opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-21 05:45:37 +08:00
Code Issues Packages Projects Releases Wiki Activity

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

Browse Source
This commit is contained in:
Daniel Blankenberg
2014-06-27 14:44:55 -04:00
parent 3e01352f44
commit 3f78f9a449
9 changed files with 199 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tool_conf.xml.main
+5
View File
@@ -7,7 +7,12 @@
<tool file="data_source/ebi_sra.xml" />
<tool file="data_source/biomart.xml" />
<tool file="data_source/gramene_mart.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/eupathdb.xml" />
tool_conf.xml.sample
+7
View File
@@ -12,6 +12,13 @@
<tool file="data_source/cbi_rice_mart.xml" />
<tool file="data_source/gramene_mart.xml" />
<tool file="data_source/fly_modencode.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/metabolicmine.xml" />
<tool file="data_source/worm_modencode.xml" />
<tool file="data_source/wormbase.xml" />
<tool file="data_source/wormbase_test.xml" />
tools/data_source/flymine.xml
+35
View File
@@ -0,0 +1,35 @@
<?xml version="1.0"?>
<!--
If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="Flymine" id="flymine" tool_type="data_source">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.flymine.org" check_values="false" method="get">
<display>go to Flymine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
<request_param galaxy_name="URL" remote_name="URL" missing="" />
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
<request_param galaxy_name="organism" remote_name="organism" missing="" />
<request_param galaxy_name="table" remote_name="table" missing="" />
<request_param galaxy_name="description" remote_name="description" missing="" />
<request_param galaxy_name="name" remote_name="name" missing="FlyMine query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
<value_translation>
<value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
</value_translation>
</request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/flymine_test.xml
+31
View File
@@ -0,0 +1,31 @@
<?xml version="1.0"?>
<!--
If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="Flymine test" id="flymine_test" tool_type="data_source">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get">
<display>go to Flymine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
<request_param galaxy_name="URL" remote_name="URL" missing="" />
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
<request_param galaxy_name="organism" remote_name="organism" missing="" />
<request_param galaxy_name="table" remote_name="table" missing="" />
<request_param galaxy_name="description" remote_name="description" missing="" />
<request_param galaxy_name="name" remote_name="name" missing="FlyMine query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/metabolicmine.xml
+13
View File
@@ -0,0 +1,13 @@
<?xml version="1.0"?>
<tool name="metabolicMine" id="metabolicmine" tool_type="data_source">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get">
<display>go to metabolicMine server $GALAXY_URL</display>
</inputs>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/modmine.xml
+19
View File
@@ -0,0 +1,19 @@
<?xml version="1.0"?>
<!--
If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="modENCODE modMine" id="modmine" tool_type="data_source">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://intermine.modencode.org/" check_values="false" method="get">
<display>go to modENCODE modMine server $GALAXY_URL</display>
</inputs>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/mousemine.xml
+35
View File
@@ -0,0 +1,35 @@
<?xml version="1.0"?>
<!--
If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="MouseMine" id="mousemine" tool_type="data_source">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get">
<display>go to MouseMine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=mousemine" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
<request_param galaxy_name="URL" remote_name="URL" missing="" />
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
<request_param galaxy_name="organism" remote_name="organism" missing="" />
<request_param galaxy_name="table" remote_name="table" missing="" />
<request_param galaxy_name="description" remote_name="description" missing="" />
<request_param galaxy_name="name" remote_name="name" missing="MouseMine query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
<value_translation>
<value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
</value_translation>
</request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/ratmine.xml
+34
View File
@@ -0,0 +1,34 @@
<?xml version="1.0"?>
<!--
If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="Ratmine" id="ratmine" tool_type="data_source">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get">
<display>go to Ratmine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
<request_param galaxy_name="URL" remote_name="URL" missing="" />
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
<request_param galaxy_name="organism" remote_name="organism" missing="" />
<request_param galaxy_name="table" remote_name="table" missing="" />
<request_param galaxy_name="description" remote_name="description" missing="" />
<request_param galaxy_name="name" remote_name="name" missing="Ratmine query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
<value_translation>
<value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
</value_translation>
</request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/yeastmine.xml
+20
View File
@@ -0,0 +1,20 @@
<?xml version="1.0"?>
<tool name="YeastMine" id="yeastmine" tool_type="data_source">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get">
<display>go to yeastMine server $GALAXY_URL</display>
</inputs>
<request_param_translation>
<request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
<value_translation>
<value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
</value_translation>
</request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>