<tool name="SRA" id="sra_source" tool_type="data_source" version="1.0.1" profile="16.04">
    <description>server</description>
    <edam_operations>
        <edam_operation>operation_0224</edam_operation>
    </edam_operations>
    <command><![CDATA[
    python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit &&
    python '$csv_to_tsv'
    ]]></command>
    <configfiles>
    <configfile name="csv_to_tsv">
import csv


with open('$output') as in_fh:
    rows = [r for r in csv.reader(in_fh)]
with open('$output', 'w') as out_fh:
    tsvout = csv.writer(out_fh, delimiter='\t')
    for row in rows:
        tsvout.writerow(row)
    </configfile>
    </configfiles>
    <inputs action="https://www.ncbi.nlm.nih.gov/sra" check_values="false" method="get">
        <display>go to SRA server $GALAXY_URL</display>
        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=sra_source" />
    </inputs>
    <outputs>
        <data name="output" format="sra_manifest.tabular"/>
    </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>