Mercurial > repos > dfornika > match_plasmid_to_reference

view match_plasmid_to_reference.xml @ 0:8bb674372911 draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 00:08:43 -0500
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children 3616b6eda1da
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<tool id="match_plasmid_to_reference" name="Match plasmid to reference" version="0.1.0">
    <description>Pick plasmids containing specific genes</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        '$__tool_directory__/match_plasmid_to_reference.py'
        --plasmid '${plasmid}'
        --reference_plasmids
        #for $reference_plasmid in $reference_plasmids:
          '${reference_plasmid}'
        #end for
        --concatenated_mob_typer_reports '${concatenated_mob_typer_reports}'
        --outdir outdir
    ]]></command>
    <inputs>
        <param name="plasmid" type="data" format="fasta" />
        <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" />
        <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
    </inputs>
    <outputs>
        <data name="plasmid" from_work_dir="outdir/plasmid.fasta" />
        <data name="reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" />
	<data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" />
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>