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Add a tool config for the new bx_browser data source tool.

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Greg Von Kuster
2010-01-14 10:24:37 -05:00
parent 927cfe685c
commit 826da3acac
2 changed files with 42 additions and 0 deletions
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tool_conf.xml.sample
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<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/bx_browser.xml" />
<tool file="data_source/microbial_import.xml" />
<tool file="data_source/biomart.xml" />
<tool file="data_source/biomart_test.xml" />
tools/data_source/bx_browser.xml
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<?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="BX main" id="bx_browser" tool_type="data_source">
<description>browser</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://main.genome-browser.bx.psu.edu/" check_values="false" method="get">
<display>go to BX Browser $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
<param name="tool_id" type="hidden" value="bx_browser" />
<param name="sendToGalaxy" type="hidden" value="1" />
<param name="hgta_compressType" type="hidden" value="none" />
<param name="hgta_outputType" type="hidden" value="bed" />
</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="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
<value_translation>
<value galaxy_value="tabular" remote_value="primaryTable" />
<value galaxy_value="tabular" remote_value="selectedFields" />
<value galaxy_value="wig" remote_value="wigData" />
<value galaxy_value="interval" remote_value="tab" />
<value galaxy_value="html" remote_value="hyperlinks" />
<value galaxy_value="fasta" remote_value="sequence" />
</value_translation>
</request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>