flymine.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.
-->
<tool name="Flymine" id="flymine" tool_type="data_source" version="1.0.0">
<description>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.flymine.org" check_values="false" method="get">
<display>go to Flymine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
</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="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="FlyMine query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
<value_translation>
<value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
</value_translation>
</request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="txt" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>