cpo_mash.xml

<tool id="cpo_mash" name="cpo_mash" version="2.0">
  <description>Modified version of mash 2.0 with custom bcplasmid database</description>
  <requirements>
     <requirement type="package" version="2.0">mash</requirement>
  </requirements>   
  <command detect_errors="exit_code">
  <![CDATA[  
    mash screen $__tool_directory__/databases/bcPlasmidDB.msh $input | sort -gr | head -10 > mashresult.tsv 
  ]]>  
  </command>
  <inputs>
    <param name="input" type="data" format="fasta" label="contig" help="FASTA file with contig(s)"/>
  </inputs>
  <outputs>
    <data name="mashResult" format="tabular" from_work_dir="mashresult.tsv"/> 
  </outputs>
  <help>
    Modified version of mash 2.0 with custom bcplasmid database. 
	Required input: first argument: bcplasmid database (available in databases folder), second argument: contig input
  </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>