ucsc_tablebrowser.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="UCSC Main" id="ucsc_table_direct1" tool_type="data_source" version="1.0.0" profile="20.09">
    <description>table browser</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="https://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
        <display>go to UCSC Table Browser $GALAXY_URL</display>
        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
        <param name="tool_id" type="hidden" value="ucsc_table_direct1" />
        <param name="sendToGalaxy" type="hidden" value="1" />
        <param name="hgta_compressType" type="hidden" value="none" />
        <param name="hgta_outputType" type="hidden" value="bed" />
    </inputs>
    <request_param_translation>
        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
        <request_param galaxy_name="URL" remote_name="URL" missing="" />
        <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
        <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
        <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
        <request_param galaxy_name="position" remote_name="position" missing="unknown position" />
        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" >
            <value_translation>
                <value galaxy_value="auto" remote_value="primaryTable" />
                <value galaxy_value="auto" remote_value="selectedFields" />
                <value galaxy_value="wig" remote_value="wigData" />
                <value galaxy_value="interval" remote_value="tab" />
                <value galaxy_value="html" remote_value="hyperlinks" />
                <value galaxy_value="fasta" remote_value="sequence" />
                <value galaxy_value="gtf" remote_value="gff" />
            </value_translation>
        </request_param>
    </request_param_translation>
    <uihints minwidth="800"/>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $position else $description#)"/>
    </outputs>
    <options sanitize="False" refresh="True"/>
    <citations>
        <citation type="doi">10.1093/database/bar011</citation>
        <citation type="doi">10.1101/gr.229102</citation>
    </citations>
</tool>