<tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0">
  <description>Removes scans with identified PSMs from the mzML file(s).</description>
  <requirements>
      <requirement type="package" version="3.0.9016">proteowizard</requirement>
      <requirement type="package" version="3.4">pyteomics</requirement>
  </requirements>
  <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]}]]></command>
  <inputs>
    <param name="spectrumfile" type="data" format="mzml">
      <label>Input mzML File</label>
    </param>
    <param name="psmreportfile" type="data" format="tabular">
      <label>Input PSM Report File</label>
    </param>
  </inputs>

  <outputs>
    <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
  </outputs>
  

  <help>
MSMS_Extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and removes it from the mzML file.
  </help>
</tool>