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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
author public-health-bioinformatics
date Tue, 12 Nov 2019 22:47:36 -0500
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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_genbank
        #for $reference_plasmid in $reference_plasmids_genbank:
          '${reference_plasmid}'
        #end for
        --reference_plasmids_fasta
        #for $reference_plasmid in $reference_plasmids_fasta:
          '${reference_plasmid}'
        #end for
        --mob_typer_report '${concatenated_mob_typer_reports}'
        --outdir outdir
    ]]></command>
    <inputs>
        <param name="plasmid" type="data" format="fasta" />
        <param name="reference_plasmids_genbank" type="data_collection" collection_type="list" format="genbank" />
	<param name="reference_plasmids_fasta" type="data_collection" collection_type="list" format="fasta" />
        <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
    </inputs>
    <outputs>
        <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/>
        <data name="matched_reference_plasmid_genbank" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid (genbank)" format="genbank"/>
	<data name="matched_reference_plasmid_fasta" from_work_dir="outdir/reference_plasmid.fasta" label="Reference Plasmid (fasta)" format="fasta"/>
	<data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
            <param name="reference_plasmids_genbank">
                <collection type="list">
                    <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
                    <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
                </collection>
            </param>
            <param name="reference_plasmids_fasta">
                <collection type="list">
                    <element name="CP008719" value="CP008719.fa" ftype="fasta" />
                    <element name="JQ739157" value="JQ739157.fa" ftype="fasta" />
                </collection>
            </param>
            <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
            <output name="output_plasmid" file="outdir/plasmid.fasta" />
            <output name="matched_reference_plasmid_genbank" file="outdir/reference_plasmid.gbk" />
            <output name="matched_reference_plasmid_fasta" file="outdir/reference_plasmid.fasta" />
            <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>