<tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.1.0">
  <description>Extract scans based on PSM report 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]} $removeretain.doremoveretain $removeretain.num_random_scans]]></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>
    
    <conditional name="removeretain">
        <param name="doremoveretain" type="boolean" truevalue="retain" falsevalue="remove" label="Retain or Remove the given Scans" help="Retain=Yes; Remove=No (default)" />
        <when value="remove">
            <param name="num_random_scans" type="hidden" value="0" />
        </when>
        <when value="retain">
            <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="false" />
        </when>
      </conditional>
      
  </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 gives option to create a new mzml file, either with those scans or without those scans.

Remove option:
Creates a new mzml file with all the unidentified scans (removes those that are in the PSM report).

Retain option:
Creates a new mzml file with only those scans that is present in the PSM report. In addition to this, it also has an option to add N number of randomly selected scans to the output mzml file.


Please Note: This tool currently works only with PeptideShaker generated PSM report file.

  </help>
</tool>