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Wolfgang Maier
bd0f257452
Allows moving all data source tools using the script to profile 20.09. For more recent profiles data_source.py would have to work outside of Galaxy's Python environment.
36 lines
1.2 KiB
XML
36 lines
1.2 KiB
XML
<tool name="SRA" id="sra_source" tool_type="data_source" version="1.0.1" profile="20.09">
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<description>server</description>
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<edam_operations>
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<edam_operation>operation_0224</edam_operation>
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</edam_operations>
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<command><![CDATA[
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python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit &&
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python '$csv_to_tsv'
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]]></command>
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<configfiles>
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<configfile name="csv_to_tsv">
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import csv
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with open('$output') as in_fh:
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rows = [r for r in csv.reader(in_fh)]
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with open('$output', 'w') as out_fh:
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tsvout = csv.writer(out_fh, delimiter='\t')
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for row in rows:
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tsvout.writerow(row)
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</configfile>
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</configfiles>
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<inputs action="https://www.ncbi.nlm.nih.gov/sra" check_values="false" method="get">
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<display>go to SRA server $GALAXY_URL</display>
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<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=sra_source" />
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</inputs>
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<outputs>
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<data name="output" format="sra_manifest.tabular"/>
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</outputs>
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<options sanitize="False" refresh="True"/>
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<citations>
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<citation type="doi">10.1093/database/bar011</citation>
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<citation type="doi">10.1101/gr.229102</citation>
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</citations>
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</tool>
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