mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-31 02:28:09 +08:00
Remove mako
This commit is contained in:
guerler
@@ -1,249 +0,0 @@
|
||||
<%!
|
||||
def inherit(context):
|
||||
if context.get('use_panels'):
|
||||
return '/webapps/galaxy/base_panels.mako'
|
||||
else:
|
||||
return '/base.mako'
|
||||
%>
|
||||
<%inherit file="${inherit(context)}"/>
|
||||
|
||||
<%def name="init()">
|
||||
<%
|
||||
self.has_left_panel=False
|
||||
self.has_right_panel=False
|
||||
self.message_box_visible=False
|
||||
self.active_view="user"
|
||||
self.overlay_visible=False
|
||||
%>
|
||||
</%def>
|
||||
|
||||
<%def name="title()">Custom Database Builds</%def>
|
||||
|
||||
<%def name="stylesheets()">
|
||||
${parent.stylesheets()}
|
||||
<style type="text/css">
|
||||
#custom_dbkeys * {
|
||||
min-width: 100px;
|
||||
vertical-align: text-top;
|
||||
}
|
||||
pre {
|
||||
padding: 0;
|
||||
margin: 0;
|
||||
}
|
||||
## If page is displayed in panels, pad from edges for readability.
|
||||
%if context.get('use_panels'):
|
||||
div#center {
|
||||
padding: 10px;
|
||||
}
|
||||
%endif
|
||||
div.def_tab {
|
||||
float: left;
|
||||
padding: 0.2em 0.5em;
|
||||
background-color: white;
|
||||
}
|
||||
div.def_tab.active {
|
||||
background-color: #CCF;
|
||||
border: solid 1px #66A;
|
||||
}
|
||||
</style>
|
||||
</%def>
|
||||
|
||||
<%def name="javascripts()">
|
||||
${parent.javascripts()}
|
||||
|
||||
<script type="text/javascript">
|
||||
|
||||
$(function() {
|
||||
$(".db_hide").each(function() {
|
||||
var pre = $(this);
|
||||
pre.hide();
|
||||
pre.siblings("span").wrap( "<a href='javascript:void(0);'></a>" ).click( function() {
|
||||
pre.toggle();
|
||||
});
|
||||
});
|
||||
$("#installed_builds").hide();
|
||||
$("#show_installed_builds").click(function() {
|
||||
$("#installed_builds").show();
|
||||
});
|
||||
|
||||
// Set up behavior for build definition tab controls.
|
||||
$("div.def_tab > a").each(function() {
|
||||
$(this).click(function() {
|
||||
var tab_id = $(this).attr("id");
|
||||
|
||||
// Hide all build inputs, help.
|
||||
$("div.build_definition").children(":input").hide();
|
||||
$(".infomessagesmall > div").hide();
|
||||
|
||||
// Show input item, help corresponding to tab id.
|
||||
$("#" + tab_id + "_input").show();
|
||||
$("." + tab_id + "_help").show();
|
||||
|
||||
// Update tabs.
|
||||
$("div.def_tab").removeClass("active");
|
||||
$(this).parent().addClass("active");
|
||||
});
|
||||
});
|
||||
|
||||
## If there are fasta HDAs available, show fasta tab; otherwise show len file tab.
|
||||
// Set starting tab.
|
||||
% if fasta_hdas.first():
|
||||
$("#fasta").click();
|
||||
% else:
|
||||
$("#len_file").click();
|
||||
% endif
|
||||
|
||||
// Before submit, remove inputs not associated with the active tab.
|
||||
$("#submit").click(function() {
|
||||
var id = $(this).parents("form").find(".active > a").attr("id");
|
||||
$("div.build_definition").children(":input").each(function() {
|
||||
if ( $(this).attr("id") !== (id + "_input") ) {
|
||||
$(this).remove();
|
||||
}
|
||||
});
|
||||
});
|
||||
});
|
||||
|
||||
</script>
|
||||
</%def>
|
||||
|
||||
<%def name="center_panel()">
|
||||
${self.body()}
|
||||
</%def>
|
||||
|
||||
<%def name="body()">
|
||||
% if message:
|
||||
<div class="errormessagelarge">${message}</div>
|
||||
% elif lines_skipped > 0:
|
||||
<div class="warningmessagelarge">Skipped ${lines_skipped} lines that could not be parsed. (Line was either blank or not 2-column, with 2nd column being an integer)</div>
|
||||
% endif
|
||||
|
||||
<h3>Current Custom Builds:</h3>
|
||||
|
||||
% if dbkeys:
|
||||
<table id="custom_dbkeys" class="colored" cellspacing="0" cellpadding="0">
|
||||
<tr class="header">
|
||||
<th>Name</th>
|
||||
<th>Key</th>
|
||||
<th>Number of chroms/contigs</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
% for key, dct in dbkeys.iteritems():
|
||||
<tr>
|
||||
<td>${dct['name'] | h}</td>
|
||||
<td>${key | h}</td>
|
||||
<td>
|
||||
## <span>${len(dct["chroms"])} entries</span>
|
||||
## <pre id="pre_${key}" class="db_hide">
|
||||
## <table cellspacing="0" cellpadding="0">
|
||||
## <tr><th>Chrom</th><th>Length</th></tr>
|
||||
## % for chrom, chrom_len in dct["chroms"].iteritems():
|
||||
## <tr><td>${chrom | h}</td><td>${chrom_len | h}</td></tr>
|
||||
## % endfor
|
||||
## </table>
|
||||
## </pre>
|
||||
% if 'count' in dct:
|
||||
${dct['count']}
|
||||
% else:
|
||||
Processing
|
||||
% endif
|
||||
</td>
|
||||
<td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key | h}" /><input type="submit" name="delete" value="Delete" /></form></td>
|
||||
</tr>
|
||||
% endfor
|
||||
</table>
|
||||
% else:
|
||||
<p>You currently have no custom builds.</p>
|
||||
% endif
|
||||
|
||||
<p>
|
||||
<a id="show_installed_builds" href="javascript:void(0);">Show loaded, system-installed builds</a>
|
||||
<blockquote id="installed_builds">${installed_len_files}</blockquote>
|
||||
</p>
|
||||
|
||||
<hr />
|
||||
<h3>Add a Custom Build</h3>
|
||||
<form action="dbkeys" method="post" enctype="multipart/form-data">
|
||||
## Include hidden param for panels:
|
||||
%if use_panels:
|
||||
<input type="hidden" name="use_panels" value="True">
|
||||
%endif
|
||||
## Custom build via fasta in history.
|
||||
<div class="toolForm" style="float: left;">
|
||||
<div class="toolFormTitle">New Build</div>
|
||||
<div class="toolFormBody">
|
||||
<div class="form-row">
|
||||
<label for="name">Name (eg: Hamster):</label>
|
||||
<input type="text" id="name" name="name" />
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label for="key">Key (eg: hamster_v1):</label>
|
||||
<input type="text" id="key" name="key" />
|
||||
</div>
|
||||
<div class="form-row build_definition">
|
||||
<label>Definition:</label>
|
||||
<div class="def_tab">
|
||||
<a id="fasta" href="javascript:void(0)">FASTA</a>
|
||||
</div>
|
||||
<div class="def_tab">
|
||||
<a id="len_file" href="javascript:void(0)">Len File</a>
|
||||
</div>
|
||||
<div class="def_tab">
|
||||
<a id="len_entry" href="javascript:void(0)">Len Entry</a>
|
||||
</div>
|
||||
<div style="clear: both; padding-bottom: 0.5em"></div>
|
||||
<select id="fasta_input" name="dataset_id">
|
||||
%for dataset in fasta_hdas:
|
||||
<option value="${trans.security.encode_id( dataset.id )}">${dataset.hid | h}: ${dataset.name | h}</option>
|
||||
%endfor
|
||||
</select>
|
||||
<input type="file" id="len_file_input" name="len_file" /></input>
|
||||
<textarea id="len_entry_input" name="len_text" cols="30" rows="8"></textarea>
|
||||
</div>
|
||||
<div class="form-row"><input id="submit" type="submit" name="add" value="Submit"/></div>
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
<div class="infomessagesmall" style="float: left; margin-left: 10px; width: 40%;">
|
||||
<div class="fasta_help">
|
||||
<h3>FASTA format</h3>
|
||||
<p>
|
||||
This is a multi-fasta file from your current history that provides the genome
|
||||
sequences for each chromosome/contig in your build.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
Here is a snippet from an example multi-fasta file:
|
||||
<pre>
|
||||
>chr1
|
||||
ATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...
|
||||
>chr2
|
||||
GGCGGCCGCGGCGATATAGAACTACTCATTATATATA...
|
||||
...
|
||||
</pre>
|
||||
</p>
|
||||
</div>
|
||||
<div class="len_file_help len_entry_help">
|
||||
<h3>Length Format</h3>
|
||||
<p>
|
||||
The length format is two-column, separated by whitespace, of the form:
|
||||
<pre>chrom/contig length of chrom/contig</pre>
|
||||
</p>
|
||||
<p>
|
||||
For example, the first few entries of <em>mm9.len</em> are as follows:
|
||||
<pre>
|
||||
chr1 197195432
|
||||
chr2 181748087
|
||||
chr3 159599783
|
||||
chr4 155630120
|
||||
chr5 152537259
|
||||
</pre>
|
||||
</p>
|
||||
|
||||
<p>Trackster uses this information to populate the select box for chrom/contig, and
|
||||
to set the maximum basepair of the track browser. You may either upload a .len file
|
||||
of this format (Len File option), or directly enter the information into the box
|
||||
(Len Entry option).</p>
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
Reference in New Issue
Block a user