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Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server.

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Greg Von Kuster
2008-12-15 10:37:39 -05:00
parent 7ecfd7c61e
commit dfd5e9827f
3 changed files with 33 additions and 7 deletions
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tool_conf.xml.sample
+2 -1
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@@ -9,7 +9,8 @@
<tool file="data_source/microbial_import.xml" />
<tool file="data_source/biomart.xml" />
<tool file="data_source/biomart_test.xml" />
<tool file="data_source/gbrowse_elegans.xml" />
<tool file="data_source/wormbase.xml" />
<tool file="data_source/wormbase_test.xml" />
<tool file="data_source/flymine.xml" />
<tool file="data_source/encode_db.xml" />
<tool file="data_source/epigraph_import.xml" />
tools/data_source/wormbase.xml
+26
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@@ -0,0 +1,26 @@
<?xml version="1.0"?>
<tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="get">
<description>server</description>
<command interpreter="python">data_source.py $output</command>
<inputs action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top">
<display>go to Wormbase server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL" remote_name="URL" missing="">
<add_to_url>
<param_from_source name="d" missing="" />
<param_from_source name="dbkey" missing="" />
<param_from_source name="q" missing="" />
<param_from_source name="s" missing="" />
<param_from_source name="t" missing="" />
</add_to_url>
</request_param>
<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/gbrowse_elegans.xml → tools/data_source/wormbase_test.xml
+5 -6
View File
@@ -1,10 +1,10 @@
<?xml version="1.0"?>
<tool name="C. Elegans" id="gbrowse_elegans" tool_type="data_source" URL_method="get">
<description>server</description>
<tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="get">
<description>test server</description>
<command interpreter="python">data_source.py $output</command>
<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top">
<display>go to C. Elegans server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=gbrowse_elegans" />
<display>go to Wormbase test server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL" remote_name="URL" missing="">
@@ -16,7 +16,7 @@
<param_from_source name="t" missing="" />
</add_to_url>
</request_param>
<request_param galaxy_name="data_type" remote_name="data_type" missing="gff3" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
@@ -24,4 +24,3 @@
</outputs>
<options sanitize="False" refresh="True"/>
</tool>