gramene_mart.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="GrameneMart" id="gramenemart" tool_type="data_source" version="1.0.1">
<description> Central server</description>
<edam_operations>
<edam_operation>operation_0224</edam_operation>
</edam_operations>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></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="">
<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"/>
</tool>