<tool id="msms_extractor" name="msms_extractor" version="1.0.0">
  <description>Extract MS/MS scans from the mzML file(s) based on PSM report</description>
  <requirements>
      <requirement type="package" version="3_0_9992">proteowizard</requirement>
      <requirement type="package" version="3.7.3">python</requirement>
      <requirement type="package" version="4.1.2">pyteomics</requirement>
      <requirement type="package" version="0.25.2">pandas</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[python '$__tool_directory__/msms_extractor.py' '$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"/>
    <param name="psmreportfile" type="data" format="tabular" label="Input PSM Report File"/>
    
    <conditional name="removeretain">
        <param name="doremoveretain" type="select" display="radio" label="Retain or Remove the MS/MS scans that were identified in PSM report">
            <option value="remove" selected="True">Remove the scans reported in the PSM Report File</option>
            <option value="retain">Retain the scans reported in the PSM Report File </option>
        </param>
        
        <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="true" />
        </when>
      </conditional>
      
  </inputs>

  <outputs>
    <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
  </outputs>
  
  <tests>
    <test>
        <param name="spectrumfile" value="Mo_Tai_iTRAQ_f1.mzml"/>
        <param name="psmreportfile" value="test_psmreport.tabular"/>
        <conditional name="removeretain">
            <param name="doremoveretain" value="retain"/>
            <param name="num_random_scans" value="5"/>
        </conditional>
        <output name="output">
            <assert_contents>
                <has_text text="Mo_Tai_iTRAQ_f1" />
            </assert_contents>
        </output>
    </test>
  </tests>

  <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.


This tool uses msconvert from ProteoWizard: Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. and Mallick, P. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology 30, 918-920 (2012).

  </help>
    <citations>
        <citation type="bibtex">
@misc{A cross-platform toolkit for mass spectrometry and proteomics,
    author={Matt Chambers et al.},
    year={2012},
    title={ProteoWizard}
}
        </citation>
    </citations>
</tool>