https://github.com/galaxyproject/galaxy
Tip revision: 90de3f2588a61382e70b6209ea39293c6a3987f1 authored by Martin Cech on 22 February 2017, 15:56:56 UTC
Update version to 17.01
Update version to 17.01
Tip revision: 90de3f2
biomart.xml
<?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="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
<description>Ensembl server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.ensembl.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to BioMart Ensembl $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="">
<append_param separator="&" first_separator="?" join="=">
<value name="_export" missing="1" />
<value name="GALAXY_URL" missing="0" />
</append_param>
</request_param>
<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
<value_translation>
<value galaxy_value="tabular" remote_value="TSV" />
</value_translation>
</request_param>
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
<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"/>
<citations>
<citation type="doi">10.1093/database/bar011</citation>
<citation type="doi">10.1093/nar/gkv350</citation>
</citations>
</tool>