cpo_clustalw.xml

<tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
  <description>Modified version of clustalw2 v2.1 to produce NJ trees from an SNIPPY produced alignment</description>
  <requirements>
     <requirement type="package" version="2.1">clustalw</requirement>
  </requirements>   
  <command detect_errors="exit_code">
  <![CDATA[  
    clustalw2 -tree -infile=$input && mv `ls $input | cut -d$'.' -f 1`.ph ./result.ph
  ]]>  
  </command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
  </inputs>
  <outputs>
    <data name="phylip" format="txt" from_work_dir="result.ph"/> 
  </outputs>
  <help>
    clustalw2 -tree -infile=$input -outputtree=nj
  </help>
  <citations>
    <citation type="bibtex">
  @misc{githubmob-suite,
  author = {Robertson J, Nash J},
  title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
  publisher = {GitHub},
  journal = {GitHub repository},
  doi = {10.1099/mgen.0.000206},
  url = {https://github.com/phac-nml/mob-suite}
    }</citation>
  </citations>
</tool>