shed_tools">
</toolbox>
config/shed_tool_data_table_conf.xml.sample
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<?xml version="1.0"?>
<tables>
</tables>
config/swarm_manager_conf.yml.sample
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---
# Galaxy docker swarm manager configuration file
#
# To configure the location of this file, use the `swarm_manager_config_file`
# setting in galaxy.ini
# When the swarm manager daemonizes, it writes a pid file so that only one
# manager will run at a time. This is the path to that pid file.
# {xdg_data_home} will be templated automatically and defaults to
# ~/.local/share as per the XDG specification
#pid_file: '{xdg_data_home}/galaxy_swarm_manager.pid'
# Program output will be written to the log
#log_file: '{xdg_data_home}/galaxy_swarm_manager.log'
# As with GIE plugins, you can modify the base docker command ({docker_args}
# must be present and will be filled in with the docker subcommand and
# arguments)
#command: 'docker {docker_args}'
# Managed services should be started with this string at the beginning of their
# name. It should match the value of CONTAINER_NAME_PREFIX in
# lib/galaxy/web/base/interactive_environments.py, so you should not change
# this unless you change both.
#service_prefix: galaxy_gie_
# Limits:
#
# - max_waiting_services: number of services that should be waiting of each
# "CPU class" (number of CPUs requested e.g. with --reserve-cpu) before
# attempting to spawn a node
# - max_wait_time: number of seconds a service should be waiting before
# attempting to spawn a node
# - max_node_idle_time: number of seconds a node should be idle before
# terminating it
# - max_node_counts: a dictionary controlling the maximum number of nodes of
# each CPU class that the swarm manager will attempt to spawn, e.g.:
# max_node_counts:
# 1: 10 # spawn up to 10 x 1-CPU nodes
# 2: 3 # spawn up to 3 x 2-CPU nodes
# 4: 1 # spawn up to 1 x 4-CPU nodes
#max_waiting_services: 0
#max_wait_time: 5
#max_node_idle_time: 120
#max_node_counts: {}
# If set, only manage nodes whose swarm hostnames begin with this prefix.
# Otherwise, attempt to manage all nodes
#node_prefix: null
# Amount of time to wait for a spawning node to appear in `docker node ls`
# before considering it failed
#spawn_wait_time: 30
# Command to run to spawn new nodes. This command should join the node to the
# swarm. Can include template variables:
# - {cpu_class}: CPU class as explained above (the value of --reserve-cpu)
# - {cpus_needed}: Total number of CPUs of the given class needed to run the
# waiting services
# If this command does not block until the node is joined to the swarm, make
# sure it at least completes that step in `spawn_wait_time` once it returns
# control. This command should return a space-separated list of nodes. If the
# nodes have a different number of CPUs than the class that they were started
# for, you can include that number after a colon (e.g. `node1:4`).
#spawn_command: /bin/true
# Command to run to destroy idle nodes. Can include template variables:
# - {nodes}: Space-separated list of node names to destroy
# This command should block until at least the point at which any nodes being
# deallocated no longer appear in `docker node ls`.
#destroy_command: /bin/true
# Command to run if either of the above commands failed (e.g. to notify an
# administrator). Can include template variables:
# - {failed_command}: Command line of the command that failed
#command_failure_command: /bin/true
# Number of times to retry spawn/destroy commands before considering them to
# have failed, and seconds to wait between retries
#command_retries: 0
#command_retry_wait: 10
# Stop the swarm manager daemon when there are no services or nodes to manage
#terminate_when_idle: True
config/swarm_manager_conf.yml.sample
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<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="true">
<section id="getext" name="Get Data">
<tool file="data_source/upload.xml" />
<tool file="data_source/ucsc_tablebrowser.xml" />
<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
<tool file="data_source/ebi_sra.xml" />
<tool file="data_source/intermine.xml" />
<tool file="data_source/flymine.xml" />
<tool file="data_source/fly_modencode.xml" />
<tool file="data_source/modmine.xml" />
<tool file="data_source/mousemine.xml" />
<tool file="data_source/ratmine.xml" />
<tool file="data_source/yeastmine.xml" />
<tool file="data_source/worm_modencode.xml" />
<tool file="data_source/wormbase.xml" />
<tool file="data_source/zebrafishmine.xml" />
<tool file="data_source/eupathdb.xml" />
<tool file="genomespace/genomespace_importer.xml" />
<tool file="genomespace/genomespace_push.xml" />
</section>
<section id="send" name="Send Data">
<tool file="cloud/send.xml" />
<tool file="genomespace/genomespace_exporter.xml" />
</section>
<section id="liftOver" name="Lift-Over">
<tool file="extract/liftOver_wrapper.xml" />
</section>
<section id="collection_operations" name="Collection Operations">
<tool file="${model_tools_path}/unzip_collection.xml" labels="new" />
<tool file="${model_tools_path}/zip_collection.xml" labels="new" />
<tool file="${model_tools_path}/filter_failed_collection.xml" labels="new" />
<tool file="${model_tools_path}/flatten_collection.xml" labels="new" />
<tool file="${model_tools_path}/merge_collection.xml" labels="new" />
<tool file="${model_tools_path}/relabel_from_file.xml" />
<tool file="${model_tools_path}/filter_from_file.xml" />
<tool file="${model_tools_path}/sort_collection_list.xml" />
<tool file="${model_tools_path}/apply_rules.xml" />
</section>
<section id="textutil" name="Text Manipulation">
<tool file="filters/fixedValueColumn.xml" />
<tool file="filters/catWrapper.xml" hidden="true" />
<tool file="filters/condense_characters.xml" />
<tool file="filters/convert_characters.xml" />
<tool file="filters/mergeCols.xml" />
<tool file="filters/CreateInterval.xml" />
<tool file="filters/cutWrapper.xml" hidden="true" />
<tool file="filters/changeCase.xml" />
<tool file="filters/pasteWrapper.xml" />
<tool file="filters/remove_beginning.xml" />
<tool file="filters/randomlines.xml" />
<tool file="filters/headWrapper.xml" />
<tool file="filters/tailWrapper.xml" />
<tool file="filters/trimmer.xml" />
<tool file="filters/wc_gnu.xml" />
<tool file="filters/secure_hash_message_digest.xml" />
</section>
<section id="convert" name="Convert Formats">
<tool file="filters/bed2gff.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="maf/maf_to_bed.xml" />
<tool file="maf/maf_to_interval.xml" />
<tool file="maf/maf_to_fasta.xml" />
<tool file="filters/sff_extractor.xml" />
<tool file="filters/wig_to_bigwig.xml" />
<tool file="filters/bed_to_bigbed.xml" />
</section>
<section id="filter" name="Filter and Sort">
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.xml" />
<label id="gff" text="GFF" />
<tool file="filters/gff/extract_GFF_Features.xml" />
<tool file="filters/gff/gff_filter_by_attribute.xml" />
<tool file="filters/gff/gff_filter_by_feature_count.xml" />
<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
</section>
<section id="group" name="Join, Subtract and Group">
<tool file="filters/joiner.xml" />
<tool file="filters/compare.xml" />
<tool file="stats/grouping.xml" />
</section>
<section id="fetchAlignSeq" name="Fetch Alignments/Sequences">
<tool file="maf/interval2maf_pairwise.xml" />
<tool file="maf/interval2maf.xml" />
<tool file="maf/interval_maf_to_merged_fasta.xml" />
<tool file="maf/genebed_maf_to_fasta.xml" />
<tool file="maf/maf_stats.xml" />
<tool file="maf/maf_thread_for_species.xml" />
<tool file="maf/maf_limit_to_species.xml" />
<tool file="maf/maf_limit_size.xml" />
<tool file="maf/maf_by_block_number.xml" />
<tool file="maf/maf_filter.xml" />
<tool file="maf/maf_reverse_complement.xml" />
<tool file="extract/extract_genomic_dna.xml" />
</section>
<section id="bxops" name="Operate on Genomic Intervals" version="">
<tool file="filters/wiggle_to_simple.xml" />
<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
</section>
<section id="stats" name="Statistics">
<tool file="stats/gsummary.xml" />
<tool file="filters/uniq.xml" />
</section>
<section id="plots" name="Graph/Display Data">
<tool file="plotting/boxplot.xml" hidden="true" />
<tool file="maf/vcf_to_maf_customtrack.xml" />
</section>
<section id="hgv" name="Phenotype Association">
<tool file="evolution/codingSnps.xml" />
<tool file="evolution/add_scores.xml" />
<tool file="phenotype_association/sift.xml" />
<tool file="phenotype_association/linkToGProfile.xml" />
<tool file="phenotype_association/linkToDavid.xml" />
<tool file="phenotype_association/ldtools.xml" />
<tool file="phenotype_association/pass.xml" />
<tool file="phenotype_association/gpass.xml" />
<tool file="phenotype_association/beam.xml" />
<tool file="phenotype_association/lps.xml" />
<tool file="phenotype_association/master2pg.xml" />
</section>
<section id="cshl_library_information" name="NGS: QC and manipulation">
<label id="illumina" text="Illumina data" />
<label id="454" text="Roche-454 data" />
<label id="solid" text="AB-SOLiD data" />
<tool file="next_gen_conversion/solid2fastq.xml" />
<tool file="solid_tools/solid_qual_stats.xml" />
<tool file="solid_tools/solid_qual_boxplot.xml" />
<label id="generic_fastq" text="Generic FASTQ manipulation" />
<label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" />
</section>
<section id="ngs_mapping" name="NGS: Mapping">
<label id="illumina" text="Illumina" />
<label id="roche_454" text="Roche-454" />
<label id="ab_solid" text="AB-SOLiD" />
</section>
<label id="deprecated" text="DEPRECATED" />
<section id="gatk" name="NGS: GATK Tools (beta)">
</section>
</toolbox>
config/tool_conf.xml.main
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config/tool_conf.xml.sample
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<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="true">
<section id="getext" name="Get Data">
<tool file="data_source/upload.xml" />
<tool file="data_source/ucsc_tablebrowser.xml" />
<!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->
<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
<tool file="data_source/ebi_sra.xml" />
<tool file="data_source/fly_modencode.xml" />
<tool file="data_source/intermine.xml" />
<tool file="data_source/flymine.xml" />
<!-- <tool file="data_source/flymine_test.xml" /> -->
<tool file="data_source/modmine.xml" />
<tool file="data_source/mousemine.xml" />
<tool file="data_source/ratmine.xml" />
<tool file="data_source/yeastmine.xml" />
<tool file="data_source/worm_modencode.xml" />
<tool file="data_source/wormbase.xml" />
<!-- <tool file="data_source/wormbase_test.xml" /> -->
<tool file="data_source/zebrafishmine.xml" />
<tool file="data_source/eupathdb.xml" />
<tool file="data_source/hbvar.xml" />
<tool file="genomespace/genomespace_importer.xml" />
<tool file="genomespace/genomespace_push.xml" />
</section>
<section id="send" name="Send Data">
<tool file="cloud/send.xml" />
<tool file="genomespace/genomespace_exporter.xml" />
</section>
<section id="collection_operations" name="Collection Operations">
<tool file="${model_tools_path}/unzip_collection.xml" />
<tool file="${model_tools_path}/zip_collection.xml" />
<tool file="${model_tools_path}/filter_failed_collection.xml" />
<tool file="${model_tools_path}/filter_empty_collection.xml" />
<tool file="${model_tools_path}/flatten_collection.xml" />
<tool file="${model_tools_path}/merge_collection.xml" />
<tool file="${model_tools_path}/relabel_from_file.xml" />
<tool file="${model_tools_path}/filter_from_file.xml" />
<tool file="${model_tools_path}/sort_collection_list.xml" />
<tool file="${model_tools_path}/tag_collection_from_file.xml" />
<tool file="${model_tools_path}/apply_rules.xml" />
<tool file="${model_tools_path}/build_list.xml" />
<tool file="${model_tools_path}/extract_dataset.xml" />
</section>
<section id="expression_tools" name="Expression Tools">
<tool file="expression_tools/parse_values_from_file.xml"/>
</section>
<section id="liftOver" name="Lift-Over">
<tool file="extract/liftOver_wrapper.xml" />
</section>
<section id="textutil" name="Text Manipulation">
<tool file="filters/fixedValueColumn.xml" />
<tool file="filters/catWrapper.xml" />
<tool file="filters/cutWrapper.xml" />
<tool file="filters/mergeCols.xml" />
<tool file="filters/convert_characters.xml" />
<tool file="filters/CreateInterval.xml" />
<tool file="filters/cutWrapper.xml" />
<tool file="filters/changeCase.xml" />
<tool file="filters/pasteWrapper.xml" />
<tool file="filters/remove_beginning.xml" />
<tool file="filters/randomlines.xml" />
<tool file="filters/headWrapper.xml" />
<tool file="filters/tailWrapper.xml" />
<tool file="filters/trimmer.xml" />
<tool file="filters/wc_gnu.xml" />
<tool file="filters/secure_hash_message_digest.xml" />
</section>
<section id="convert" name="Convert Formats">
<tool file="filters/bed2gff.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="maf/maf_to_bed.xml" />
<tool file="maf/maf_to_interval.xml" />
<tool file="maf/maf_to_fasta.xml" />
<tool file="filters/sff_extractor.xml" />
<tool file="filters/wig_to_bigwig.xml" />
<tool file="filters/bed_to_bigbed.xml" />
</section>
<section id="filter" name="Filter and Sort">
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.xml" />
<label id="gff" text="GFF" />
<tool file="filters/gff/extract_GFF_Features.xml" />
<tool file="filters/gff/gff_filter_by_attribute.xml" />
<tool file="filters/gff/gff_filter_by_feature_count.xml" />
<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
</section>
<section id="group" name="Join, Subtract and Group">
<tool file="filters/joiner.xml" />
<tool file="filters/compare.xml" />
<tool file="stats/grouping.xml" />
</section>
<section id="fetchAlignSeq" name="Fetch Alignments/Sequences">
<tool file="maf/interval2maf_pairwise.xml" />
<tool file="maf/interval2maf.xml" />
<tool file="maf/maf_split_by_species.xml" />
<tool file="maf/interval_maf_to_merged_fasta.xml" />
<tool file="maf/genebed_maf_to_fasta.xml" />
<tool file="maf/maf_stats.xml" />
<tool file="maf/maf_thread_for_species.xml" />
<tool file="maf/maf_limit_to_species.xml" />
<tool file="maf/maf_limit_size.xml" />
<tool file="maf/maf_by_block_number.xml" />
<tool file="maf/maf_reverse_complement.xml" />
<tool file="maf/maf_filter.xml" />
</section>
<section id="bxops" name="Operate on Genomic Intervals" version="">
<tool file="filters/wiggle_to_simple.xml" />
<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
</section>
<section id="stats" name="Statistics">
<tool file="stats/gsummary.xml" />
<tool file="filters/uniq.xml" />
</section>
<section id="plots" name="Graph/Display Data">
<tool file="maf/vcf_to_maf_customtrack.xml" />
</section>
<section id="hgv" name="Phenotype Association">
<tool file="evolution/codingSnps.xml" />
<tool file="evolution/add_scores.xml" />
<tool file="phenotype_association/sift.xml" />
<tool file="phenotype_association/linkToGProfile.xml" />
<tool file="phenotype_association/linkToDavid.xml" />
<tool file="phenotype_association/ldtools.xml" />
<tool file="phenotype_association/master2pg.xml" />
</section>
</toolbox>
config/tool_conf.xml.sample
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<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
<tables>
<!-- Locations of all fasta files under genome directory -->
<table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/all_fasta.loc" />
</table>
<!-- Locations of indexes in the BFAST mapper format -->
<table name="bfast_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, formats, name, path</columns>
<file path="tool-data/bfast_indexes.loc" />
</table>
<!-- Locations of nucleotide BLAST databases -->
<table name="blastdb" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, path</columns>
<file path="tool-data/blastdb.loc" />
</table>
<!-- Locations of protein BLAST databases -->
<table name="blastdb_p" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, path</columns>
<file path="tool-data/blastdb_p.loc" />
</table>
<!-- Locations of protein domain BLAST databases -->
<table name="blastdb_d" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, path</columns>
<file path="tool-data/blastdb_d.loc" />
</table>
<!-- Locations of indexes in the BWA mapper format -->
<table name="bwa_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bwa_index.loc" />
</table>
<!-- Locations of indexes in the BWA color-space mapper format -->
<table name="bwa_indexes_color" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bwa_index_color.loc" />
</table>
<!-- Locations of MAF files that have been indexed with bx-python -->
<table name="indexed_maf_files">
<columns>name, value, dbkey, species</columns>
<file path="tool-data/maf_index.loc" />
</table>
<!-- Locations of fasta files appropriate for NGS simulation -->
<table name="ngs_sim_fasta" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/ngs_sim_fasta.loc" />
</table>
<!-- Locations of PerM base index files -->
<table name="perm_base_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, path</columns>
<file path="tool-data/perm_base_index.loc" />
</table>
<!-- Locations of PerM color-space index files -->
<table name="perm_color_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, path</columns>
<file path="tool-data/perm_color_index.loc" />
</table>
<!-- Location of Picard dict file and other files -->
<table name="picard_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/picard_index.loc" />
</table>
<!-- Location of SRMA dict file and other files -->
<table name="srma_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/picard_index.loc" />
</table>
<!-- Location of Mosaik files -->
<table name="mosaik_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/mosaik_index.loc" />
</table>
<!-- Locations of indexes in the 2bit format -->
<table name="twobit" comment_char="#" allow_duplicate_entries="False">
<columns>value, path</columns>
<file path="tool-data/twobit.loc" />
</table>
<!-- Available IGV builds, loaded from URL -->
<table name="igv_broad_genomes" comment_char="#" allow_duplicate_entries="False">
<columns>name, url, value</columns>
<file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
</table>
<!-- Available liftOver chain file -->
<table name="liftOver" comment_char="#" allow_duplicate_entries="False">
<columns>dbkey, name, value</columns>
<file path="tool-data/liftOver.loc" />
</table>
<!-- iobio bam servers -->
<table name="bam_iobio" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, url</columns>
<file path="tool-data/bam_iobio.loc" />
</table>
<!-- iobio vcf servers -->
<table name="vcf_iobio" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, url</columns>
<file path="tool-data/vcf_iobio.loc" />
</table>
<!-- simple biom servers -->
<table name="biom_simple_display" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, url</columns>
<file path="tool-data/biom_simple_display.loc" />
</table>
<!-- simple intermine servers -->
<table name="intermine_simple_display" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, url</columns>
<file path="tool-data/intermine_simple_display.loc" />
</table>
</tables>
config/tool_data_table_conf.xml.sample
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# Dynamic Tool Destinations config has four main levels (or key properties) - tools,
# default_destination, users, and verbose.
#
# Under tools is where you put the IDs of the tools. Tool IDs must be
# distinct. In each tool is a list of rules, each of which contain rule-specific
# parameters. Dynamic Tool Destination is set up to allow and fix a few light errors
# in the config, but it's best to follow the specified template.
#
# default_destination, the second key property, specifies which global destination
# to default to in case none of the rules apply.
#
# users, the third key property, can be used to assign a priority to a user. Three priorities
# are available low, med, and high. By default all users are assumed to be med priority. If
# a rule has priority destinations the user will be set to the destination which matches their priority
# or if their priority isn't available they will be matched to the next closest one.
#
# A fourth key property is verbose. When this is set to True, Dynamic Tool Destination
# gives much more descriptive output regarding the steps it's taking in mapping your tools to
# the appropriate destinations, including config validation and any potential errors found in the
# config.
#
# Note: Configurations can be validated with the following command:
#
# python lib/galaxy/jobs/dynamic_tool_destination.py -c
#
# or
#
# python lib/galaxy/jobs/dynamic_tool_destination.py -c /path/to/tool_destinations.yml
#
# The general template is as follows (note that this template
# does not use quote symbols), using spades and smalt as an example
# (spades for showing what each field is for, and smalt
# to give a fairly real-world example):
#
# Ex:
#
# tools:
# spades:
# rules:
# - rule_type: what kind of rule is it?
# nice_value: what kind of priority does this rule have over others?
# destination: how should this tool be run?
# lower_bound: what's the max file size?
# upper_bound: what's the minimum file size?
# users: #(optional) which users does this rule apply to
# - user@example.com
# default_destination: this tool-specific field is optional
# smalt_map:
# rules:
# - rule_type: file_size
# nice_value: 0
# lower_bound: 0
# upper_bound: 2 GB
# destination: cluster_low_4
# - rule_type: file_size
# nice_value: 0
# lower_bound: 2 GB
# upper_bound: 4 GB
# destination: cluster_low_8
# - rule_type: file_size
# nice_value: 0
# lower_bound: 4 GB
# upper_bound: Infinity
# destination: cluster_low_16
# default_destination: cluster_default
# users:
# user_low@example.com:
# priority: low
# user_med@example.com:
# priority: med
# user_high@example.com:
# priority: high
# default_destination: this global field is mandatory
# verbose: True
#
#
#
# Looking at this example, some things must be clarified: each entry in the list of
# rules per tool is specified by '-'. Per rule, regardless of rule type,
# the following fields are mandatory:
# rule_type, nice_value, and destination.
#
# Some of the other fields are mandatory only for specific rule types, which will be
# further discussed below.
#
# Starting with rule_type, there are currently 3 rule types: file_size, records,
# and arguments.
#
# file_size and records rules are based on how large the files are: if they fall
# within specified limits, then the rule is satisfied, and the tool may proceed
# with the appropriate destination.
#
# file_size and records rules have the following required parameters on top of the base
# mandatory parameters:
# upper_bound
# lower_bound
#
# Bounds are allowed to be specified in bytes (48000 for example) or a higher size unit,
# including the unit abbreviation (4 GB or 10 TB for example). Additionally, upper_bound
# is allowed to be Infinite; simply specify Infinite in order to do so.
#
# **The rule will allow the lower_bound, up to but not including the upper_bound
#
# The third rule_type is arguments, which has arguments as a mandatory parameter on top of
# the base mandatory parameters. The arguments parameter is specified using the following
# template:
#
#
# arguments:
# argument_name: the_argument
#
#
# A real world example is shown below:
#
#
# tools:
# spades:
# rules:
# - rule_type: arguments
# nice_value: -19
# destination: fail
# fail_message: Don't do that
# arguments:
# my_section:
# my_condition:
# careful: true
# default_destination: cluster_low
# default_destination: cluster
# verbose: False
#
#
# Next up, nice_value is used for prioritizing rules over others in case two rules
# match. nice_value basically translates to, "the higher the nice_value, the 'nicer'
# the tool is about being picked last". So based off of that idea, a rule with a nice
# value of -5 is guaranteed to be picked over a rule with a nice value of 10. nice_value
# is allowed to go from -20 to 20. If two rules have the same nice value and both were
# satisfied, the first rule in the config file will be picked. In summary, first-come-
# first-serve basis unless nice_value overrides that.
#
#
# Finally, destination simply refers to the specific way the tool will run. Each
# destination ID refers to a specific configuration to run the tool with.
#
# Some rules may call for the job to fail if certain conditions are encountered. In
# this case, destination simply refers to 'fail'.
#
# For example, the following rule is set to fail the job if a file that is too large
# (more than 4GB) is encountered:
#
#
# tools:
# spades:
# rules:
# - rule_type: file_size
# nice_value: 0
# destination: fail
# fail_message: Data too large
# lower_bound: 4 GB
# upper_bound: Infinity
#
#
# As shown above, a rule with 'fail' as the destination requires an additional
# parameter, 'fail_message', which DynamicToolDestination uses to print a helpful error
# message to the user indicating why the job failed (showing up inside the job log in
# Galaxy's history panel).
tools:
spades:
rules:
- rule_type: file_size
nice_value: 0
lower_bound: 0
upper_bound: 10 MB
fail_message: Too few reads for spades to work
destination: fail
- rule_type: file_size
nice_value: 0
lower_bound: 10 MB
upper_bound: 2 GB
destination:
priority:
low: slurm_low_24
med: slurm_med_24
high: slurm_high_24
- rule_type: file_size
nice_value: 0
lower_bound: 2 GB
upper_bound: 4 GB
destination:
priority:
low: slurm_low_48
med: slurm_med_48
high: slurm_high_48
- rule_type: file_size
nice_value: 0
lower_bound: 4 GB
upper_bound: Infinity
fail_message: Too much data, shoudn't run
destination: fail
- rule_type: arguments
nice_value: 0
arguments:
careful: true
destination:
priority:
low: slurm_low_48
med: slurm_med_48
high: slurm_high_48
default_destination:
priority:
low: slurm_low_16
med: slurm_med_16
high: slurm_high_16
srst2:
rules:
- rule_type: records
nice_value: 0
lower_bound: 0
upper_bound: 100
destination:
priority:
low: slurm_low_4
med: slurm_med_4
high: slurm_high_4
- rule_type: records
nice_value: 0
lower_bound: 100
upper_bound: 1000
destination:
priority:
low: slurm_low_8
med: slurm_med_8
high: slurm_high_8
- rule_type: records
nice_value: 0
lower_bound: 1000
upper_bound: 10000
destination:
priority:
low: slurm_low_8
med: slurm_med_8
high: slurm_high_8
- rule_type: records
nice_value: 0
lower_bound: 1000000
upper_bound: Infinity
fail_message: Using the wrong tool
destination: fail
smalt_map:
rules:
- rule_type: file_size
nice_value: 0
lower_bound: 0
upper_bound: 2 GB
destination:
priority:
low: slurm_low_4
med: slurm_med_4
high: slurm_high_4
- rule_type: file_size
nice_value: 0
lower_bound: 2 GB
upper_bound: 4 GB
destination:
priority:
low: slurm_low_8
med: slurm_med_8
high: slurm_high_8
- rule_type: file_size
nice_value: 0
lower_bound: 4 GB
upper_bound: Infinity
destination:
priority:
low: slurm_low_16
med: slurm_med_16
high: slurm_high_16
fastqc:
rules:
- rule_type: file_size
nice_value: 0
lower_bound: 0
upper_bound: 400 MB
fail_message: File size too small
destination: fail
- rule_type: file_size
nice_value: 0
lower_bound: 400 MB
upper_bound: Infinity
destination:
priority:
low: slurm_low_4
med: slurm_med_4
high: slurm_high_4
default_destination:
priority:
low: slurm_low_16
med: slurm_med_16
high: slurm_high_16
default_destination:
priority:
low: slurm_low_default
med: slurm_med_default
high: slurm_high_default
users:
user@email.com:
priority: high
verbose: True
config/tool_destinations.yml.sample
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config/tool_shed.yml.sample
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uwsgi:
# The address and port on which to listen. By default, only listen to
# localhost (tool_shed will not be accessible over the network). Use
# ':9009' to listen on all available network interfaces.
http: 127.0.0.1:9009
# By default uWSGI allocates a very small buffer (4096 bytes) for the
# headers of each request. If you start receiving "invalid request
# block size" in your logs, it could mean you need a bigger buffer. We
# recommend at least 16384.
buffer-size: 16384
# Number of web server (worker) processes to fork after the
# application has loaded. If this is set to greater than 1, thunder-
# lock likely should be enabled below.
processes: 1
# Number of threads for each web server process.
threads: 4
# Number of threads for serving static content and handling internal
# routing requests.
offload-threads: 2
# Mapping to serve style content.
static-map: /static/style=static/style/blue
# Mapping to serve the remainder of the static content.
static-map: /static=static
# Mapping to serve the favicon.
static-map: /favicon.ico=static/favicon.ico
# Enable the master process manager. Disabled by default for maximum
# compatibility with CTRL+C, but should be enabled for use with
# --daemon and/or production deployments.
master: false
# Path to the application's Python virtual environment. If using Conda
# for Galaxy's framework dependencies (not tools!), do not set this.
virtualenv: .venv
# Path to the application's Python library.
pythonpath: lib
# The entry point which returns the web application (e.g. Galaxy,
# Reports, etc.) that you are loading.
module: galaxy.webapps.tool_shed.buildapp:uwsgi_app()
# Mount the web application (e.g. Galaxy, Reports, etc.) at the given
# URL prefix. Cannot be used together with 'module:' above.
#mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-
# points. Set this to true if a URL prefix is used.
manage-script-name: false
# It is usually a good idea to set this to ``true`` if processes is
# greater than 1.
thunder-lock: false
# Cause uWSGI to respect the traditional behavior of dying on SIGTERM
# (its default is to brutally reload workers)
die-on-term: true
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGINT (its default is to brutally kill workers)
hook-master-start: unix_signal:2 gracefully_kill_them_all
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGTERM (its default is to brutally kill workers)
hook-master-start: unix_signal:15 gracefully_kill_them_all
# Feature necessary for proper mule signal handling
py-call-osafterfork: true
# Ensure application threads will run if `threads` is unset.
enable-threads: true
tool_shed:
# Verbosity of console log messages. Acceptable values can be found
# here: https://docs.python.org/library/logging.html#logging-levels
#log_level: DEBUG
# By default, the Tool Shed uses a SQLite database at
# 'database/community.sqlite'. You may use a SQLAlchemy connection
# string to specify an external database instead. This string takes
# many options which are explained in detail in the config file
# documentation.
#database_connection: sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
# Where the hgweb.config file is stored. The default is the Galaxy
# installation directory.
#hgweb_config_dir: null
# Where Tool Shed repositories are stored.
#file_path: database/community_files
# Where temporary files are stored.
#new_file_path: database/tmp
# File containing old-style genome builds
#builds_file_path: tool-data/shared/ucsc/builds.txt
# Format string used when showing date and time information. The
# string may contain: - the directives used by Python time.strftime()
# function (see
# https://docs.python.org/library/time.html#time.strftime ), - $locale
# (complete format string for the server locale), - $iso8601 (complete
# format string as specified by ISO 8601 international standard).
#pretty_datetime_format: $locale (UTC)
# -- Repository and Tool search Using the script located at
# scripts/build_ts_whoosh_index.py you can generate search index and
# allow full text API searching over the repositories and tools within
# the Tool Shed given that you specify the following two config
# options.
#toolshed_search_on: true
# -- Repository and Tool search Using the script located at
# scripts/build_ts_whoosh_index.py you can generate search index and
# allow full text API searching over the repositories and tools within
# the Tool Shed given that you specify the following two config
# options.
#whoosh_index_dir: database/toolshed_whoosh_indexes
# For searching repositories at /api/repositories:
#repo_name_boost: 0.9
# For searching repositories at /api/repositories:
#repo_description_boost: 0.6
# For searching repositories at /api/repositories:
#repo_long_description_boost: 0.5
# For searching repositories at /api/repositories:
#repo_homepage_url_boost: 0.3
# For searching repositories at /api/repositories:
#repo_remote_repository_url_boost: 0.2
# For searching repositories at /api/repositories:
#repo_owner_username_boost: 0.3
# For searching repositories at /api/repositories:
#categories_boost: 0.5
# For searching tools at /api/tools
#tool_name_boost: 1.2
# For searching tools at /api/tools
#tool_description_boost: 0.6
# For searching tools at /api/tools
#tool_help_boost: 0.4
# For searching tools at /api/tools
#tool_repo_owner_username: 0.3
# You can enter tracking code here to track visitor's behavior through
# your Google Analytics account. Example: UA-XXXXXXXX-Y
#ga_code: null
# The Tool Shed encodes various internal values when these values will
# be output in some format (for example, in a URL or cookie). You
# should set a key to be used by the algorithm that encodes and
# decodes these values. It can be any string. If left unchanged,
# anyone could construct a cookie that would grant them access to
# others' sessions. One simple way to generate a value for this is
# with the shell command: python -c 'from __future__ import
# print_function; import time; print(time.time())' | md5sum | cut -f 1
# -d ' '
#id_secret: changethisinproductiontoo
# User authentication can be delegated to an upstream proxy server
# (usually Apache). The upstream proxy should set a REMOTE_USER
# header in the request. Enabling remote user disables regular logins.
# For more information, see: https://galaxyproject.org/admin/config
# /apache-external-user-auth/
#use_remote_user: false
# If use_remote_user is enabled, anyone who can log in to the Galaxy
# host may impersonate any other user by simply sending the
# appropriate header. Thus a secret shared between the upstream proxy
# server, and Galaxy is required. If anyone other than the Galaxy user
# is using the server, then apache/nginx should pass a value in the
# header 'GX_SECRET' that is identical the one below
#remote_user_secret: changethisinproductiontoo
# If use_remote_user is enabled and your external authentication
# method just returns bare usernames, set a default mail domain to be
# appended to usernames, to become your Galaxy usernames (email
# addresses).
#remote_user_maildomain: null
# If use_remote_user is enabled, the header that the upstream proxy
# provides the remote username in defaults to HTTP_REMOTE_USER (the
# 'HTTP_' is prepended by WSGI). This option allows you to change the
# header. Note, you still need to prepend 'HTTP_' to the header in
# this option, but your proxy server should *not* include 'HTTP_' at
# the beginning of the header name.
#remote_user_header: HTTP_REMOTE_USER
# If use_remote_user is enabled, you can set this to a URL that will
# log your users out.
#remote_user_logout_href: null
# Configuration for debugging middleware
#debug: false
# Check for WSGI compliance.
#use_lint: false
# Intercept print statements and show them on the returned page.
#use_printdebug: true
# NEVER enable this on a public site (even test or QA)
#use_interactive: false
# Administrative users - set this to a comma-separated list of valid
# Tool Shed users (email addresses). These users will have access to
# the Admin section of the server, and will have access to create
# users, groups, roles, libraries, and more.
#admin_users: null
# Force everyone to log in (disable anonymous access)
#require_login: false
# Allow unregistered users to create new accounts (otherwise, they
# will have to be created by an admin).
#allow_user_creation: true
# Allow administrators to delete accounts.
#allow_user_deletion: false
# For use by email messages sent from the Tool Shed.
#smtp_server: smtp.your_tool_shed_server
# For use by email messages sent from the Tool Shed.
#email_from: your_tool_shed_email@server
# If your SMTP server requires a username and password, you can
# provide them here (password in cleartext here, but if your server
# supports STARTTLS it will be sent over the network encrypted).
#smtp_username: null
# If your SMTP server requires a username and password, you can
# provide them here (password in cleartext here, but if your server
# supports STARTTLS it will be sent over the network encrypted).
#smtp_password: null
# If your SMTP server requires SSL from the beginning of the
# connection
#smtp_ssl: false
# The URL linked by the "Support" link in the "Help" menu.
#support_url: https://galaxyproject.org/support/
# Address to join mailing list
#mailing_join_addr: galaxy-announce-join@bx.psu.edu
# Write thread status periodically to 'heartbeat.log' (careful, uses
# disk space rapidly!)
#use_heartbeat: true
# Profiling middleware (cProfile based)
#use_profile: true
# Enable creation of Galaxy flavor Docker Image
#enable_galaxy_flavor_docker_image: false
# Show a message box under the masthead.
#message_box_visible: false
# Show a message box under the masthead.
#message_box_content: null
# Class of the message box under the masthead. Possible values are:
# 'info' (the default), 'warning', 'error', 'done'.
#message_box_class: info
# Serving static files (needed if running standalone)
#static_enabled: true
# Serving static files (needed if running standalone)
#static_cache_time: 360
# Serving static files (needed if running standalone)
#static_dir: static/
# Serving static files (needed if running standalone)
#static_images_dir: static/images
# Serving static files (needed if running standalone)
#static_favicon_dir: static/favicon.ico
# Serving static files (needed if running standalone)
#static_scripts_dir: static/scripts/
# Serving static files (needed if running standalone)
#static_style_dir: static/style/blue
# Enables GDPR Compliance mode. This makes several changes to the way
# Galaxy logs and exposes data externally such as removing
# emails/usernames from logs and bug reports. You are responsible for
# removing personal data from backups. Please read the GDPR section
# under the special topics area of the admin documentation.
#enable_beta_gdpr: false
# For help on configuring the Advanced proxy features, see:
# https://docs.galaxyproject.org/en/master/admin/production.html
# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile.
# Set this to True to inform Galaxy that mod_xsendfile is enabled
# upstream.
#apache_xsendfile: false
# The same download handling can be done by nginx using X-Accel-
# Redirect. This should be set to the path defined in the nginx
# config as an internal redirect with access to Galaxy's data files
# (see documentation linked above).
#nginx_x_accel_redirect_base: null
# This value overrides the action set on the file upload form, e.g.
# the web path where the nginx_upload_module has been configured to
# intercept upload requests.
#nginx_upload_path: null
# E-mail domains blacklist is used for filtering out users that are
# using disposable email address during the registration. If their
# address domain matches any domain in the blacklist, they are refused
# the registration.
#blacklist_file: config/disposable_email_blacklist.conf
# Append "/{brand}" to the "Galaxy" text in the masthead.
#brand: null
# Citation related caching. Tool citations information maybe fetched
# from external sources such as https://doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
#citation_cache_type: file
# Citation related caching. Tool citations information maybe fetched
# from external sources such as https://doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
#citation_cache_data_dir: database/citations/data
# Citation related caching. Tool citations information maybe fetched
# from external sources such as https://doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
#citation_cache_lock_dir: database/citations/lock
# Turn on logging of user actions to the database. Actions currently
# logged are grid views, tool searches, and use of "recently" used
# tools menu. The log_events and log_actions functionality will
# eventually be merged.
#log_actions: true
# Password expiration period (in days). Users are required to change
# their password every x days. Users will be redirected to the change
# password screen when they log in after their password expires. Enter
# 0 to disable password expiration.
#password_expiration_period: 0
# Log to Sentry Sentry is an open source logging and error aggregation
# platform. Setting sentry_dsn will enable the Sentry middleware and
# errors will be sent to the indicated sentry instance. This
# connection string is available in your sentry instance under
# <project_name> -> Settings -> API Keys.
#sentry_dsn: null
# Galaxy Session Timeout This provides a timeout (in minutes) after
# which a user will have to log back in. A duration of 0 disables this
# feature.
#session_duration: 0
# The URL linked by the "Terms and Conditions" link in the "Help"
# menu, as well as on the user registration and login forms and in the
# activation emails.
#terms_url: null
config/tool_shed.yml.sample
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@@ -0,0 +1 @@
../lib/galaxy/config/sample/tool_shed.yml.sample
config/tool_sheds_conf.xml.sample
-7
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@@ -1,7 +0,0 @@
<?xml version="1.0"?>
<tool_sheds>
<tool_shed name="Galaxy Main Tool Shed" url="https://toolshed.g2.bx.psu.edu/"/>
<!-- Test Tool Shed should be used only for testing purposes.
<tool_shed name="Galaxy Test Tool Shed" url="https://testtoolshed.g2.bx.psu.edu/"/>
-->
</tool_sheds>
config/tool_sheds_conf.xml.sample
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@@ -0,0 +1 @@
../lib/galaxy/config/sample/tool_sheds_conf.xml.sample
config/user_preferences_extra_conf.yml.sample
-65
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@@ -1,65 +0,0 @@
preferences:
# the key you can refer to
apollo_url_01:
# description that is displayed to the user
description: The URL to your personal Apollo instance
inputs:
# the content can be accessed by apollo_url_01.apollo_url
- name: apollo_url
label: Apollo URL
# type of input field that will be displayed to the user
# can be string or password
type: text
# by defaul all inputs are required
required: True
- name: apollo_text
label: Apollo Text
# type of input field that will be displayed to the user
# can be string or password
type: text
# by defaul all inputs are required
required: True
openstack_account:
description: Your own Open Stack account
inputs:
- name: username
label: Username
type: text
required: False
- name: url
label: Open Stack URL
type: text
required: True
webhook_overlay_search:
description: Configuration option for your search results
inputs:
- name: max_search_results
label: Maximum number of search results
type: text
required: False
use_cached_job:
description: Do you want to be able to re-use previously run jobs ?
inputs:
- name: use_cached_job_checkbox
label: Do you want to be able to re-use equivalent jobs ?
type: boolean
checked: false
value: false
help: If you select yes, you will be able to select for each tool and workflow run if you would like to use this feature.
localization:
description: Localization
inputs:
- name: locale
label: Prefered language
type: select
required: False
options:
- [Navigator default, auto]
- [Chinese, zh]
- [English, en]
- [French, fr]
- [Japanese, ja]
config/user_preferences_extra_conf.yml.sample
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../lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
config/workflow_resource_mapper_conf.yml.sample
-14
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@@ -1,14 +0,0 @@
by_group:
default: default
groups:
default: [project, priority]
prio_basic: [{name: priority, options: ["low", "med"]}]
prio_advanced: [{name: priority, options: ["low", "med", "high"]}]
prio_super:
- time
- memory
- processors
- name: priority
options:
- ultra
- plus_ultra
config/workflow_resource_mapper_conf.yml.sample
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../lib/galaxy/config/sample/workflow_resource_mapper_conf.yml.sample
config/workflow_resource_params_conf.xml.sample
-13
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@@ -1,13 +0,0 @@
<parameters>
<param label="Processors" name="processors" type="integer" min="1" max="64" value="" help="Number of processing cores, 'ppn' value (1-64). Leave blank to use default value." />
<param label="Memory" name="memory" type="integer" min="1" max="256" value="" help="Memory size in gigabytes, 'pmem' value (1-256). Leave blank to use default value." />
<param label="Time" name="time" type="integer" min="1" max="744" value="" help="Maximum job time in hours, 'walltime' value (1-744). Leave blank to use default value." />
<param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value." />
<param label="Workflow Job Priority" name="priority" type="select" value="med" help="What priority should the jobs in this workflow run at? (Overrides any declared job priority)">
<option value="low" label="Low"/>
<option value="med" label="Medium"/>
<option value="high" label="High"/>
<option value="ultra" label="Ultra"/>
<option value="plus_ultra" label="Plus Ultra"/>
</param>
</parameters>
config/workflow_resource_params_conf.xml.sample
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../lib/galaxy/config/sample/workflow_resource_params_conf.xml.sample
config/workflow_schedulers_conf.xml.sample
-42
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@@ -1,42 +0,0 @@
<?xml version="1.0"?>
<!-- If workflow_schedulers_conf.xml exists it defines the workflow scheduling
plugins to load and how to configure them. Currently only the core workflow
scheduling is available.
-->
<workflow_schedulers default="core">
<!-- Each element in this file corresponds to a workflow scheduling plugin
in lib/galaxy/workflow/schedulers. -->
<!-- Core plugin schedules whole workflow at outset inside Galaxy and doesn't
require any external dependencies. -->
<core id="core" />
<!-- Handlers (Galaxy server processes that perform the scheduling work) can
be defined here in the same format as in job_conf.xml. By default, the
handlers defined in job_conf.xml will be used (or the web process that
receives the workflow scheduling request if handlers are not configured
in job_conf.xml).
The options here are the same as is documented for <handlers> in
job_conf.xml.sample_advanced with two exceptions:
- If a uWSGI farm named `workflow-schedulers` is present, it will be
preferred, followed by `job-handlers`. If any untagged handlers are
defined in this configuration they are eligible to schedule workflows
in addition to any matching mules.
- If uWSGI farms are present, the default assignment method is
`db-preassign` rather than `uwsgi-mule-message`, because `db-preassign`
is deterministic. All workflows scheduled in a single history will be
assigned to the same handler, ensuring they are scheduled serially
(preventing their outputs from being interleaved in the history). You
can override this by explicitly setting
`assign_with="uwsgi-mule-message"`.
-->
<!--
<handlers>
<handler id="handler0"/>
<handler id="handler1"/>
</handlers>
-->
</workflow_schedulers>
config/workflow_schedulers_conf.xml.sample
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../lib/galaxy/config/sample/workflow_schedulers_conf.xml.sample
doc/Makefile
+1 -1
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@@ -57,7 +57,7 @@ source/api/ts_api.rst: source/lib/galaxy.webapps.tool_shed.api.rst
sed -i.bak -e 's/^galaxy\\\.webapps\\\.tool\\_shed\\\.api\\\.//' $@
rm -f $@.bak
source/admin/config_logging_default_yaml.rst: ../lib/galaxy/config.py
source/admin/config_logging_default_yaml.rst: ../lib/galaxy/config/__init__.py
printf '.. code-block:: yaml\n\n' > $@
printf ' galaxy:\n' >> $@
printf ' logging:\n ' >> $@
doc/source/admin/galaxy_options.rst
+82 -78
View File
@@ -222,7 +222,7 @@
functionality is largely untested in modern Galaxy releases and
has serious issues such as #7273 and the possibility of slowing
down Galaxy startup, so the default and recommended value is
False.
false.
:Default: ``false``
:Type: bool
@@ -271,14 +271,13 @@
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to the directory in which tool dependencies are placed. This
is used by the Tool Shed to install dependencies and can also be
used by administrators to manually install or link to
dependencies. For details, see:
https://galaxyproject.org/admin/config/tool-dependencies Set the
Various dependency resolver configuration parameters will have
defaults set relative to this path, such as the default conda
prefix, default Galaxy packages path, legacy tool shed
dependencies path, and the dependency cache directory. Set the
string to None to explicitly disable tool dependency handling. If
this option is set to none or an invalid path, installing tools
with dependencies from the Tool Shed will fail.
with dependencies from the Tool Shed or in Conda will fail.
:Default: ``database/dependencies``
:Type: str
@@ -360,7 +359,7 @@
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set to True to instruct Galaxy to look for and install missing
Set to true to instruct Galaxy to look for and install missing
tool dependencies before each job runs.
:Default: ``false``
:Type: bool
@@ -371,7 +370,7 @@
~~~~~~~~~~~~~~~~~~~
:Description:
Set to True to instruct Galaxy to install Conda from the web
Set to true to instruct Galaxy to install Conda from the web
automatically if it cannot find a local copy and conda_exec is not
configured.
:Default: ``true``
@@ -383,7 +382,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
You must set this to True if conda_prefix and
You must set this to true if conda_prefix and
job_working_directory are not on the same volume, or some conda
dependencies will fail to execute at job runtime. Conda will copy
packages content instead of creating hardlinks or symlinks. This
@@ -402,10 +401,12 @@
Certain dependency resolvers (namely Conda) take a considerable
amount of time to build an isolated job environment in the
job_working_directory if the job working directory is on a network
share. Set the following option to True to cache the dependencies
in a folder. This option is beta and should only be used if you
share. Set this option to true to cache the dependencies in a
folder. This option is beta and should only be used if you
experience long waiting times before a job is actually submitted
to your cluster.
to your cluster. This only affects tools where some requirements
can be resolved but not others, most modern best practice tools
can use prebuilt environments in the Conda directory.
:Default: ``false``
:Type: bool
@@ -428,7 +429,7 @@
:Description:
By default, when using a cached dependency manager, the
dependencies are cached when installing new tools and when using
tools for the first time. Set this to False if you prefer
tools for the first time. Set this to false if you prefer
dependencies to be cached only when installing new tools.
:Default: ``true``
:Type: bool
@@ -451,7 +452,7 @@
~~~~~~~~~~~~~~~
:Description:
Set to True to enable monitoring of tools and tool directories
Set to true to enable monitoring of tools and tool directories
listed in any tool config file specified in tool_config_file
option. If changes are found, tools are automatically reloaded.
Watchdog ( https://pypi.org/project/watchdog/ ) must be installed
@@ -469,7 +470,7 @@
~~~~~~~~~~~~~~~~~~~
:Description:
Set to True to enable monitoring of dynamic job rules. If changes
Set to true to enable monitoring of dynamic job rules. If changes
are found, rules are automatically reloaded. Takes the same values
as the 'watch_tools' option.
:Default: ``false``
@@ -535,7 +536,7 @@
`requirement`s. The following path is the location of involucro on
the Galaxy host. This is ignored if the relevant container
resolver isn't enabled, and will install on demand unless
involucro_auto_init is set to False.
involucro_auto_init is set to false.
:Default: ``database/dependencies/involucro``
:Type: str
@@ -660,7 +661,7 @@
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set to True to enable monitoring of the tool_data and
Set to true to enable monitoring of the tool_data and
shed_tool_data_path directories. If changes in tool data table
files are found, the tool data tables for that data manager are
automatically reloaded. Watchdog (
@@ -716,7 +717,7 @@
:Description:
Enable sniffing of compressed datatypes. This can be
configured/overridden on a per-datatype basis in the
datatypes_conf.xml file. With this option set to False the
datatypes_conf.xml file. With this option set to false the
compressed datatypes will be unpacked before sniffing.
:Default: ``true``
:Type: bool
@@ -767,7 +768,7 @@
:Description:
To run interactive environment containers in Docker Swarm mode (on
an existing swarm), set this option to True and set
an existing swarm), set this option to true and set
`docker_connect_port` in the IE plugin config (ini) file(s) of any
IE plugins you have enabled and ensure that you are not using any
`docker run`-specific options in your plugins' `command_inject`
@@ -1099,9 +1100,9 @@
~~~~~~~~~~~~~~~~~~~~~~
:Description:
User account activation feature global flag. If set to "False",
the rest of the Account activation configuration is ignored and
user activation is disabled (i.e. accounts are active since
User account activation feature global flag. If set to false, the
rest of the Account activation configuration is ignored and user
activation is disabled (i.e. accounts are active since
registration). The activation is also not working in case the SMTP
server is not defined.
:Default: ``false``
@@ -1176,9 +1177,9 @@
Galaxy can display data at various external browsers. These
options specify which browsers should be available. URLs and
builds available at these browsers are defined in the specified
files. If use_remote_user = True, display application servers
will be denied access to Galaxy and so displaying datasets in
these sites will fail. display_servers contains a list of
files. If use_remote_user is set to true, display application
servers will be denied access to Galaxy and so displaying datasets
in these sites will fail. display_servers contains a list of
hostnames which should be allowed to bypass security to display
datasets. Please be aware that there are security implications if
this is allowed. More details (including required changes to the
@@ -1197,15 +1198,15 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
To disable the old-style display applications that are hardcoded
into datatype classes, set enable_old_display_applications =
False. This may be desirable due to using the new-style, XML-
defined, display applications that have been defined for many of
the datatypes that have the old-style. There is also a potential
security concern with the old-style applications, where a
malicious party could provide a link that appears to reference the
Galaxy server, but contains a redirect to a third-party server,
tricking a Galaxy user to access said site.
Set this to false to disable the old-style display applications
that are hardcoded into datatype classes. This may be desirable
due to using the new-style, XML-defined, display applications that
have been defined for many of the datatypes that have the old-
style. There is also a potential security concern with the old-
style applications, where a malicious party could provide a link
that appears to reference the Galaxy server, but contains a
redirect to a third-party server, tricking a Galaxy user to access
said site.
:Default: ``true``
:Type: bool
@@ -1576,7 +1577,7 @@
For help on configuring the Advanced proxy features, see:
https://docs.galaxyproject.org/en/master/admin/production.html
Apache can handle file downloads (Galaxy-to-user) via
mod_xsendfile. Set this to True to inform Galaxy that
mod_xsendfile. Set this to true to inform Galaxy that
mod_xsendfile is enabled upstream.
:Default: ``false``
:Type: bool
@@ -1697,9 +1698,9 @@
other services based on Galaxy's session cookie. It will attempt
to do this by default though you do need to install node+npm and
do an npm install from `lib/galaxy/web/proxy/js`. It is generally
more robust to configure this externally, managing it however
Galaxy is managed. If True, Galaxy will only launch the proxy if
it is actually going to be used (e.g. for Jupyter).
more robust to configure this externally, managing it in the same
way Galaxy itself is managed. If true, Galaxy will only launch
the proxy if it is actually going to be used (e.g. for Jupyter).
:Default: ``true``
:Type: bool
@@ -1733,7 +1734,8 @@
:Description:
Set the port and IP for the dynamic proxy to bind to, this must
match the external configuration if dynamic_proxy_manage is False.
match the external configuration if dynamic_proxy_manage is set to
false.
:Default: ``8800``
:Type: int
@@ -1744,7 +1746,8 @@
:Description:
Set the port and IP for the dynamic proxy to bind to, this must
match the external configuration if dynamic_proxy_manage is False.
match the external configuration if dynamic_proxy_manage is set to
false.
:Default: ``0.0.0.0``
:Type: str
@@ -1837,7 +1840,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If True, Galaxy will attempt to configure a simple root logger if
If true, Galaxy will attempt to configure a simple root logger if
a "loggers" section does not appear in this configuration file.
:Default: ``true``
:Type: bool
@@ -1984,8 +1987,7 @@
By default Galaxy will serve non-HTML tool output that may
potentially contain browser executable JavaScript content as plain
text. This will for instance cause SVG datasets to not render
properly and so may be disabled by setting the following option to
True.
properly and so may be disabled by setting this option to true.
:Default: ``false``
:Type: bool
@@ -2011,12 +2013,11 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the following to True to use Jupyter nbconvert to build HTML
from Jupyter notebooks in Galaxy histories. This process may
allow users to execute arbitrary code or serve arbitrary HTML. If
enabled, Jupyter must be available and on Galaxy's PATH, to do
this run `pip install jinja2 pygments jupyter` in Galaxy's
virtualenv.
Set to true to use Jupyter nbconvert to build HTML from Jupyter
notebooks in Galaxy histories. This process may allow users to
execute arbitrary code or serve arbitrary HTML. If enabled,
Jupyter must be available and on Galaxy's PATH, to do this run
`pip install jinja2 pygments jupyter` in Galaxy's virtualenv.
:Default: ``false``
:Type: bool
@@ -2294,7 +2295,7 @@
allowing admins to paste filesystem paths to files and directories
in a box, and these paths will be added to a library. For history
uploads, this allows pasting in paths as URIs. (i.e. prefixed with
file://). Set to True to enable. Please note the security
file://). Set to true to enable. Please note the security
implication that this will give Galaxy Admins access to anything
your Galaxy user has access to.
:Default: ``false``
@@ -2559,8 +2560,8 @@
:Description:
If your proxy and/or authentication source does not normalize
e-mail addresses or user names being passed to Galaxy - set the
following option to True to force these to lower case.
e-mail addresses or user names being passed to Galaxy - set this
option to true to force these to lower case.
:Default: ``false``
:Type: bool
@@ -2609,7 +2610,7 @@
:Description:
Show the site's welcome page (see welcome_url) alongside the login
page (even if require_login is True)
page (even if require_login is true).
:Default: ``false``
:Type: bool
@@ -2641,7 +2642,7 @@
:Description:
Allow administrators to log in as other users (useful for
debugging)
debugging).
:Default: ``false``
:Type: bool
@@ -2674,7 +2675,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
By default, users' data will be public, but setting this to True
By default, users' data will be public, but setting this to true
will cause it to be private. Does not affect existing users and
data, only ones created after this option is set. Users may still
change their default back to public.
@@ -2687,14 +2688,14 @@
~~~~~~~~~~~~~~~~~~~~
:Description:
Expose user list. Setting this to True will expose the user list
Expose user list. Setting this to true will expose the user list
to authenticated users. This makes sharing datasets in smaller
galaxy instances much easier as they can type a name/email and
have the correct user show up. This makes less sense on large
public Galaxy instances where that data shouldn't be exposed. For
semi-public Galaxies, it may make sense to expose just the
username and not email, or vice versa. If enable_beta_gdpr is set
to True, then this option will be overridden and set to False.
to true, then this option will be overridden and set to false.
:Default: ``false``
:Type: bool
@@ -2704,14 +2705,14 @@
~~~~~~~~~~~~~~~~~~~~~
:Description:
Expose user list. Setting this to True will expose the user list
Expose user list. Setting this to true will expose the user list
to authenticated users. This makes sharing datasets in smaller
galaxy instances much easier as they can type a name/email and
have the correct user show up. This makes less sense on large
public Galaxy instances where that data shouldn't be exposed. For
semi-public Galaxies, it may make sense to expose just the
username and not email, or vice versa. If enable_beta_gdpr is set
to True, then this option will be overridden and set to False.
to true, then this option will be overridden and set to false.
:Default: ``false``
:Type: bool
@@ -2753,17 +2754,6 @@
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_beta_ts_api_install``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable the new interface for installing tools from Tool Shed via
the API. Admin menu will list both if enabled.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_beta_containers_interface``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -3000,9 +2990,9 @@
datasets are selected for "Set at Runtime" inputs from the history
such that the same input will not be selected twice, unless there
are more inputs than compatible datasets in the history. When
False, the most recently added compatible item in the history will
false, the most recently added compatible item in the history will
be used for each "Set at Runtime" input, independent of others in
the Workflow
the workflow.
:Default: ``false``
:Type: bool
@@ -3013,7 +3003,7 @@
:Description:
The URL to the myExperiment instance being used (omit scheme but
include port)
include port).
:Default: ``www.myexperiment.org:80``
:Type: str
@@ -3073,8 +3063,8 @@
~~~~~~~~~~~~~~~~~~~~
:Description:
This should be set to False to prevent Galaxy from deleting
uploaded FTP files as it imports them.
Set to false to prevent Galaxy from deleting uploaded FTP files as
it imports them.
:Default: ``true``
:Type: bool
@@ -3210,6 +3200,20 @@
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~
``dependency_resolution``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Alternative representation of various dependency resolution
parameters. Takes the dictified version of a DependencyManager
object - so this is ideal for automating the configuration of
dependency resolution from one application that uses a
DependencyManager to another.
:Default: ``None``
:Type: map
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``default_job_resubmission_condition``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -3290,7 +3294,7 @@
fail. In these instances, you can choose to retry setting it
internally or leave it in a failed state (since retrying
internally may cause the Galaxy process to be unresponsive). If
this option is set to False, the user will be given the option to
this option is set to false, the user will be given the option to
retry externally, or set metadata manually (when possible).
:Default: ``true``
:Type: bool
@@ -3510,7 +3514,7 @@
several extra database queries must be performed to determine the
number of jobs a user has dispatched to a given destination. By
default, these queries will happen for every job that is waiting
to run, but if cache_user_job_count is set to True, it will only
to run, but if cache_user_job_count is set to true, it will only
happen once per iteration of the handler queue. Although better
for performance due to reduced queries, the trade-off is a greater
possibility that jobs will be dispatched past the configured
doc/source/lib/log_tempfile.rst
-7
View File
@@ -1,7 +0,0 @@
log\_tempfile module
====================
.. automodule:: log_tempfile
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/mimeparse.rst
-7
View File
@@ -1,7 +0,0 @@
mimeparse module
================
.. automodule:: mimeparse
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/modules.rst
-3
View File
@@ -6,7 +6,4 @@ lib
galaxy
galaxy_ext
log_tempfile
mimeparse
psyco_full
tool_shed
doc/source/lib/psyco_full.rst
-7
View File
@@ -1,7 +0,0 @@
psyco\_full module
==================
.. automodule:: psyco_full
:members:
:undoc-members:
:show-inheritance:
lib/galaxy/app.py
+1 -1
View File
@@ -11,6 +11,7 @@ import galaxy.queues
import galaxy.quota
import galaxy.security
from galaxy import config, job_metrics, jobs
from galaxy.config_watchers import ConfigWatchers
from galaxy.containers import build_container_interfaces
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.folders import FolderManager
@@ -41,7 +42,6 @@ from galaxy.visualization.plugins.registry import VisualizationsRegistry
from galaxy.web import url_for
from galaxy.web.proxy import ProxyManager
from galaxy.web_stack import application_stack_instance
from galaxy.webapps.galaxy.config_watchers import ConfigWatchers
from galaxy.webhooks import WebhooksRegistry
from tool_shed.galaxy_install import (
installed_repository_manager,
lib/galaxy/auth/__init__.py
+1 -1
View File
@@ -15,7 +15,7 @@ class AuthManager(object):
def __init__(self, app):
self.__app = app
self.redact_username_in_logs = app.config.redact_username_in_logs
self.authenticators = get_authenticators(app.config.auth_config_file)
self.authenticators = get_authenticators(app.config.auth_config_file, app.config.auth_config_file_set)
def check_registration_allowed(self, email, username, password):
"""Checks if the provided email/username is allowed to register."""
lib/galaxy/auth/util.py
+21 -3
View File
@@ -1,3 +1,4 @@
import errno
import logging
import xml.etree.ElementTree
from collections import namedtuple
@@ -10,14 +11,31 @@ from galaxy.util import plugin_config, string_as_bool
log = logging.getLogger(__name__)
AUTH_CONF_XML = """<?xml version="1.0"?>
<auth>
<authenticator>
<type>localdb</type>
<options>
<allow-password-change>true</allow-password-change>
</options>
</authenticator>
</auth>
"""
Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
def get_authenticators(auth_config_file):
def get_authenticators(auth_config_file, auth_config_file_set):
__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, 'plugin_type')
# parse XML
ct = xml.etree.ElementTree.parse(auth_config_file)
conf_root = ct.getroot()
try:
ct = xml.etree.ElementTree.parse(auth_config_file)
conf_root = ct.getroot()
except (OSError, IOError) as exc:
if exc.errno == errno.ENOENT and not auth_config_file_set:
conf_root = xml.etree.ElementTree.fromstring(AUTH_CONF_XML)
else:
raise
authenticators = []
# process authenticators
lib/galaxy/config.py → lib/galaxy/config/__init__.py
+214 -162
View File
@@ -5,6 +5,7 @@ Universe configuration builder.
from __future__ import absolute_import
import collections
import errno
import ipaddress
import logging
import logging.config
@@ -25,6 +26,8 @@ from six.moves import configparser
from galaxy.containers import parse_containers_config
from galaxy.exceptions import ConfigurationError
from galaxy.model import mapping
from galaxy.model.tool_shed_install.migrate.check import create_or_verify_database as tsi_create_or_verify_database
from galaxy.tool_util.deps.container_resolvers.mulled import DEFAULT_CHANNELS
from galaxy.util import (
ExecutionTimer,
@@ -34,59 +37,16 @@ from galaxy.util import (
)
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.util.logging import LOGLV_TRACE
from galaxy.util.properties import find_config_file, running_from_source
from galaxy.web.formatting import expand_pretty_datetime_format
from galaxy.web_stack import (
get_stack_facts,
register_postfork_function
)
from .version import VERSION_MAJOR
from ..version import VERSION_MAJOR
log = logging.getLogger(__name__)
PATH_DEFAULTS = dict(
auth_config_file=['config/auth_conf.xml', 'config/auth_conf.xml.sample'],
data_manager_config_file=['config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample'],
datatypes_config_file=['config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample'],
build_sites_config_file=['config/build_sites.yml', 'config/build_sites.yml.sample'],
job_config_file=['config/job_conf.xml', 'job_conf.xml'],
tool_destinations_config_file=['config/tool_destinations.yml', 'config/tool_destinations.yml.sample'],
job_metrics_config_file=['config/job_metrics_conf.xml', 'job_metrics_conf.xml', 'config/job_metrics_conf.xml.sample'],
error_report_file=['config/error_report.yml', 'config/error_report.yml.sample'],
oidc_config_file=['config/oidc_config.yml', 'config/oidc_config.yml.sample'],
oidc_backends_config_file=['config/oidc_backends_config.yml', 'config/oidc_backends_config.yml.sample'],
dependency_resolvers_config_file=['config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml', None],
job_resource_params_file=['config/job_resource_params_conf.xml', 'job_resource_params_conf.xml'],
workflow_resource_params_file=['config/workflow_resource_params_conf.xml', 'workflow_resource_params_conf.xml'],
migrated_tools_config=['migrated_tools_conf.xml', 'config/migrated_tools_conf.xml'],
object_store_config_file=['config/object_store_conf.xml', 'object_store_conf.xml'],
shed_data_manager_config_file=['shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml'],
shed_tool_data_table_config=['shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml'],
tool_sheds_config_file=['config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample'],
workflow_schedulers_config_file=['config/workflow_schedulers_conf.xml', 'config/workflow_schedulers_conf.xml.sample'],
modules_mapping_files=['config/environment_modules_mapping.yml', 'config/environment_modules_mapping.yml.sample'],
local_conda_mapping_file=['config/local_conda_mapping.yml', 'config/local_conda_mapping.yml.sample'],
containers_config_file=['config/containers_conf.yml'],
)
PATH_LIST_DEFAULTS = dict(
tool_data_table_config_path=['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample'],
# rationale:
# [0]: user has explicitly created config/tool_conf.xml but did not
# move their existing shed_tool_conf.xml, don't use
# config/shed_tool_conf.xml, which is probably the empty
# version copied from the sample, or else their shed tools
# will disappear
# [1]: user has created config/tool_conf.xml and, having passed
# [0], probably moved their shed_tool_conf.xml as well
# [2]: user has done nothing, use the old files
# [3]: fresh install
tool_config_file=['config/tool_conf.xml,shed_tool_conf.xml',
'config/tool_conf.xml,config/shed_tool_conf.xml',
'tool_conf.xml,shed_tool_conf.xml',
'config/tool_conf.xml.sample,config/shed_tool_conf.xml']
)
LOGGING_CONFIG_DEFAULT = {
'version': 1,
'root': {
@@ -139,40 +99,112 @@ def resolve_path(path, root):
return path
def find_path(kwargs, var, root):
"""Find a configuration path that may exist at different defaults."""
defaults = PATH_DEFAULTS[var]
if kwargs.get(var, None) is not None:
path = kwargs.get(var)
else:
for default in defaults:
if default is None:
# if None is the final default - just return that.
return None
if os.path.exists(resolve_path(default, root)):
path = default
break
else:
path = defaults[-1]
return resolve_path(path, root)
def find_root(kwargs):
root = kwargs.get('root_dir', '.')
return root
class Configuration(object):
class BaseAppConfiguration(object):
def _set_config_base(self, config_kwargs):
self.sample_config_dir = os.path.join(os.path.dirname(__file__), 'sample')
self.config_file = find_config_file('galaxy')
# Parse global_conf and save the parser
self.global_conf = config_kwargs.get('global_conf', None)
self.global_conf_parser = configparser.ConfigParser()
if not self.config_file and self.global_conf and "__file__" in self.global_conf:
self.config_file = self.global_conf['__file__']
if self.config_file is None:
log.warning("No Galaxy config file found, running from current working directory: %s", os.getcwd())
else:
try:
self.global_conf_parser.read(self.config_file)
except (IOError, OSError):
raise
except Exception:
# Not an INI file
pass
self.config_dir = config_kwargs.get('config_dir', os.path.dirname(self.config_file or os.getcwd()))
self.data_dir = config_kwargs.get('data_dir', None)
# mutable_config_dir is intentionally not configurable. You can
# override individual mutable configs with config options, but they
# should be considered Galaxy-controlled data files and will by default
# just live in the data dir
if running_from_source:
if self.data_dir is None:
self.data_dir = os.path.join(self.root, 'database')
if self.config_file is None:
self.config_dir = os.path.join(self.root, 'config')
self.mutable_config_dir = self.config_dir
# TODO: do we still need to support ../shed_tools?
self.shed_tools_dir = os.path.join(self.data_dir, 'shed_tools')
else:
if self.data_dir is None:
self.data_dir = os.path.join(self.config_dir, 'data')
self.mutable_config_dir = os.path.join(self.data_dir, 'config')
self.shed_tools_dir = os.path.join(self.data_dir, 'shed_tools')
log.debug("Configuration directory is %s", self.config_dir)
log.debug("Data directory is %s", self.data_dir)
log.debug("Mutable config directory is %s", self.mutable_config_dir)
def _in_mutable_config_dir(self, path):
return os.path.join(self.mutable_config_dir, path)
def _in_config_dir(self, path):
return os.path.join(self.config_dir, path)
def _in_sample_dir(self, path):
return os.path.join(self.sample_config_dir, path)
def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
for var, defaults in defaults.items():
if config_kwargs.get(var, None) is not None:
path = config_kwargs.get(var)
setattr(self, var + '_set', True)
else:
for default in defaults:
if os.path.exists(resolve_path(default, self.root)):
path = default
break
else:
path = defaults[-1]
setattr(self, var + '_set', False)
setattr(self, var, resolve_path(path, self.root))
for var, defaults in listify_defaults.items():
paths = []
if config_kwargs.get(var, None) is not None:
paths = listify(config_kwargs.get(var))
else:
for default in defaults:
for path in listify(default):
if not os.path.exists(resolve_path(path, self.root)):
break
else:
paths = listify(default)
break
else:
paths = listify(defaults[-1])
setattr(self, var, [resolve_path(x, self.root) for x in paths])
class GalaxyAppConfiguration(BaseAppConfiguration):
deprecated_options = ('database_file', 'track_jobs_in_database')
default_config_file_name = 'galaxy.yml'
def __init__(self, **kwargs):
self.config_dict = kwargs
self.root = find_root(kwargs)
self._set_config_base(kwargs)
# Configs no longer read from samples
self.migrated_tools_config = resolve_path(kwargs.get('migrated_tools_conf', 'migrated_tools_conf.xml'), self.mutable_config_dir)
self.shed_tool_conf = resolve_path(kwargs.get('shed_tool_conf', 'shed_tool_conf.xml'), self.mutable_config_dir)
for name in ('migrated_tools_config', 'shed_tool_conf'):
setattr(self, name + '_set', kwargs.get(name, None) is not None)
# Resolve paths of other config files
self.__parse_config_file_options(kwargs)
self.parse_config_file_options(kwargs)
# Collect the umask and primary gid from the environment
self.umask = os.umask(0o77) # get the current umask
@@ -182,8 +214,8 @@ class Configuration(object):
self.version_major = VERSION_MAJOR
# Database related configuration
self.check_migrate_databases = kwargs.get('check_migrate_databases', True)
self.database = resolve_path(kwargs.get("database_file", "database/universe.sqlite"), self.root)
self.database_connection = kwargs.get("database_connection", False)
self.database_connection = kwargs.get("database_connection",
"sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path("universe.sqlite", self.data_dir))
self.database_engine_options = get_database_engine_options(kwargs)
self.database_create_tables = string_as_bool(kwargs.get("database_create_tables", "True"))
self.database_query_profiling_proxy = string_as_bool(kwargs.get("database_query_profiling_proxy", "False"))
@@ -210,19 +242,21 @@ class Configuration(object):
self.database_wait_sleep = float(kwargs.get("database_wait_sleep", 1))
# Where dataset files are stored
self.file_path = resolve_path(kwargs.get("file_path", "database/files"), self.root)
self.file_path = resolve_path(kwargs.get("file_path", "files"), self.data_dir)
# new_file_path and legacy_home_dir can be overridden per destination in job_conf.
self.new_file_path = resolve_path(kwargs.get("new_file_path", "database/tmp"), self.root)
self.new_file_path = resolve_path(kwargs.get("new_file_path", "tmp"), self.data_dir)
override_tempdir = string_as_bool(kwargs.get("override_tempdir", "True"))
if override_tempdir:
tempfile.tempdir = self.new_file_path
self.shared_home_dir = kwargs.get("shared_home_dir", None)
self.openid_consumer_cache_path = resolve_path(kwargs.get("openid_consumer_cache_path", "database/openid_consumer_cache"), self.root)
self.openid_consumer_cache_path = resolve_path(kwargs.get("openid_consumer_cache_path", "openid_consumer_cache"), self.data_dir)
self.cookie_path = kwargs.get("cookie_path", None)
self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False))
self.enable_unique_workflow_defaults = string_as_bool(kwargs.get('enable_unique_workflow_defaults', False))
self.tool_path = resolve_path(kwargs.get("tool_path", "tools"), self.root)
self.tool_data_path = resolve_path(kwargs.get("tool_data_path", "tool-data"), os.getcwd())
if not running_from_source and kwargs.get("tool_data_path", None) is None:
self.tool_data_path = resolve_path("tool-data", self.data_dir)
self.builds_file_path = resolve_path(kwargs.get("builds_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt')), self.root)
self.len_file_path = resolve_path(kwargs.get("len_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom')), self.root)
# Galaxy OIDC settings.
@@ -231,8 +265,8 @@ class Configuration(object):
self.oidc_backends_config = kwargs.get("oidc_backends_config_file", self.oidc_backends_config_file)
self.oidc = []
# The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution
# and moved to the tool shed.
self.integrated_tool_panel_config = resolve_path(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'), self.root)
# and moved to the tool shed. It is created on demand.
self.integrated_tool_panel_config = resolve_path(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'), self.mutable_config_dir)
integrated_tool_panel_tracking_directory = kwargs.get('integrated_tool_panel_tracking_directory', None)
if integrated_tool_panel_tracking_directory:
self.integrated_tool_panel_tracking_directory = resolve_path(integrated_tool_panel_tracking_directory, self.root)
@@ -317,13 +351,14 @@ class Configuration(object):
self.show_user_prepopulate_form = string_as_bool(kwargs.get("show_user_prepopulate_form", "False"))
self.new_user_dataset_access_role_default_private = string_as_bool(kwargs.get("new_user_dataset_access_role_default_private", "False"))
self.template_path = resolve_path(kwargs.get("template_path", "templates"), self.root)
self.template_cache = resolve_path(kwargs.get("template_cache_path", "database/compiled_templates"), self.root)
self.template_cache = resolve_path(kwargs.get("template_cache_path", "compiled_templates"), self.data_dir)
self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
self.cluster_files_directory = os.path.abspath(kwargs.get("cluster_files_directory", "database/pbs"))
self.cluster_files_directory = os.path.abspath(resolve_path(kwargs.get("cluster_files_directory", "pbs"), self.data_dir))
# Fall back to legacy job_working_directory config variable if set.
default_jobs_directory = kwargs.get("job_working_directory", "database/jobs_directory")
self.jobs_directory = resolve_path(kwargs.get("jobs_directory", default_jobs_directory), self.root)
default_jobs_directory = kwargs.get("job_working_directory", "jobs_directory")
self.jobs_directory = resolve_path(kwargs.get("jobs_directory", default_jobs_directory), self.data_dir)
self.default_job_shell = kwargs.get("default_job_shell", "/bin/bash")
self.cleanup_job = kwargs.get("cleanup_job", "always")
preserve_python_environment = kwargs.get("preserve_python_environment", "legacy_only")
@@ -334,7 +369,7 @@ class Configuration(object):
self.nodejs_path = kwargs.get("nodejs_path", None)
# Older default container cache path, I don't think anyone is using it anymore and it wasn't documented - we
# should probably drop the backward compatiblity to save the path check.
self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", "database/container_images"))
self.container_image_cache_path = resolve_path(kwargs.get("container_image_cache_path", "container_images"), self.data_dir)
if not os.path.exists(self.container_image_cache_path):
self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", "database/container_cache"))
self.outputs_to_working_directory = string_as_bool(kwargs.get('outputs_to_working_directory', False))
@@ -385,10 +420,6 @@ class Configuration(object):
# Tasked job runner.
self.use_tasked_jobs = string_as_bool(kwargs.get('use_tasked_jobs', False))
self.local_task_queue_workers = int(kwargs.get("local_task_queue_workers", 2))
# Enable new interface for API installations from TS.
# Admin menu will list both if enabled.
self.enable_beta_ts_api_install = string_as_bool(kwargs.get('enable_beta_ts_api_install', 'True'))
# The transfer manager and deferred job queue
self.enable_beta_job_managers = string_as_bool(kwargs.get('enable_beta_job_managers', 'False'))
# Set this to go back to setting the object store in the tool request instead of
@@ -525,7 +556,7 @@ class Configuration(object):
involucro_path = kwargs.get('involucro_path', None)
if involucro_path is None:
target_dir = kwargs.get("tool_dependency_dir", "database/dependencies")
target_dir = resolve_path(kwargs.get("tool_dependency_dir", "dependencies"), self.data_dir)
if target_dir == "none":
target_dir = "database"
involucro_path = os.path.join(target_dir, "involucro")
@@ -554,7 +585,7 @@ class Configuration(object):
self.nginx_upload_store = os.path.abspath(self.nginx_upload_store)
self.object_store = kwargs.get('object_store', 'disk')
self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
self.object_store_cache_path = resolve_path(kwargs.get("object_store_cache_path", "database/object_store_cache"), self.root)
self.object_store_cache_path = resolve_path(kwargs.get("object_store_cache_path", "database/object_store_cache"), self.data_dir)
self.object_store_store_by = kwargs.get("object_store_store_by", "id")
# Handle AWS-specific config options for backward compatibility
@@ -578,17 +609,9 @@ class Configuration(object):
self.distributed_object_store_config_file = resolve_path(self.distributed_object_store_config_file, self.root)
self.irods_root_collection_path = kwargs.get('irods_root_collection_path', None)
self.irods_default_resource = kwargs.get('irods_default_resource', None)
# Parse global_conf and save the parser
global_conf = kwargs.get('global_conf', None)
global_conf_parser = configparser.ConfigParser()
self.config_file = None
self.global_conf_parser = global_conf_parser
if global_conf and "__file__" in global_conf and ".yml" not in global_conf["__file__"]:
self.config_file = global_conf['__file__']
global_conf_parser.read(global_conf['__file__'])
# Heartbeat log file name override
if global_conf is not None and 'heartbeat_log' in global_conf:
self.heartbeat_log = global_conf['heartbeat_log']
if self.global_conf is not None and 'heartbeat_log' in self.global_conf:
self.heartbeat_log = self.global_conf['heartbeat_log']
if self.heartbeat_log is None:
self.heartbeat_log = 'heartbeat_{server_name}.log'
# Determine which 'server:' this is
@@ -605,7 +628,7 @@ class Configuration(object):
self.config_dict['base_server_name'] = self.base_server_name = self.server_name
# Store all configured server names for the message queue routing
self.server_names = []
for section in global_conf_parser.sections():
for section in self.global_conf_parser.sections():
if section.startswith('server:'):
self.server_names.append(section.replace('server:', '', 1))
@@ -620,7 +643,7 @@ class Configuration(object):
# so dependending on the context a better default can be used (
# request url in a web thread, Docker parent in IE stuff, etc...)
galaxy_infrastructure_url = "http://localhost"
web_port = self.galaxy_infrastructure_web_port or self.guess_galaxy_port()
web_port = self.galaxy_infrastructure_web_port
if web_port:
galaxy_infrastructure_url += ":%s" % (web_port)
galaxy_infrastructure_url_set = False
@@ -649,7 +672,7 @@ class Configuration(object):
elif 'database_connection' in kwargs:
self.amqp_internal_connection = "sqlalchemy+" + self.database_connection
else:
self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path("database/control.sqlite", self.root)
self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path("control.sqlite", self.data_dir)
self.pretty_datetime_format = expand_pretty_datetime_format(kwargs.get('pretty_datetime_format', '$locale (UTC)'))
self.user_preferences_extra_config_file = kwargs.get('user_preferences_extra_conf_path', 'config/user_preferences_extra_conf.yml')
try:
@@ -697,7 +720,7 @@ class Configuration(object):
self.gie_swarm_mode = string_as_bool(kwargs.get('interactive_environment_swarm_mode', False))
self.proxy_session_map = self.resolve_path(kwargs.get("dynamic_proxy_session_map", "database/session_map.sqlite"))
self.proxy_session_map = resolve_path(kwargs.get("dynamic_proxy_session_map", "session_map.sqlite"), self.data_dir)
self.manage_dynamic_proxy = string_as_bool(kwargs.get("dynamic_proxy_manage", "True")) # Set to false if being launched externally
self.dynamic_proxy_debug = string_as_bool(kwargs.get("dynamic_proxy_debug", "False"))
self.dynamic_proxy_bind_port = int(kwargs.get("dynamic_proxy_bind_port", "8800"))
@@ -717,8 +740,8 @@ class Configuration(object):
self.display_chunk_size = int(kwargs.get('display_chunk_size', 65536))
self.citation_cache_type = kwargs.get("citation_cache_type", "file")
self.citation_cache_data_dir = self.resolve_path(kwargs.get("citation_cache_data_dir", "database/citations/data"))
self.citation_cache_lock_dir = self.resolve_path(kwargs.get("citation_cache_lock_dir", "database/citations/locks"))
self.citation_cache_data_dir = resolve_path(kwargs.get("citation_cache_data_dir", "citations/data"), self.data_dir)
self.citation_cache_lock_dir = resolve_path(kwargs.get("citation_cache_lock_dir", "citations/locks"), self.data_dir)
self.containers_conf = parse_containers_config(self.containers_config_file)
@@ -790,6 +813,76 @@ class Configuration(object):
else:
return None
def parse_config_file_options(self, kwargs):
"""
Backwards compatibility for config files moved to the config/ dir.
"""
defaults = dict(
auth_config_file=[self._in_config_dir('auth_conf.xml')],
build_sites_config_file=[self._in_config_dir('build_sites.yml')],
containers_config_file=[self._in_config_dir('containers_conf.yml')],
data_manager_config_file=[self._in_config_dir('data_manager_conf.xml')],
datatypes_config_file=[self._in_config_dir('datatypes_conf.xml'), self._in_sample_dir('datatypes_conf.xml.sample')],
dependency_resolvers_config_file=[self._in_config_dir('dependency_resolvers_conf.xml')],
error_report_file=[self._in_config_dir('error_report.yml')],
job_config_file=[self._in_config_dir('job_conf.xml')],
job_metrics_config_file=[self._in_config_dir('job_metrics_conf.xml')],
job_resource_params_file=[self._in_config_dir('job_resource_params_conf.xml')],
local_conda_mapping_file=[self._in_config_dir('local_conda_mapping.yml')],
migrated_tools_config=[self._in_config_dir('migrated_tools_conf.xml')],
modules_mapping_files=[self._in_config_dir('environment_modules_mapping.yml')],
object_store_config_file=[self._in_config_dir('object_store_conf.xml')],
oidc_backends_config_file=[self._in_config_dir('config/oidc_backends_config.yml')],
oidc_config_file=[self._in_config_dir('oidc_config.yml')],
shed_data_manager_config_file=[self._in_mutable_config_dir('shed_data_manager_conf.xml')],
shed_tool_data_table_config=[self._in_mutable_config_dir('shed_tool_data_table_conf.xml')],
tool_destinations_config_file=[self._in_config_dir('config/tool_destinations.yml')],
tool_sheds_config_file=[self._in_config_dir('tool_sheds_conf.xml')],
workflow_resource_params_file=[self._in_config_dir('workflow_resource_params_conf.xml')],
workflow_schedulers_config_file=[self._in_config_dir('config/workflow_schedulers_conf.xml')],
)
if running_from_source:
listify_defaults = {
'tool_data_table_config_path': ['config/tool_data_table_conf.xml',
'tool_data_table_conf.xml',
'lib/galaxy/config/sample/tool_data_table_conf.xml.sample'],
# rationale:
# [0]: user has explicitly created config/tool_conf.xml but did not
# move their existing shed_tool_conf.xml, don't use
# config/shed_tool_conf.xml, which is probably the empty
# version copied from the sample, or else their shed tools
# will disappear
# [1]: user has created config/tool_conf.xml and, having passed
# [0], probably moved their shed_tool_conf.xml as well
# [2]: user has done nothing, use the old files
# [3]: fresh install (shed_tool_conf will be added later)
'tool_config_file': ['config/tool_conf.xml,shed_tool_conf.xml',
'config/tool_conf.xml,config/shed_tool_conf.xml',
'tool_conf.xml,shed_tool_conf.xml',
'lib/galaxy/config/sample/tool_conf.xml.sample']
}
else:
listify_defaults = {
'tool_data_table_config_path': [
self._in_config_dir('tool_data_table_conf.xml'),
self._in_sample_dir('tool_data_table_conf.xml.sample')],
'tool_config_file': [
self._in_config_dir('tool_conf.xml'),
self._in_sample_dir('tool_conf.xml.sample')]
}
self._parse_config_file_options(defaults, listify_defaults, kwargs)
# If the user has configured a shed tool config in tool_config_file
# this would add a second, but since we're not parsing them yet we
# don't know if that's the case.
if not running_from_source and self.shed_tool_conf not in self.tool_config_file:
self.tool_config_file.append(self.shed_tool_conf)
# Backwards compatibility for names used in too many places to fix
self.datatypes_config = self.datatypes_config_file
self.tool_configs = self.tool_config_file
def reload_sanitize_whitelist(self, explicit=True):
self.sanitize_whitelist = []
try:
@@ -801,34 +894,6 @@ class Configuration(object):
if explicit:
log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
def __parse_config_file_options(self, kwargs):
"""
Backwards compatibility for config files moved to the config/ dir.
"""
for var in PATH_DEFAULTS:
setattr(self, var, find_path(kwargs, var, self.root))
for var, defaults in PATH_LIST_DEFAULTS.items():
paths = []
if kwargs.get(var, None) is not None:
paths = listify(kwargs.get(var))
else:
for default in defaults:
for path in listify(default):
if not os.path.exists(resolve_path(path, self.root)):
break
else:
paths = listify(default)
break
else:
paths = listify(defaults[-1])
setattr(self, var, [resolve_path(x, self.root) for x in paths])
# Backwards compatibility for names used in too many places to fix
self.datatypes_config = self.datatypes_config_file
self.tool_configs = self.tool_config_file
def get(self, key, default):
return self.config_dict.get(key, default)
@@ -849,7 +914,7 @@ class Configuration(object):
raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
def check(self):
paths_to_check = [self.root, self.tool_path, self.tool_data_path, self.template_path]
paths_to_check = [self.tool_data_path, self.data_dir, self.mutable_config_dir]
# Check that required directories exist
for path in paths_to_check:
if path not in [None, False] and not os.path.isdir(path):
@@ -864,10 +929,10 @@ class Configuration(object):
self._ensure_directory(path)
# Check that required files exist
tool_configs = self.tool_configs
if self.migrated_tools_config not in tool_configs:
if self.migrated_tools_config not in tool_configs and os.path.exists(self.migrated_tools_config):
tool_configs.append(self.migrated_tools_config)
for path in tool_configs:
if not os.path.exists(path):
if not os.path.exists(path) and path != self.shed_tool_conf:
raise ConfigurationError("Tool config file not found: %s" % path)
for datatypes_config in listify(self.datatypes_config):
if not os.path.isfile(datatypes_config):
@@ -892,19 +957,6 @@ class Configuration(object):
"""
return resolve_path(path, self.root)
def guess_galaxy_port(self):
# Code derived from Jupyter work ie.mako
config = configparser.SafeConfigParser({'port': '8080'})
if self.config_file:
config.read(self.config_file)
try:
port = config.getint('server:%s' % self.server_name, 'port')
except Exception:
# uWSGI galaxy installations don't use paster and only speak uWSGI not http
port = None
return port
@staticmethod
def _parse_allowed_origin_hostnames(kwargs):
"""
@@ -925,6 +977,10 @@ class Configuration(object):
return [parse(v) for v in allowed_origin_hostnames if v]
# legacy naming
Configuration = GalaxyAppConfiguration
def get_database_engine_options(kwargs, model_prefix=''):
"""
Allow options for the SQLAlchemy database engine to be passed by using
@@ -954,16 +1010,12 @@ def get_database_engine_options(kwargs, model_prefix=''):
def get_database_url(config):
if config.database_connection:
db_url = config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database
db_url = config.database_connection
return db_url
def init_models_from_config(config, map_install_models=False, object_store=None, trace_logger=None):
db_url = get_database_url(config)
from galaxy.model import mapping
model = mapping.init(
config.file_path,
db_url,
@@ -1092,9 +1144,14 @@ class ConfiguresGalaxyMixin(object):
self.tool_data_tables = ToolDataTableManager(tool_data_path=self.config.tool_data_path,
config_filename=self.config.tool_data_table_config_path)
# Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables.
self.tool_data_tables.load_from_config_file(config_filename=self.config.shed_tool_data_table_config,
tool_data_path=self.tool_data_tables.tool_data_path,
from_shed_config=from_shed_config)
try:
self.tool_data_tables.load_from_config_file(config_filename=self.config.shed_tool_data_table_config,
tool_data_path=self.tool_data_tables.tool_data_path,
from_shed_config=from_shed_config)
except (OSError, IOError) as exc:
# Missing shed_tool_data_table_config is okay if it's the default
if exc.errno != errno.ENOENT or self.config.shed_tool_data_table_config_set:
raise
def _configure_datatypes_registry(self, installed_repository_manager=None):
from galaxy.datatypes import registry
@@ -1131,7 +1188,7 @@ class ConfiguresGalaxyMixin(object):
if os.path.isfile(self.config.tool_sheds_config_file):
self.tool_shed_registry = tool_shed.tool_shed_registry.Registry(self.config.tool_sheds_config_file)
else:
self.tool_shed_registry = None
self.tool_shed_registry = tool_shed.tool_shed_registry.Registry()
def _configure_models(self, check_migrate_databases=False, check_migrate_tools=False, config_file=None):
"""
@@ -1143,6 +1200,7 @@ class ConfiguresGalaxyMixin(object):
# database file under the hood.
combined_install_database = not(install_db_url and install_db_url != db_url)
install_db_url = install_db_url or db_url
install_database_options = self.config.database_engine_options if combined_install_database else self.config.install_database_engine_options
if self.config.database_wait:
self._wait_for_database(db_url)
@@ -1155,18 +1213,13 @@ class ConfiguresGalaxyMixin(object):
# Initialize database / check for appropriate schema version. # If this
# is a new installation, we'll restrict the tool migration messaging.
from galaxy.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self)
create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self, map_install_models=combined_install_database)
if not combined_install_database:
from galaxy.model.tool_shed_install.migrate.check import create_or_verify_database as tsi_create_or_verify_database
tsi_create_or_verify_database(install_db_url, self.config.install_database_engine_options, app=self)
tsi_create_or_verify_database(install_db_url, install_database_options, app=self)
if check_migrate_tools:
# Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed.
from tool_shed.galaxy_install.migrate.check import verify_tools
if combined_install_database:
install_database_options = self.config.database_engine_options
else:
install_database_options = self.config.install_database_engine_options
verify_tools(self, install_db_url, config_file, install_database_options)
self.model = init_models_from_config(
@@ -1182,9 +1235,8 @@ class ConfiguresGalaxyMixin(object):
from galaxy.model.tool_shed_install import mapping as install_mapping
install_db_url = self.config.install_database_connection
log.info("Install database using its own connection %s" % install_db_url)
install_db_engine_options = self.config.install_database_engine_options
self.install_model = install_mapping.init(install_db_url,
install_db_engine_options)
install_database_options)
def _configure_signal_handlers(self, handlers):
for sig, handler in handlers.items():
lib/galaxy/config/sample/auth_conf.xml.sample
+128
View File
@@ -0,0 +1,128 @@
<?xml version="1.0"?>
<auth>
<!--<authenticator>
<type>ldap</type>
-->
<!-- Replacement fields: instances of {email}, {username} and {password}
are replaced with the corresponding user's values inside the
<filter>, <server>, <ldap-options>, <search-fields>,
<search-filter>, <search-base>, <search-user> and <search-password>
elements. -->
<!-- Filter users for which this authenticator applies. This is a Python
expression which is evaluated after field replacement. -->
<!-- <filter>'{email}'.endswith('@example.com')</filter>
<options>
-->
<!-- Whether to allow user registration. Possible values are True,
False and Challenge (i.e. allow registration in case of
successful authentication). Default is True. -->
<!-- <allow-register>False</allow-register>
-->
<!-- Whether Galaxy should automatically register users when they
first login. Default is False. -->
<!-- <auto-register>True</auto-register>
-->
<!-- Whether users are allowed to change their password. Default is
False. -->
<!-- <allow-password-change>False</allow-password-change>
-->
<!-- Whether roles should be automatically created if
the attribute specified under auto-register-roles can be found.
Default is False. -->
<!-- <auto-create-roles>False</auto-create-roles>
-->
<!-- Whether groups should be automatically created if
the attribute specified under auto-register-roles can be found.
Can be used in combination with auto-create-roles
Default is False. -->
<!-- <auto-create-groups>False</auto-create-groups>
-->
<!-- If set, roles will be assigned to the auto generated groups,
not to the individual users. Can only be used if auto-create-roles and
auto-create-groups are True. Default is False. -->
<!-- <auto-assign-roles-to-groups-only>False</auto-assign-roles-to-groups-only>
-->
<!-- LDAP-specific options -->
<!-- <server>ldap://dc1.example.com</server>
-->
<!-- Additional options for the LDAP connection. The syntax is:
option1=value1,option2=value2,...
Options and values should match those from the python-ldap
documentation.
The following example allows connecting to ldaps:// (SSL/TLS)
when self-signed certificates are used -->
<!-- <ldap-options>OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW</ldap-options>
-->
<!-- Whether unregistered users should use their LDAP username
instead of the email at their first login when auto-register is
True. Default is False. -->
<!-- <login-use-username>False</login-use-username>
-->
<!-- Whether to continue with the following authenticators if LDAP
fails. Default is False. -->
<!-- <continue-on-failure>False</continue-on-failure>
-->
<!-- If search-fields is not specified, all other search-* elements
are ignored.
If search-user is not specified, Galaxy will bind anonymously
to the LDAP server for search. -->
<!-- For Active Directory: -->
<!-- <search-fields>sAMAccountName,mail</search-fields>
<search-base>dc=dc1,dc=example,dc=com</search-base>
-->
<!-- If login-use-username is False -->
<!-- <search-filter>(&amp;(objectClass=user)(mail={email}))</search-filter>
-->
<!-- If login-use-username is True -->
<!-- <search-filter>(&amp;(objectClass=user)(sAMAccountName={username}))</search-filter>
-->
<!-- <search-user>jsmith@dc1.example.com</search-user>
<search-password>mysecret</search-password>
-->
<!-- For OpenLDAP: -->
<!-- <search-fields>uid,mail</search-fields>
<search-base>ou=People,dc=example,dc=com</search-base>
-->
<!-- If login-use-username is False -->
<!-- <search-filter>(mail={email})</search-filter>
-->
<!-- If login-use-username is True -->
<!-- <search-filter>(uid={username})</search-filter>
-->
<!-- <search-user>cn=jsmith,ou=People,dc=domain,dc=com</search-user>
<search-password>mysecret</search-password>
-->
<!-- Replacement fields: instances of {email}, {username},
{password}, {dn} plus all fields defined in <search-fields> are
replaced with the corresponding user's values inside the
<bind-user>, <bind-password>, <auto-register-username> and
<auto-register-email> elements. -->
<!-- For Active Directory: -->
<!-- <bind-user>{sAMAccountName}@dc1.example.com</bind-user>
<bind-password>{password}</bind-password>
<auto-register-username>{sAMAccountName}</auto-register-username>
<auto-register-email>{mail}</auto-register-email>
<auto-register-roles>{gidNumber}</auto-register-roles>
-->
<!-- For OpenLDAP: -->
<!-- <bind-user>{dn}</bind-user>
<bind-password>{password}</bind-password>
<auto-register-username>{uid}</auto-register-username>
<auto-register-email>{mail}</auto-register-email>
<auto-register-roles>{gid}</auto-register-roles>
-->
<!-- </options>
</authenticator>
-->
<authenticator>
<type>localdb</type>
<options>
<!-- Whether users are allowed to change their password. Default is
False. -->
<allow-password-change>true</allow-password-change>
</options>
</authenticator>
</auth>
lib/galaxy/config/sample/build_sites.yml.sample
+22
View File
@@ -0,0 +1,22 @@
# Build sites define the builds (dbkeys) available at sites used by display
# applications and the URL to those sites.
# The `display` attributes on the `ucsc` and `gbrowse` sites replace the
# `ucsc_display_sites` and `gbrowse_display_sites` options in galaxy.ini.
# Because these are used by "old-style" display applications, their types
# cannot change if you want the old-style display links for these sites to
# work.
- type: ucsc
file: tool-data/shared/ucsc/ucsc_build_sites.txt
display: [main,test,archaea,ucla]
- type: gbrowse
file: tool-data/shared/gbrowse/gbrowse_build_sites.txt
display: [modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225]
- type: ensembl
file: tool-data/shared/ensembl/ensembl_sites.txt
- type: ensembl_data_url
file: tool-data/shared/ensembl/ensembl_sites_data_URL.txt
- type: igv
file: tool-data/shared/igv/igv_build_sites.txt
- type: rviewer
file: tool-data/shared/rviewer/rviewer_build_sites.txt
lib/galaxy/config/sample/container_resolvers_conf.xml.sample
+59
View File
@@ -0,0 +1,59 @@
<containers_resolvers>
<explicit />
<!-- explicit: resolves container URI for a job through explict container
tags in the tool XML wrapper. -->
<!-- All mulled flavors below only work if enable_beta_mulled_containers is
set to true in the galaxy.yaml config file. -->
<!-- <cached_mulled /> -->
<!-- cached_mulled: resolves container URI through bioconda to mulled
automatic mapping, preferring cached images in the accessible docker
engine. Requires docker engine. -->
<!-- <cached_mulled_singularity /> -->
<!-- cached_mulled_singularity: resolves container URI through
bioconda to mulled automatic mapping, preferring cached singularity
images to building local singularity images. Only works with
enable_beta_mulled_containers set to true in the galaxy.yaml config file.
-->
<!-- <mulled auto_install="True"/> -->
<!-- mulled: only resolves container URI through bioconda to mulled automatic
mapping. Should be the method of choice if mulled resolution is required
but the container execution is handled by a container orchestration
instead of docker directly (ie. Galaxy has no access to a docker client
binary). It works of course with direct docker engine tool executions.
Set auto_install to False if Galaxy should pull container images
through the admin interface or API, but not automatically when
a tool is run.
-->
<!-- <mulled_singularity auto_install="True"/> -->
<!-- mulled_singularity: only resolves container URI through bioconda to mulled automatic
mapping. Should be the method of choice if mulled resolution is required
but the container execution is handled by a container orchestration
instead of singularity directly (ie. Galaxy has no access to a singularity client
binary). It works of course with direct singularity tool executions.
Set auto_install to False if Galaxy should pull container images
through the admin interface or API, but not automatically when
a tool is run.
-->
<!-- <build_mulled auto_install="True"/> -->
<!-- build_mulled: builds a docker image locally for one or more bioconda
packages listed in the tools definition.
Set auto_install to False if Galaxy should build container images
through the admin interface or API, but not automatically when
a tool is run.
-->
<!-- <build_mulled_singularity auto_install="True"/> -->
<!-- build_mulled_singularity: builds a singularity image locally for one
or more package requirements listed as part of the tool's definition.
Set auto_install to False if Galaxy should build container images
through the admin interface or API, but not automatically when
a tool is run.
-->
</containers_resolvers>
lib/galaxy/config/sample/containers_conf.yml.sample
+278
View File
@@ -0,0 +1,278 @@
---
# Galaxy container interface configuration file
#
# To configure the location of this file, use the `containers_config_file` setting in galaxy.yml. Additionally, the
# containers interface is only used if `enable_beta_containers_interface` is set in galaxy.yml.
###
### Container Interfaces
###
# Define container interfaces beneath the top-level `containers` dictionary. By default, a single `_default_` interface
# of type `docker` is defined, equivalent to:
#containers:
# _default_:
# type: docker
# The interface name is arbitrary and allows multiple distinct configurations to be defined. The name can be any string,
# but `_default_` is used if a component that uses the containers interface does not specify an interface. Currently
# only Galaxy Interactive Environments use the containers interface, and do not have a way to specify which interface to
# use, so configure under the `_default_` key for now.
# Additional options can be specified are specific to the container type:
#containers:
# _default_:
# type: docker
# host: docker.example.org:2376
# force_tlsverify: yes
# Keys in `containers` are used to map container consumers to specific # container consumers. If a mapping is not
# configured, the _default_ configuration will be used. An example of multiple container configurations would be:
#containers:
# _default_:
# type: docker
# ... additional options ...
# example_swarm:
# type: docker_swarm
# ... additional options ...
#
###
### Container Types and Supported Options
###
# Command-line equivalent arguments are in [brackets] (if applicable)
containers:
#
# Supported options for all container types
#
_default_:
# [`--name` (partial)] Prepend this string to the name of containers created
#name_prefix: galaxy_
#
# Supported options for `docker` container type
#
local_docker:
type: docker
# [`-H`/`--host] Daemon socket(s) to connect to
#host: null
# [`--tlsverify`] Use TLS and verify the remote
#force_tlsverify: no
# [`--cpus`] Number of CPUs (default 0.000)
#cpus: null
# [`-m`/`--memory`] Memory limit
#memory: null
# Default image to run if one is not provided to the run method
#image: null
#
# Supported options for `docker_swarm` container type
#
swarm:
type: docker_swarm
# All of the `docker` interface type arguments are supported. Additionally:
# [`-H`/`--host] Daemon socket(s) to connect to. This can be a list, which allows failing over to another
# manager when one is down, e.g.:
# host:
# - tcp://swarm1.example.org:2376
# - tcp://swarm2.example.org:2376
#host: null
# [`--reserve-cpu` and `--limit-cpu`] Reserve the given number of CPUs when containers are run to prevent other
# containers from being scheduled on the same node once all of its CPUs are allocated. Additionally, prevent
# container from using more than the given number of CPUs.
#cpus: null
# [`--reserve-memory` and `--limit-memory`] Reserve the given amount of memory when containers are run to
# prevent other containers from being scheduled on the same node once all of its memory is allocated.
# Additionally, prevent container from using more than the given amount of memory.
#memory: null
# If set, only nodes whose names begin with this string will be visible to and managed by the swarm manager.
# Note that regardless of whether this is set, the swarm manager will not attempt to control manager nodes
#node_prefix: null
# Convert image from name[:tag] form to name@digest form when possible, to avoid dependency on the image
# registry (e.g. Docker Hub or wherever the image was pulled from) at service creation time. For details see:
# https://github.com/docker/docker/issues/31427
#resolve_image_digest: no
# If a container run request is received that defines volumes to attach, should those volumes be ignored? Swarm
# mode does not support mounting volumes.
#ignore_volumes: no
#
# For the following `service_create_*_constraint` options, if set, the swarm manager automatically sets a
# corresponding label on nodes it spawns for services with the given constraints.
#
# [`--constraint node.labels._galaxy_image=={image}`] Automatically create a constraint based on the requested
# image name when new services are created (the image name is the resolved form if `resolve_image_digest` is
# set). This is useful if your nodes do not all have all of the possible images you'll want to run. Note: It's
# currently only possible for nodes to have a single image constraint defined. If your nodes have multiple
# images available, do not use this option.
#service_create_image_constraint: no
# [`--constraint node.labels._galaxy_cpus=={cpus}`] Automatically create a constraint based on the requested
# number of CPUs (or 1, if `cpus` is unset). This is useful if you are spawning nodes with a mixture of CPU
# counts and want to prevent (for example) 1-cpu services from being scheduled on 2-cpu nodes when 2-cpu jobs
# are waiting.
#service_create_cpus_constraint: no
#
# Galaxy can manage a Docker swarm using a built-in daemon and callouts to commands to add/remove nodes from
# your swarm.
#
# Use the swarm manager to manage services on this swarm. Even if your swarm is static, using the manager is
# recommended as the manager will automatically remove services after they have terminated.
#managed: yes
# Automatically start the swarm manager when new services are created. Useful if you want to run the swarm
# manager but control it separately from Galaxy.
#manager_autostart: yes
# Configuration dictionary for the swarm manager
manager_conf:
#
# In order to use the swarm manager for more than just service cleanup, (e.g. its node spawn and destroy
# features), you'll need to configure the `cpus` option in the interface. Otherwise, there are no limits on
# the number of services that will be assigned to a given node, so the swarm manager has no way to determine
# that more nodes should be spawned.
#
# Each service consumes one "slot", and the number of slots available on a node is its number of CPUs
# divided by the value of `cpus`.
#
# When the swarm manager daemonizes, it writes a pid file so that only one manager will run at a time. This
# is the path to that pid file. {xdg_data_home} will be templated automatically and defaults to
# ~/.local/share as per the XDG specification
#pid_file: '{xdg_data_home}/galaxy_swarm_manager.pid'
# Program output will be written to the log
#log_file: '{xdg_data_home}/galaxy_swarm_manager.log'
# Level of log messages (levels are Python logging module level names (case insensitive))
#log_level: INFO
# Log message format
#log_format: %(name)s %(levelname)s %(asctime)s %(message)s
# List of services' environment variables that should be logged when performing periodic service logging. By
# default, none are logged, but `USER_EMAIL` is useful for GIE containers to log the user who is running the
# container.
#log_environment_variables:
# - USER_EMAIL
# Command to run to spawn new nodes. This command should join the node to the swarm. It is run once per
# unique set of constraints of waiting services. Can include template variables:
#
# - {cpus}: Number of CPUs needed by the requested service(s) or minimum limits
# - {slots}: Number of "slots" needed by the requested service(s) or minimum limits, where slots are CPU
# fractions determined by use of the "cpus" option in the `docker_swarm` section.
# - {image}: Image requested by service
# - {service_ids}: Comma-separated list of service ids with these constraints currently waiting
# - {service_count}: Number of services with these constraints currently waiting
#
# If this command does not block until the node is joined to the swarm, make sure it at least completes that
# step in `spawn_wait_time` once it returns control. How the `spawn_command` exits controls the swarm
# manager's behavior:
#
# - return code: 0, output: space-separated list of spawned nodes:
# Swarm manager will wait for the nodes to appear in the swarm and manage them. You are responsible for ensuring
# the names returned match the name as it will appear in the output of `docker node ls`.
# - return code: 0, output: empty:
# Refusing to allocate nodes and the swarm manager should not attempt to spawn nodes for the given service(s)
# again. This is useful for controlling the maximum number of nodes that will be spawned.
# - return code: 2, output: anything (it will be logged as a message)
# Refusing/failed to allocate nodes but the swarm manager should attempt to spawn nodes for the given
# service(s) again.
#
#spawn_command: /bin/true
# Command to run to destroy idle nodes. Can include template variables:
#
# - {nodes}: Space-separated list of node names to destroy
#
# This command should block until at least the point at which any nodes being destroyed no longer appear in
# the swarm. It should return the names of nodes destroyed, separated by spaces.
#
#destroy_command: /bin/true
# Command to run if either of the above commands failed (e.g. to notify an administrator). Can include
# template variables:
#
# - {failed_command}: Command line of the command that failed
#
#command_failure_command: /bin/true
# Number of times to retry spawn/destroy commands before considering them to have failed, and seconds to
# wait between retries.
#command_retries: 0
#command_retry_wait: 10
# Amount of time to wait for a spawning node to appear in the swarm before considering it failed
#spawn_wait_time: 30
# Stop the swarm manager daemon when there are no services or nodes to manage
#terminate_when_idle: yes
#
# Limits control when the swarm manager will spawn and terminate nodes.
#
# Number of services that must be waiting to run before attempting to spawn a node. If using constraints,
# then waiting services are grouped by constraint.
#service_wait_count_limit: 0
# Number of seconds a service must be waiting before attempting to spawn a node.
#service_wait_time_limit: 5
# Number of seconds a node must be idle before terminating it.
#node_idle_limit: 120
# Minimum number of worker slots that should be started and active.
#slots_min_limit: 0
# Number of spare (unused) worker slots that should be started and active
#slots_min_spare: 0
#
# Each set of limits can also be set on a per-constraint basis under the `limits` list. Each member of
# `limits` is a dictionary dictionary with at least the key `constraints`, whose value is a list of
# constraint strings matching constraint strings that jobs will be created with, either by the use of
# `service_create_*_constraint` or manually setting constraints. Other keys match the `node_*` and `slots_*`
# limits above. Any limits unset will default to the "global" limits as set above, or their defaults.
#
# If you are using constraints, you should at least define them in the limits section, even if using all
# "global" values for the limits. This allows the swarm manager to know what node types to keep around if
# you're using `slots_min_limit`.
#
# Limits section example:
#limits:
# constraints:
# - node.labels._galaxy_image==bgruening/docker-jupyter-notebook:16.01.1
# - node.labels._galaxy_cpus==1
# slots_min_limit: 2
# slots_min_spare: 1
lib/galaxy/config/sample/datatypes_conf.xml.sample
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<?xml version="1.0"?>
<datatypes>
<registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
<datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/>
<datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/>
<datatype extension="anvio_cog_profile" type="galaxy.datatypes.anvio:AnvioComposite" display_in_upload="false" subclass="true" />
<datatype extension="anvio_composite" type="galaxy.datatypes.anvio:AnvioComposite" display_in_upload="false" />
<datatype extension="anvio_classifier" type="galaxy.datatypes.data:Data" display_in_upload="false" subclass="true" />
<datatype extension="anvio_contigs_db" type="galaxy.datatypes.anvio:AnvioContigsDB" display_in_upload="false" />
<datatype extension="anvio_db" type="galaxy.datatypes.anvio:AnvioDB" display_in_upload="false" />
<datatype extension="anvio_genomes_db" type="galaxy.datatypes.anvio:AnvioGenomesDB" display_in_upload="false" />
<datatype extension="anvio_pan_db" type="galaxy.datatypes.anvio:AnvioPanDB" display_in_upload="false" />
<datatype extension="anvio_pfam_profile" type="galaxy.datatypes.anvio:AnvioComposite" display_in_upload="false" subclass="true" />
<datatype extension="anvio_profile_db" type="galaxy.datatypes.anvio:AnvioProfileDB" display_in_upload="false" />
<datatype extension="anvio_samples_db" type="galaxy.datatypes.anvio:AnvioSamplesDB" display_in_upload="false" />
<datatype extension="anvio_state" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false" />
<datatype extension="anvio_structure_db" type="galaxy.datatypes.anvio:AnvioStructureDB" display_in_upload="false" />
<datatype extension="anvio_variability" type="galaxy.datatypes.tabular:TSV" display_in_upload="false" subclass="true" />
<datatype extension="arff" type="galaxy.datatypes.text:Arff" mimetype="text/plain" display_in_upload="true"/>
<datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
<datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
<datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bai.xml" target_datatype="bai"/>
<converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
<display file="ucsc/bam.xml"/>
<display file="ensembl/ensembl_bam.xml"/>
<display file="igv/bam.xml"/>
<display file="igb/bam.xml"/>
<display file="iobio/bam.xml"/>
</datatype>
<datatype extension="bai" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="false"/>
<datatype extension="qname_input_sorted.bam" type="galaxy.datatypes.binary:BamInputSorted" mimetype="application/octet-stream" display_in_upload="false" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted based on the aligner output." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
</datatype>
<datatype extension="qname_sorted.bam" type="galaxy.datatypes.binary:BamQuerynameSorted" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted by queryname." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
</datatype>
<datatype extension="unsorted.bam" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
</datatype>
<datatype extension="probam" type="galaxy.datatypes.binary:ProBam" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="cram" type="galaxy.datatypes.binary:CRAM" mimetype="application/octet-stream" display_in_upload="true" description="CRAM is a file format for highly efficient and tunable reference-based compression of alignment data." description_url="http://www.ebi.ac.uk/ena/software/cram-usage">
<converter file="cram_to_bam_converter.xml" target_datatype="bam"/>
</datatype>
<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed">
<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
<converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="bed_to_fli_converter.xml" target_datatype="fli"/>
<!-- <display file="ucsc/interval_as_bed.xml" /> -->
<display file="igb/bed.xml"/>
</datatype>
<datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true">
<converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/>
<display file="igb/bedgraph.xml"/>
</datatype>
<datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" display_in_upload="true"/>
<datatype extension="bed6" type="galaxy.datatypes.interval:Bed6" display_in_upload="true">
</datatype>
<datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" display_in_upload="true"/>
<datatype extension="probed" type="galaxy.datatypes.interval:ProBed" display_in_upload="true"/>
<datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
<converter file="len_to_linecount.xml" target_datatype="linecount"/>
</datatype>
<datatype extension="daa" type="galaxy.datatypes.binary:DAA" display_in_upload="true"/>
<datatype extension="rma6" type="galaxy.datatypes.binary:RMA6" display_in_upload="true"/>
<datatype extension="dmnd" type="galaxy.datatypes.binary:DMND" display_in_upload="false"/>
<datatype extension="idat" type="galaxy.datatypes.binary:Idat" display_in_upload="true"/>
<datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
<display file="ucsc/bigbed.xml"/>
<display file="igb/bb.xml"/>
</datatype>
<datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true">
<display file="ucsc/bigwig.xml"/>
<display file="igb/bigwig.xml"/>
<display file="igv/bigwig.xml"/>
</datatype>
<datatype extension="cxb" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" description="Cuffquant output format"/>
<datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="true">
<converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
</datatype>
<datatype extension="csv" type="galaxy.datatypes.tabular:CSV" display_in_upload="true">
<converter file="csv_to_tabular.xml" target_datatype="tabular"/>
</datatype>
<datatype extension="tsv" type="galaxy.datatypes.tabular:TSV" display_in_upload="true">
<converter file="tabular_to_csv.xml" target_datatype="csv"/>
</datatype>
<datatype extension="intermine_tabular" type="galaxy.datatypes.tabular:TSV" subclass="true" display_in_upload="true">
<display file="intermine/intermine_simple.xml"/>
</datatype>
<datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
<datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="false"/>
<datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="false"/>
<datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
<datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
<datatype extension="d3_hierarchy" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="true"/>
<datatype extension="imgt.json" type="galaxy.datatypes.text:ImgtJson" mimetype="application/json" display_in_upload="True"/>
<datatype extension="geojson" type="galaxy.datatypes.text:GeoJson" mimetype="application/json" display_in_upload="True"/>
<datatype extension="data_manager_json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="dbn" type="galaxy.datatypes.sequence:DotBracket" display_in_upload="true" description="Dot-Bracket format is a text-based format for storing both an RNA sequence and its corresponding 2D structure." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Dbn"/>
<datatype extension="fai" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true" description="A Fasta Index File is a text file consisting of lines each with five TAB-delimited columns : Name, Length, offset, linebases, Linewidth" description_url="http://www.htslib.org/doc/faidx.html"/>
<datatype extension="fasta" auto_compressed_types="gz" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('&gt;') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta">
<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
<converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
<converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>
<converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
<converter file="fasta_to_len.xml" target_datatype="len"/>
<converter file="fasta_to_fai.xml" target_datatype="fai"/>
<display file="igv/genome_fasta.xml" inherit="true"/>
</datatype>
<datatype extension="fastg" type="galaxy.datatypes.sequence:Fastg" display_in_upload="true" description="fastg format faithfully represents genome assemblies in the face of allelic polymorphism and assembly uncertainty" description_url="http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"/>
<datatype extension="fastq" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqsanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqsolexa" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqcssanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fastqillumina" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
</datatype>
<datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
<datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
<datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
<datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">
<!-- <display file="genetrack.xml" /> -->
</datatype>
<datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true" description="GFF lines have nine required fields that must be tab-separated." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF">
<converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
<converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="gff_to_fli_converter.xml" target_datatype="fli"/>
<display file="ensembl/ensembl_gff.xml" inherit="true"/>
<display file="igv/gff.xml" inherit="true"/>
<!-- <display file="gbrowse/gbrowse_gff.xml" inherit="true" /> -->
</datatype>
<datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/>
<datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
<datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
<datatype extension="graph_dot" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
<converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<display file="igb/gtf.xml"/>
</datatype>
<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="true"/>
<datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="cool" type="galaxy.datatypes.binary:Cool" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="mcool" type="galaxy.datatypes.binary:MCool" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
<datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order).">
<converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
<converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/>
<converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/>
<converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
<converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/>
<!-- <display file="ucsc/interval_as_bed.xml" inherit="true" /> -->
<display file="ensembl/ensembl_interval_as_bed.xml" inherit="true"/>
<display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="true"/>
<display file="rviewer/bed.xml" inherit="true"/>
<display file="igv/interval_as_bed.xml" inherit="true"/>
</datatype>
<!-- ISA data types -->
<datatype extension="isa-tab" type="galaxy.datatypes.isa:IsaTab" mimetype="application/isa-tools" display_in_upload="true" description="ISA-Tab data type." description_url="https://isa-tools.org"/>
<datatype extension="isa-json" type="galaxy.datatypes.isa:IsaJson" mimetype="application/isa-tools" display_in_upload="true" description="ISA-JSON data type." description_url="https://isa-tools.org"/>
<datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true">
<converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/>
</datatype>
<datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
<datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff" display_in_upload="true"/>
<datatype extension="tf2" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="tf8" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="btf" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="tif" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="svs" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="scn" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="bif" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
<datatype extension="vms" type="galaxy.datatypes.images:Hamamatsu" mimetype="image/hamamatsu"/>
<datatype extension="vmu" type="galaxy.datatypes.images:Hamamatsu" subclass="true" display_in_upload="false"/>
<datatype extension="ndpi" type="galaxy.datatypes.images:Hamamatsu" subclass="true" display_in_upload="false"/>
<datatype extension="mrxs" type="galaxy.datatypes.images:Mirax" mimetype="image/mirax"/>
<datatype extension="svslide" type="galaxy.datatypes.images:Sakura" mimetype="image/sakura"/>
<datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/>
<datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/>
<datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/>
<datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/>
<datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/>
<datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/>
<datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/>
<datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/>
<datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
<datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
<datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
<datatype extension="nrrd" type="galaxy.datatypes.images:Nrrd" mimetype="image/nrrd"/>
<datatype extension="nhdr" type="galaxy.datatypes.images:Nrrd" subclass="true"/>
<datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="true"/>
<datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true"/>
<datatype extension="tar" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
<converter file="tar_to_directory.xml" target_datatype="directory"/>
</datatype>
<datatype extension="directory" type="galaxy.datatypes.data:Directory">
</datatype>
<!-- Proteomics Datatypes -->
<datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="raw_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
<datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
<datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
<datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Transformation of retention times"/>
<datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
<datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
<datatype extension="protxml.tsv" type="galaxy.datatypes.proteomics:ProtXmlReport" display_in_upload="true"/>
<datatype extension="mascotdat" type="galaxy.datatypes.proteomics:MascotDat" display_in_upload="false"/>
<datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="tandem" type="galaxy.datatypes.proteomics:TandemXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="thermo.raw" type="galaxy.datatypes.proteomics:ThermoRAW" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="brukerbaf.d.tar" type="galaxy.datatypes.binary:BafTar" display_in_upload="true"/>
<datatype extension="agilentbrukeryep.d.tar" type="galaxy.datatypes.binary:YepTar" display_in_upload="true"/>
<datatype extension="brukertdf.d.tar" type="galaxy.datatypes.binary:TdfTar" display_in_upload="true"/>
<datatype extension="agilentmasshunter.d.tar" type="galaxy.datatypes.binary:MassHunterTar" display_in_upload="true"/>
<datatype extension="watersmasslynx.raw.tar" type="galaxy.datatypes.binary:MassLynxTar" display_in_upload="true"/>
<datatype extension="wiff.tar" type="galaxy.datatypes.binary:WiffTar" display_in_upload="true"/>
<datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
<datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
<datatype extension="wiff" type="galaxy.datatypes.proteomics:Wiff" display_in_upload="true"/>
<datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="mzdata" type="galaxy.datatypes.proteomics:MzData" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true"/>
<datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true"/>
<datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true"/>
<datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true"/>
<datatype extension="blib" type="galaxy.datatypes.binary:BlibSQlite" display_in_upload="true"/>
<datatype extension="hlf" type="galaxy.datatypes.proteomics:XHunterAslFormat" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="idpdb" type="galaxy.datatypes.binary:IdpDB" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="sf3" type="galaxy.datatypes.proteomics:Sf3" display_in_upload="true"/>
<datatype extension="cps" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true"/>
<datatype extension="ct" type="galaxy.datatypes.tabular:ConnectivityTable" display_in_upload="true"/>
<datatype extension="postgresql" type="galaxy.datatypes.binary:PostgresqlArchive" display_in_upload="True"/>
<datatype extension="searchgui_archive" type="galaxy.datatypes.binary:SearchGuiArchive" display_in_upload="true"/>
<datatype extension="fast5.tar" type="galaxy.datatypes.binary:Fast5Archive" display_in_upload="true"/>
<datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>
<datatype extension="fast5.tar.bz2" type="galaxy.datatypes.binary:Fast5ArchiveBz2" display_in_upload="true"/>
<datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<datatype extension="percin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true"/>
<datatype extension="hardklor" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="imzml" type="galaxy.datatypes.proteomics:ImzML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="analyze75" type="galaxy.datatypes.proteomics:Analyze75" mimetype="application/xml" display_in_upload="true"/>
<!-- End Proteomics Datatypes -->
<datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<datatype extension="netcdf" type="galaxy.datatypes.binary:NetCDF" mimetype="application/octet-stream" display_in_upload="true" description="Format used by netCDF software library for writing and reading chromatography-MS data files."/>
<datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
<datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
<datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
<datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true" description="Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.."/>
<datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true" description="TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated 'variable=value' pairs. There should be no white space surrounding the '='." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#MAF">
<converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
</datatype>
<datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
<display file="ucsc/maf_customtrack.xml"/>
</datatype>
<datatype extension="mtx" type="galaxy.datatypes.tabular:MatrixMarket" display_in_upload="true"/>
<datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="true">
<converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
</datatype>
<datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf" display_in_upload="true"/>
<datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true">
<converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
</datatype>
<datatype extension="obo" type="galaxy.datatypes.text:Obo" mimetype="text/html" display_in_upload="true"/>
<datatype extension="owl" type="galaxy.datatypes.xml:Owl" mimetype="text/html" display_in_upload="true"/>
<datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
<datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore"/>
<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
<datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/>
<datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
<datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
<datatype extension="roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
<datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
<converter file="sam_to_unsorted_bam.xml" target_datatype="unsorted.bam"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
<converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
</datatype>
<datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/>
<datatype extension="sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
<datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="true"/>
<datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="true"/>
<datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true">
<converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/>
</datatype>
<datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/>
<datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true" description="A binary file archive format from the NCBI Sequence Read Archive with a '.sra' file extension." description_url="http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure"/>
<datatype extension="svg" type="galaxy.datatypes.xml:GenericXml" mimetype="image/svg+xml" subclass="true"/>
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29">
<converter file="tabular_to_csv.xml" target_datatype="csv"/>
</datatype>
<datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>
<datatype extension="gafa.sqlite" type="galaxy.datatypes.binary:GAFASQLite" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/>
<datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/>
<datatype extension="memepsp" type="galaxy.datatypes.sequence:MemePsp" display_in_upload="true" description="The MEME Position Specific Priors (PSP) format includes the name of the sequence for which a prior distribution corresponds." description_url="http://meme-suite.org/doc/psp-format.html"/>
<datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
<converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/>
<converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<display file="ucsc/vcf.xml"/>
<display file="igv/vcf.xml"/>
<display file="rviewer/vcf.xml" inherit="true"/>
<display file="iobio/vcf.xml"/>
</datatype>
<datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="true">
<converter file="bcf_to_bcf_uncompressed_converter.xml" target_datatype="bcf_uncompressed"/>
</datatype>
<!-- bcf_bgzip is just an alias for bcf for backward-compatibility -->
<datatype extension="bcf_bgzip" type="galaxy.datatypes.binary:Bcf" subclass="true"/>
<datatype extension="bcf_uncompressed" type="galaxy.datatypes.binary:BcfUncompressed" mimetype="application/octet-stream">
<converter file="bcf_uncompressed_to_bcf_converter.xml" target_datatype="bcf"/>
</datatype>
<datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="true"/>
<datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig">
<converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
<!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
<display file="igb/wig.xml"/>
</datatype>
<datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
<datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
<datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
<datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
<display file="igv/vcf.xml"/>
<converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>
</datatype>
<datatype extension="kallisto.ec" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
<datatype extension="kallisto.idx" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
<!-- Phylogenetic tree datatypes -->
<datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true"/>
<datatype extension="newick" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
<datatype extension="nhx" type="galaxy.datatypes.data:Newick" subclass="true" display_in_upload="true"/>
<datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true"/>
<datatype extension="iqtree" type="galaxy.datatypes.text:IQTree"/>
<datatype extension="mldist" type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
<!-- Start RGenetics Datatypes -->
<datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
<!-- eigenstrat pedigree input file -->
<datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
<!-- eigenstrat pca output file for adjusted eigenQTL eg -->
<datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
<datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true"/>
<!-- fbat/pbat format pedigree (header row of marker names) -->
<datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
<!-- phenotype file - fbat format -->
<datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
<!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
<datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
<!-- part of linkage format pedigree -->
<!-- information redundancy (LD) filtered plink pbed -->
<datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true">
</datatype>
<datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
<!-- linkage format pedigree (separate .map file) -->
<datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
<converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
<converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
</datatype>
<!-- plink compressed file - has bed extension unfortunately -->
<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
<converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
<converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/>
</datatype>
<datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
<!-- phenotype file - plink format -->
<datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/>
<datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
<datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
<datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
<!-- deprecated, should use excel.xls -->
<datatype extension="xls" type="galaxy.datatypes.binary:ExcelXls"/>
<!-- End RGenetics Datatypes -->
<datatype extension="ipynb" type="galaxy.datatypes.text:Ipynb" display_in_upload="true"/>
<datatype extension="json" type="galaxy.datatypes.text:Json" display_in_upload="true"/>
<datatype extension="expression.json" type="galaxy.datatypes.text:ExpressionJson" display_in_upload="true"/>
<!-- graph datatypes -->
<datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/>
<datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/>
<!-- datatypes storing triples -->
<datatype extension="triples" type="galaxy.datatypes.triples:Triples" display_in_upload="false"/>
<datatype extension="hdt" type="galaxy.datatypes.triples:HDT" display_in_upload="true"/>
<datatype extension="nt" type="galaxy.datatypes.triples:NTriples" display_in_upload="true"/>
<datatype extension="n3" type="galaxy.datatypes.triples:N3" display_in_upload="true"/>
<datatype extension="ttl" type="galaxy.datatypes.triples:Turtle" display_in_upload="true"/>
<datatype extension="rdf" type="galaxy.datatypes.triples:Rdf" display_in_upload="true"/>
<datatype extension="jsonld" type="galaxy.datatypes.triples:Jsonld" display_in_upload="true"/>
<!-- Excel datatypes -->
<datatype extension="excel.xls" type="galaxy.datatypes.binary:ExcelXls" display_in_upload="true"/>
<datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true"/>
<datatype extension="btwisted" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cai" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="charge" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="checktrans" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="chips" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="codcmp" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="coderet" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="compseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cpgplot" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cpgreport" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cusp" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="cut" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="dan" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="digest" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="dreg" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="einverted" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="epestfind" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="equicktandem" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="est2genome" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="etandem" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="freak" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="hmoment" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="isochore" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="match" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="nametable" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="needle" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="newcpgreport" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="newcpgseek" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="noreturn" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="palindrome" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pepcoil" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pepinfo" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pepstats" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="polydot" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="preg" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="prettyseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="primersearch" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="showfeat" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="showorf" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="sixpack" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="strider" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="supermatcher" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="syco" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="textsearch" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="vectorstrip" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="wobble" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="wordcount" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Report formats http://emboss.sourceforge.net/docs/themes/ReportFormats.html -->
<datatype extension="dbmotif" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="diffseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="excel" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="feattable" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="motif" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="regions" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="seqtable" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="simple" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="table" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="tagseq" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Sequence formats http://emboss.sourceforge.net/docs/themes/SequenceFormats.html -->
<datatype extension="acedb" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="clustal" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="codata" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="genbank" auto_compressed_types="gz" sniff_compressed_types="true" type="galaxy.datatypes.sequence:Genbank" display_in_upload="True"/>
<datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="jackknifernon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="mega" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="meganon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="ncbi" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="nexus" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="nexusnon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="phylip" type="galaxy.datatypes.phylip:Phylip" display_in_upload="true"/>
<datatype extension="phylipnon" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pir" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="staden" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="swiss" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Alignment Formats http://emboss.sourceforge.net/docs/themes/AlignFormats.html -->
<datatype extension="markx0" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx1" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx10" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx2" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="markx3" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="pair" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="score" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="srs" type="galaxy.datatypes.data:Text" subclass="true"/>
<datatype extension="srspair" type="galaxy.datatypes.data:Text" subclass="true"/>
<!-- Annotation Datatypes -->
<datatype extension="snaphmm" type="galaxy.datatypes.annotation:SnapHmm" display_in_upload="true"/>
<datatype extension="augustus" type="galaxy.datatypes.annotation:Augustus" display_in_upload="true"/>
<datatype extension="icm" type="galaxy.datatypes.binary:ICM" display_in_upload="true"/>
<!-- MSA Datatypes -->
<datatype extension="cm" type="galaxy.datatypes.msa:InfernalCM" display_in_upload="False"/>
<datatype extension="hmm2" type="galaxy.datatypes.msa:Hmmer2" display_in_upload="true"/>
<datatype extension="hmm3" type="galaxy.datatypes.msa:Hmmer3" display_in_upload="true"/>
<datatype extension="stockholm" type="galaxy.datatypes.msa:Stockholm_1_0" display_in_upload="true"/>
<datatype extension="xmfa" type="galaxy.datatypes.msa:MauveXmfa" display_in_upload="true"/>
<datatype extension="cel" type="galaxy.datatypes.microarrays:Cel" display_in_upload="true"/>
<datatype extension="gpr" type="galaxy.datatypes.microarrays:Gpr" display_in_upload="true"/>
<datatype extension="gal" type="galaxy.datatypes.microarrays:Gal" display_in_upload="true"/>
<datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
<datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" display_in_upload="true"/>
<datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxlits" type="galaxy.datatypes.binary:OxliTagSet" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxlist" type="galaxy.datatypes.binary:OxliStopTags" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxliss" type="galaxy.datatypes.binary:OxliSubset" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="oxligl" type="galaxy.datatypes.binary:OxliGraphLabels" mimetype="application/octet-stream" display_in_upload="true"/>
<!-- Constructive solid geometry datatypes -->
<datatype extension="stl" type="galaxy.datatypes.constructive_solid_geometry:STL" display_in_upload="true"/>
<datatype extension="plyascii" type="galaxy.datatypes.constructive_solid_geometry:PlyAscii" display_in_upload="true"/>
<datatype extension="plybinary" type="galaxy.datatypes.constructive_solid_geometry:PlyBinary" display_in_upload="true"/>
<datatype extension="vtkascii" type="galaxy.datatypes.constructive_solid_geometry:VtkAscii" display_in_upload="true"/>
<datatype extension="vtkbinary" type="galaxy.datatypes.constructive_solid_geometry:VtkBinary" display_in_upload="true"/>
<!-- Metagenomic Datatypes -->
<datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="true" mimetype="application/json">
<display file="biom/biom_simple.xml"/>
<converter file="biom1_to_biom2.xml" target_datatype="biom2"/>
</datatype>
<datatype extension="biom2" type="galaxy.datatypes.binary:Biom2" mimetype="application/octet-stream" display_in_upload="true">
<converter file="biom2_to_biom1.xml" target_datatype="biom1"/>
</datatype>
<datatype extension="msh" type="galaxy.datatypes.binary:MashSketch" display_in_upload="True" />
<!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
<datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true"/>
<!--Cheminformatics Datatypes -->
<datatype extension="smi" type="galaxy.datatypes.molecules:SMILES" display_in_upload="true">
<!-- The ordering is important. The first one is considered as default converter in the build-in conversion function -> (as sdf)-->
<converter file="smi_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="smi_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="smi_to_cml_converter.xml" target_datatype="cml"/>
<converter file="smi_to_mol_converter.xml" target_datatype="mol"/>
<converter file="smi_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="smi_to_smi_converter.xml" target_datatype="smi"/>
</datatype>
<datatype extension="sdf" type="galaxy.datatypes.molecules:SDF" display_in_upload="true">
<converter file="sdf_to_smi_converter.xml" target_datatype="smi"/>
<converter file="sdf_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="sdf_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="sdf_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="inchi" type="galaxy.datatypes.molecules:InChI" display_in_upload="true">
<converter file="inchi_to_smi_converter.xml" target_datatype="smi"/>
<converter file="inchi_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="inchi_to_mol_converter.xml" target_datatype="mol"/>
<converter file="inchi_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="inchi_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="mol" type="galaxy.datatypes.molecules:MOL" display_in_upload="true">
<converter file="mol_to_smi_converter.xml" target_datatype="smi"/>
<converter file="mol_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="mol_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="mol_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="mol2" type="galaxy.datatypes.molecules:MOL2" display_in_upload="false">
<converter file="mol2_to_smi_converter.xml" target_datatype="smi"/>
<converter file="mol2_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="mol2_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="mol2_to_mol_converter.xml" target_datatype="mol"/>
<converter file="mol2_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="cml" type="galaxy.datatypes.molecules:CML" display_in_upload="true">
<converter file="cml_to_smi_converter.xml" target_datatype="smi"/>
<converter file="cml_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="cml_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="cml_to_mol2_converter.xml" target_datatype="mol2"/>
</datatype>
<datatype extension="fps" type="galaxy.datatypes.molecules:FPS" mimetype="text/html" display_in_upload="true"/>
<datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="true"/>
<datatype extension="drf" type="galaxy.datatypes.molecules:DRF" display_in_upload="true"/>
<datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="false"/>
<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="true"/>
<datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
<datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
<datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true"/>
<datatype extension="dcd" type="galaxy.datatypes.binary:Dcd" display_in_upload="true"/>
<datatype extension="top" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="itp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="mdp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="xtc" type="galaxy.datatypes.binary:Xtc" display_in_upload="true"/>
<datatype extension="cpt" type="galaxy.datatypes.binary:Cpt" display_in_upload="true"/>
<datatype extension="gro" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="vel" type="galaxy.datatypes.binary:Vel" display_in_upload="true"/>
<datatype extension="grd" type="galaxy.datatypes.molecules:grd" display_in_upload="true"/>
<datatype extension="grd.tgz" type="galaxy.datatypes.molecules:grdtgz" display_in_upload="true"/>
<!-- mothur formats -->
<datatype extension="mothur.otu" type="galaxy.datatypes.mothur:Otu" display_in_upload="true"/>
<datatype extension="mothur.list" type="galaxy.datatypes.mothur:Otu" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.sabund" type="galaxy.datatypes.mothur:Sabund" display_in_upload="true"/>
<datatype extension="mothur.rabund" type="galaxy.datatypes.mothur:Sabund" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.shared" type="galaxy.datatypes.mothur:GroupAbund" display_in_upload="true"/>
<datatype extension="mothur.relabund" type="galaxy.datatypes.mothur:GroupAbund" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.names" type="galaxy.datatypes.mothur:Names" display_in_upload="true"/>
<datatype extension="mothur.design" type="galaxy.datatypes.mothur:Group" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.summary" type="galaxy.datatypes.mothur:Summary" display_in_upload="true"/>
<datatype extension="mothur.groups" type="galaxy.datatypes.mothur:Group" display_in_upload="true"/>
<datatype extension="mothur.oligos" type="galaxy.datatypes.mothur:Oligos" display_in_upload="true"/>
<datatype extension="mothur.align" type="galaxy.datatypes.sequence:Fasta" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.accnos" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="mothur.otulabels" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="mothur.otu.corr" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.map" type="galaxy.datatypes.mothur:SecondaryStructureMap" display_in_upload="true"/>
<datatype extension="mothur.align.check" type="galaxy.datatypes.mothur:AlignCheck" display_in_upload="true"/>
<datatype extension="mothur.align.report" type="galaxy.datatypes.mothur:AlignReport" display_in_upload="true"/>
<datatype extension="mothur.filter" type="galaxy.datatypes.mothur:LaneMask" display_in_upload="true"/>
<datatype extension="mothur.dist" type="galaxy.datatypes.mothur:DistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.tre" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.pair.dist" type="galaxy.datatypes.mothur:PairwiseDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.square.dist" type="galaxy.datatypes.mothur:SquareDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.lower.dist" type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.ref.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" display_in_upload="true">
<converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="mothur.seq.taxonomy"/>
</datatype>
<datatype extension="mothur.seq.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.rdp.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.cons.taxonomy" type="galaxy.datatypes.mothur:ConsensusTaxonomy" display_in_upload="true"/>
<datatype extension="mothur.tax.summary" type="galaxy.datatypes.mothur:TaxonomySummary" display_in_upload="true"/>
<datatype extension="mothur.freq" type="galaxy.datatypes.mothur:Frequency" display_in_upload="true"/>
<datatype extension="mothur.quan" type="galaxy.datatypes.mothur:Quantile" display_in_upload="true"/>
<datatype extension="mothur.filtered.quan" type="galaxy.datatypes.mothur:Quantile" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.filtered.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="true" display_in_upload="true"/>
<datatype extension="mothur.axes" type="galaxy.datatypes.mothur:Axes" display_in_upload="true"/>
<datatype extension="mothur.sff.flow" type="galaxy.datatypes.mothur:SffFlow" display_in_upload="true"/>
<datatype extension="mothur.count_table" type="galaxy.datatypes.mothur:CountTable" display_in_upload="true"/>
<datatype extension="neostore" type="galaxy.datatypes.neo4j:Neo4jDB" mimetype="text/html" display_in_upload="false"/>
<datatype extension="neostore.zip" type="galaxy.datatypes.neo4j:Neo4jDBzip" display_in_upload="true">
<converter file="neostorezip_to_neostore_converter.xml" target_datatype="neostore"/>
</datatype>
<datatype extension="trackhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
<display file="ucsc/trackhub.xml"/>
</datatype>
<datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
<datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
<datatype extension="blastdbd" type="galaxy.datatypes.blast:BlastDomainDb" mimetype="text/html" display_in_upload="false"/>
<datatype extension="maskinfo-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true"/>
<datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true"/>
<datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true"/>
<!-- PlantTribes datatypes -->
<!--
The commented entries in this section are required by versions 1.0.0, 1.0.1 and 1.0.2 of the
PlantTribes tools in the MTS Phylogenetics category, and are not required by version 1.0.3 of
later. These datatypes will be removed in a future Galaxy release.
-->
<!--
<datatype extension="ptalign" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment" />
<datatype extension="ptalignca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment" />
<datatype extension="ptaligntrimmed" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed" />
<datatype extension="ptaligntrimmedca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment" />
<datatype extension="ptalignfiltered" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered" />
<datatype extension="ptalignfilteredca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment" />
-->
<datatype extension="ptkscmp" type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents" display_in_upload="true"/>
<!--
<datatype extension="ptortho" type="galaxy.datatypes.plant_tribes:PlantTribesOrtho" />
<datatype extension="ptorthocs" type="galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence" />
<datatype extension="ptphylip" type="galaxy.datatypes.plant_tribes:PlantTribesPhylip" />
<datatype extension="pttgf" type="galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies" />
<datatype extension="pttree" type="galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree" />
-->
<datatype extension="smat" type="galaxy.datatypes.plant_tribes:Smat" display_in_upload="true"/>
<!-- Start Haplotype / LOD Datatypes -->
<datatype extension="alohomora_gts" type="galaxy.datatypes.genetics:GenotypeMatrix"/>
<datatype extension="alohomora_map" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="alohomora_maf" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="alohomora_ped" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<!-- Common input formats: Generated by alohomora, but user may also upload these manually -->
<datatype extension="linkage_pedin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
<datatype extension="linkage_datain" type="galaxy.datatypes.genetics:DataIn"/>
<datatype extension="linkage_map" type="galaxy.datatypes.genetics:MarkerMap"/>
<!-- All output linkage is converted into the Allegro output format -->
<datatype extension="allegro_ihaplo" type="galaxy.datatypes.tabular:Tabular"/>
<datatype extension="allegro_descent" type="galaxy.datatypes.tabular:Tabular"/>
<datatype extension="allegro_fparam" type="galaxy.datatypes.genetics:AllegroLOD"/>
<!-- IDEAS datatypes -->
<datatype extension="ideaspre" type="galaxy.datatypes.genetics:IdeasPre" display_in_upload="true"/>
<!-- End IDEAS datatypes -->
<datatype extension="sbml" type="galaxy.datatypes.xml:Sbml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="spalndbnp" type="galaxy.datatypes.spaln:SpalnNuclDb" display_in_upload="true" />
<datatype extension="spalndba" type="galaxy.datatypes.spaln:SpalnProtDb" display_in_upload="true" />
<datatype extension="dada2_derep" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
<datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
<datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
<datatype extension="ckpt" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
</registration>
<sniffers>
<!--
The order in which Galaxy attempts to determine data types is
important because some formats are much more loosely defined
than others. The following list should be the most rigidly
defined format first, followed by next-most rigidly defined,
and so on.
-->
<sniffer type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents"/>
<sniffer type="galaxy.datatypes.plant_tribes:Smat"/>
<sniffer type="galaxy.datatypes.mothur:Sabund"/>
<sniffer type="galaxy.datatypes.mothur:Otu"/>
<sniffer type="galaxy.datatypes.mothur:GroupAbund"/>
<sniffer type="galaxy.datatypes.mothur:SecondaryStructureMap"/>
<sniffer type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix"/>
<sniffer type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
<sniffer type="galaxy.datatypes.mothur:PairwiseDistanceMatrix"/>
<sniffer type="galaxy.datatypes.mothur:Oligos"/>
<sniffer type="galaxy.datatypes.mothur:Quantile"/>
<sniffer type="galaxy.datatypes.mothur:Frequency"/>
<sniffer type="galaxy.datatypes.mothur:LaneMask"/>
<sniffer type="galaxy.datatypes.mothur:RefTaxonomy"/>
<sniffer type="galaxy.datatypes.mothur:Axes"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
<sniffer type="galaxy.datatypes.interval:ScIdx"/>
<sniffer type="galaxy.datatypes.tabular:Vcf"/>
<sniffer type="galaxy.datatypes.binary:TwoBit"/>
<sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
<sniffer type="galaxy.datatypes.binary:MzSQlite"/>
<sniffer type="galaxy.datatypes.binary:IdpDB"/>
<sniffer type="galaxy.datatypes.binary:BlibSQlite"/>
<sniffer type="galaxy.datatypes.binary:CuffDiffSQlite"/>
<sniffer type="galaxy.datatypes.binary:GAFASQLite"/>
<sniffer type="galaxy.datatypes.binary:SQlite"/>
<sniffer type="galaxy.datatypes.binary:Cool"/>
<sniffer type="galaxy.datatypes.binary:MCool"/>
<sniffer type="galaxy.datatypes.binary:Loom"/>
<sniffer type="galaxy.datatypes.binary:Anndata"/>
<sniffer type="galaxy.datatypes.binary:Biom2"/>
<sniffer type="galaxy.datatypes.binary:H5"/>
<sniffer type="galaxy.datatypes.binary:Bam"/>
<sniffer type="galaxy.datatypes.binary:BamQuerynameSorted"/>
<sniffer type="galaxy.datatypes.binary:BamNative"/>
<sniffer type="galaxy.datatypes.binary:CRAM"/>
<sniffer type="galaxy.datatypes.binary:Sff"/>
<sniffer type="galaxy.datatypes.binary:Sra"/>
<sniffer type="galaxy.datatypes.binary:NetCDF"/>
<sniffer type="galaxy.datatypes.binary:DAA"/>
<sniffer type="galaxy.datatypes.binary:RMA6"/>
<sniffer type="galaxy.datatypes.binary:DMND"/>
<sniffer type="galaxy.datatypes.binary:BafTar"/>
<sniffer type="galaxy.datatypes.binary:TdfTar"/>
<sniffer type="galaxy.datatypes.binary:MassHunterTar"/>
<sniffer type="galaxy.datatypes.binary:MassLynxTar"/>
<sniffer type="galaxy.datatypes.binary:YepTar"/>
<sniffer type="galaxy.datatypes.binary:WiffTar"/>
<sniffer type="galaxy.datatypes.binary:Fast5ArchiveGz"/>
<sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>
<sniffer type="galaxy.datatypes.binary:Fast5Archive"/>
<sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>
<sniffer type="galaxy.datatypes.binary:ICM"/>
<sniffer type="galaxy.datatypes.binary:Idat"/>
<sniffer type="galaxy.datatypes.binary:Trr"/>
<sniffer type="galaxy.datatypes.binary:Dcd"/>
<sniffer type="galaxy.datatypes.binary:Xtc"/>
<sniffer type="galaxy.datatypes.binary:Cpt"/>
<sniffer type="galaxy.datatypes.binary:Vel"/>
<sniffer type="galaxy.datatypes.annotation:Augustus"/>
<sniffer type="galaxy.datatypes.triples:Rdf"/>
<sniffer type="galaxy.datatypes.blast:BlastXml"/>
<sniffer type="galaxy.datatypes.xml:Phyloxml"/>
<sniffer type="galaxy.datatypes.xml:Owl"/>
<sniffer type="galaxy.datatypes.xml:Sbml"/>
<sniffer type="galaxy.datatypes.proteomics:MzML"/>
<sniffer type="galaxy.datatypes.proteomics:NmrML"/>
<sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
<sniffer type="galaxy.datatypes.proteomics:PepXml"/>
<sniffer type="galaxy.datatypes.proteomics:Mgf"/>
<sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
<sniffer type="galaxy.datatypes.proteomics:MzXML"/>
<sniffer type="galaxy.datatypes.proteomics:MzData"/>
<sniffer type="galaxy.datatypes.proteomics:TraML"/>
<sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
<sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
<sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
<sniffer type="galaxy.datatypes.proteomics:Msp"/>
<sniffer type="galaxy.datatypes.proteomics:SPLib"/>
<sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
<sniffer type="galaxy.datatypes.molecules:CML"/>
<sniffer type="galaxy.datatypes.xml:GenericXml"/>
<sniffer type="galaxy.datatypes.triples:HDT"/>
<sniffer type="galaxy.datatypes.triples:Turtle"/>
<sniffer type="galaxy.datatypes.triples:NTriples"/>
<sniffer type="galaxy.datatypes.triples:Jsonld"/>
<sniffer type="galaxy.datatypes.sequence:Maf"/>
<sniffer type="galaxy.datatypes.sequence:Lav"/>
<sniffer type="galaxy.datatypes.sequence:MemePsp"/>
<sniffer type="galaxy.datatypes.sequence:Fastg"/>
<sniffer type="galaxy.datatypes.sequence:csFasta"/>
<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
<sniffer type="galaxy.datatypes.molecules:SDF"/>
<sniffer type="galaxy.datatypes.molecules:PDB"/>
<sniffer type="galaxy.datatypes.molecules:MOL2"/>
<sniffer type="galaxy.datatypes.molecules:InChI"/>
<sniffer type="galaxy.datatypes.molecules:FPS"/>
<sniffer type="galaxy.datatypes.molecules:PQR"/>
<!-- TODO: see molecules.py <sniffer type="galaxy.datatypes.molecules:SMILES"/>-->
<sniffer type="galaxy.datatypes.phylip:Phylip"/>
<sniffer type="galaxy.datatypes.sequence:Fasta"/>
<sniffer type="galaxy.datatypes.sequence:FastqCSSanger"/>
<sniffer type="galaxy.datatypes.sequence:FastqSanger"/>
<sniffer type="galaxy.datatypes.sequence:Fastq"/>
<sniffer type="galaxy.datatypes.interval:Wiggle"/>
<sniffer type="galaxy.datatypes.text:Html"/>
<sniffer type="galaxy.datatypes.images:Pdf"/>
<sniffer type="galaxy.datatypes.sequence:Axt"/>
<sniffer type="galaxy.datatypes.sequence:Genbank"/>
<sniffer type="galaxy.datatypes.interval:Bed"/>
<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
<sniffer type="galaxy.datatypes.interval:Gtf"/>
<sniffer type="galaxy.datatypes.interval:Gff"/>
<sniffer type="galaxy.datatypes.interval:Gff3"/>
<sniffer type="galaxy.datatypes.tabular:Pileup"/>
<sniffer type="galaxy.datatypes.interval:Interval"/>
<sniffer type="galaxy.datatypes.tabular:Sam"/>
<sniffer type="galaxy.datatypes.data:Newick"/>
<sniffer type="galaxy.datatypes.data:Nexus"/>
<sniffer type="galaxy.datatypes.text:IQTree"/>
<sniffer type="galaxy.datatypes.text:Obo"/>
<sniffer type="galaxy.datatypes.text:Arff"/>
<sniffer type="galaxy.datatypes.text:Ipynb"/>
<sniffer type="galaxy.datatypes.text:Biom1"/>
<sniffer type="galaxy.datatypes.text:ImgtJson"/>
<sniffer type="galaxy.datatypes.text:GeoJson"/>
<sniffer type="galaxy.datatypes.text:Json"/>
<sniffer type="galaxy.datatypes.genetics:GenotypeMatrix"/>
<sniffer type="galaxy.datatypes.genetics:DataIn"/>
<sniffer type="galaxy.datatypes.genetics:MarkerMap"/>
<sniffer type="galaxy.datatypes.genetics:AllegroLOD"/>
<sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/>
<sniffer type="galaxy.datatypes.sequence:DotBracket"/>
<sniffer type="galaxy.datatypes.tabular:ConnectivityTable"/>
<sniffer type="galaxy.datatypes.tabular:CSV"/>
<sniffer type="galaxy.datatypes.tabular:TSV"/>
<sniffer type="galaxy.datatypes.tabular:MatrixMarket"/>
<sniffer type="galaxy.datatypes.msa:Hmmer2"/>
<sniffer type="galaxy.datatypes.msa:Hmmer3"/>
<sniffer type="galaxy.datatypes.msa:Stockholm_1_0"/>
<sniffer type="galaxy.datatypes.msa:MauveXmfa"/>
<sniffer type="galaxy.datatypes.msa:InfernalCM"/>
<sniffer type="galaxy.datatypes.annotation:SnapHmm"/>
<sniffer type="galaxy.datatypes.microarrays:Cel"/>
<sniffer type="galaxy.datatypes.microarrays:Gpr"/>
<sniffer type="galaxy.datatypes.microarrays:Gal"/>
<sniffer type="galaxy.datatypes.binary:RData"/>
<sniffer type="galaxy.datatypes.images:Jpg"/>
<sniffer type="galaxy.datatypes.images:Png"/>
<sniffer type="galaxy.datatypes.images:Tiff"/>
<sniffer type="galaxy.datatypes.images:Bmp"/>
<sniffer type="galaxy.datatypes.images:Gif"/>
<sniffer type="galaxy.datatypes.images:Im"/>
<sniffer type="galaxy.datatypes.images:Pcd"/>
<sniffer type="galaxy.datatypes.images:Pcx"/>
<sniffer type="galaxy.datatypes.images:Ppm"/>
<sniffer type="galaxy.datatypes.images:Psd"/>
<sniffer type="galaxy.datatypes.images:Xbm"/>
<sniffer type="galaxy.datatypes.images:Rgb"/>
<sniffer type="galaxy.datatypes.images:Pbm"/>
<sniffer type="galaxy.datatypes.images:Pgm"/>
<sniffer type="galaxy.datatypes.images:Xpm"/>
<sniffer type="galaxy.datatypes.images:Eps"/>
<sniffer type="galaxy.datatypes.images:Rast"/>
<!--
Keep this commented until the sniff method in the assembly.py
module is fixed to not read the entire file.
<sniffer type="galaxy.datatypes.assembly:Amos"/>
-->
<sniffer type="galaxy.datatypes.binary:OxliCountGraph"/>
<sniffer type="galaxy.datatypes.binary:OxliNodeGraph"/>
<sniffer type="galaxy.datatypes.binary:OxliTagSet"/>
<sniffer type="galaxy.datatypes.binary:OxliStopTags"/>
<sniffer type="galaxy.datatypes.binary:OxliSubset"/>
<sniffer type="galaxy.datatypes.binary:OxliGraphLabels"/>
<sniffer type="galaxy.datatypes.neo4j:Neo4jDBzip"/>
</sniffers>
</datatypes>

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