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2 <tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0">
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3 <description>Removes scans with identified PSMs from the mzML file(s).</description>
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4 <requirements>
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5 <requirement type="package" version="3.0.9016">proteowizard</requirement>
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6 <requirement type="package" version="3.4">pyteomics</requirement>
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7 </requirements>
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8 <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]}]]></command>
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9 <inputs>
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10 <param name="spectrumfile" type="data" format="mzml">
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11 <label>Input mzML File</label>
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12 </param>
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13 <param name="psmreportfile" type="data" format="tabular">
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14 <label>Input PSM Report File</label>
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15 </param>
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16 </inputs>
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17
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18 <outputs>
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19 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
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20 </outputs>
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21
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22
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23 <help>
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24 MSMS_Extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and removes it from the mzML file.
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25 </help>
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26 </tool>
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