cpo_plasmidfinder.xml

<tool id="cpo_plasmidfinder" name="cpo_plasmidfinder" version="0.8">
	<description>Modified plasmidfinder v0.8 with custom cpo database</description>
	<requirements>
		<requirement type="package" version="0.8">abricate</requirement>
	</requirements>
	<command detect_errors="exit_code">
	<![CDATA[
		abricate
		--datadir=$__tool_directory__/databases/
		--db=plasmidfinder
		'$input'
		>report.tsv
    ]]>
	</command>
    <inputs>
        <param type="data" name="input" format="fasta" />
    </inputs>
    <outputs>
        <data name="report" format="tabular" from_work_dir="report.tsv"/>
    </outputs>
	<help>
		Modified plasmidfinder v0.8 with custom carbapenemase database. required input: input: contig, --db plasmidfinder database
	</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>