<tool id="cpo_prediction_parser" name="cpo_prediction_parser" version="0.1.0">
  <description>This tool combines outputs from MLST, ResFinder, PlasmidFinder, Mobsuite, RGI into a TSV for the cpo_prediction workflow</description>
  <requirements>
		<requirement type="package" version="0.23.4">pandas</requirement>
		<requirement type="package" version="3.6">python</requirement>
	</requirements>
	<command detect_errors="exit_code">
    <![CDATA[
	    python '$__tool_directory__/cpo_galaxy_prediction.py'
		'-i $contig.element_identifier'
		'-m $mlst'
		'-c $mobsuitecontig'
		'-f $mobsuiteaggregate'
		'-a $resfinder'
		'-r $rgi'
		'-e $expected'
		'-s $__tool_directory__/scheme_species_map.tab'
    '-p $plasmidfinder'
    '-d $mash'
    ]]>
	</command>
    <inputs>
        <param type="data" name="contig"/>
        <param type="data" name="mlst" format="tabular" />
        <param type="data" name="mobsuitecontig" format="tabular" />
        <param type="data" name="mobsuiteaggregate" format="tabular" />
        <param type="data" name="resfinder" format="tabular" />
        <param type="data" name="rgi" format="tabular" />
        <param type="data" name="plasmidfinder" format="tabular" />
        <param type="data" name="mash" format ="tabular"/>
        <param type="text" name="expected" optional ="false"/>
    </inputs>
    <outputs>
        <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
        <data name="tsvSummaryExistingFormat" format="tabular" from_work_dir="summary.linda.tsv"/>
		    <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
    </outputs>
	<tests>
        <test>
            <param name="ID" value="BC11-Kpn005_S2"/>
            <param name="mlst" value="BC11-Kpn005_S2.mlst"/>
            <param name="mobsuitecontig" value="contig_report"/>
            <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/>
            <param name="abricate" value="BC11-Kpn005_S2.cp"/>
            <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/>
            <param name="plasmidfinder" value="BC11-Kpn005_S2.origins"/>
            <param name="expected" value="Klebsiella pneumoniae"/>
            <output name="tsvSummary" file="summary.tsv"/>
			      <output name="tsvSummary" file="summary.txt"/>
        </test>
    </tests>
	<help>
		This tool parses stuff.
	</help>
	<citations>
        <citation type="bibtex">
@misc{cpo,
  author = {j, j},
  year = {2018},
  title = {cpo_prediction},
  publisher = {j},
  journal = {j of j},
  url = {https://bfjia.net,
}</citation>
    </citations>
</tool>