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2 <tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.1.0">
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3 <description>Extract scans based on PSM report 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]} $removeretain.doremoveretain $removeretain.num_random_scans]]></command>
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9 <inputs>
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10 <param name="spectrumfile" type="data" format="mzml">
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11 <label>Input mzML File</label>
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12 </param>
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13 <param name="psmreportfile" type="data" format="tabular">
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14 <label>Input PSM Report File</label>
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15 </param>
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16
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17 <conditional name="removeretain">
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18 <param name="doremoveretain" type="boolean" truevalue="retain" falsevalue="remove" label="Retain or Remove the given Scans" help="Retain=Yes; Remove=No (default)" />
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19 <when value="remove">
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20 <param name="num_random_scans" type="hidden" value="0" />
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21 </when>
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22 <when value="retain">
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23 <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="false" />
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24 </when>
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25 </conditional>
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27 </inputs>
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28
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29 <outputs>
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30 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
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31 </outputs>
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32
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33
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34 <help>
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35 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.
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36
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37 ----
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38
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39 REMOVE option:
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40
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41 Creates a new mzml file with all the unidentified scans (removes those that are in the PSM report).
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42
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43
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44 RETAIN option:
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45
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46 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.
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47
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48 ----
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49
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50 Please Note: This tool currently works only with PeptideShaker generated PSM report file.
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51
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52 </help>
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53 </tool>
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