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Add tool config for GrameneMart data source.

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This commit is contained in:
Greg Von Kuster
2009-05-27 14:19:59 -04:00
parent 4dcc777df4
commit e608f904ee
3 changed files with 43 additions and 0 deletions
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tool_conf.xml.main
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@@ -6,6 +6,7 @@
<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
<tool file="data_source/microbial_import.xml" />
<tool file="data_source/biomart.xml" />
<tool file="data_source/gramene_mart.xml" />
<tool file="data_source/flymine.xml" />
<tool file="data_source/encode_db.xml" />
<tool file="data_source/epigraph_import.xml" />
tool_conf.xml.sample
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@@ -8,6 +8,7 @@
<tool file="data_source/microbial_import.xml" />
<tool file="data_source/biomart.xml" />
<tool file="data_source/biomart_test.xml" />
<tool file="data_source/gramene_mart.xml" />
<tool file="data_source/wormbase.xml" />
<tool file="data_source/wormbase_test.xml" />
<tool file="data_source/flymine.xml" />
tools/data_source/gramene_mart.xml
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@@ -0,0 +1,41 @@
<?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.
TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
-->
<tool name="GrameneMart" id="gramenemart" tool_type="data_source" URL_method="get" version="1.0.1">
<description> Central server</description>
<command interpreter="python">data_source.py $output</command>
<inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to GrameneMart Central $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL" remote_name="URL" missing="">
<add_to_url>
<param_from_source name="_export" missing="1" />
<param_from_source name="GALAXY_URL" missing="0" />
</add_to_url>
</request_param>
<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular">
<data_type_translation>
<format galaxy_format="tabular" remote_format="TSV" />
</data_type_translation>
</request_param>
<request_param galaxy_name="dbkey" remote_name="dbkey" 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="Biomart query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>