<tool id="cpo_tree_drawer" name="cpo_tree_drawer" version="0.1.0">
	<description>This tool makes a phylogenetic tree using data from snippy alignments, clustalw NJ tree and metadat from cpo_prediction workflow using ETE3</description>
	<requirements>
    <requirement type="package" version="3.6">python</requirement>
    <requirement type="package" version="0.23.4">pandas</requirement>
    <requirement type="package" version="3.1.1">ete3</requirement>
    <requirement type="package" version="5.6.0">pyqt</requirement>
	<requirement type="package" version="5.6.2">qt</requirement>

  </requirements>
	<command detect_errors="exit_code">
    <![CDATA[
	    python '$__tool_directory__/cpo_galaxy_tree.py'
		'-t $tree'
		'-d $distance'
		'-m $metadata'
    ]]>
	</command>
    <inputs>
        <param type="data" name="tree" format="txt"/>
        <param type="data" name="distance" format="tabular" />
        <param type="data" name="metadata" format="tabular" />
    </inputs>
    <outputs>
        <data name="tsvSummary" format="pdf" from_work_dir="tree.pdf"/>
    </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="txtSummary" 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>