Mercurial > repos > pravs > msms_extractor
view MSMS_Extractor.xml @ 8:5a1ec6c352e3 draft
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author | pravs |
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date | Thu, 10 Aug 2017 12:54:55 -0400 |
parents | 8741bc3644d4 |
children | b0284072f3eb |
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<tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.2.0"> <description>Extract scans based on PSM report from the mzML file(s).</description> <requirements> <requirement type="package" version="3_0_9992">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 $removeretain.num_random_scans]]></command> <inputs> <param name="spectrumfile" type="data" format="mzml"> <label>Input mzML File</label> </param> <param name="psmreportfile" type="data" format="tabular"> <label>Input PSM Report File</label> </param> <conditional name="removeretain"> <param name="doremoveretain" type="select" display="radio" label="Retain or Remove the MS/MS scans that were identified in PSM report"> <option value="remove" selected="True">Remove the scans reported in the PSM Report File</option> <option value="retain">Retain the scans reported in the PSM Report File </option> </param> <when value="remove"> <param name="num_random_scans" type="hidden" value="0" /> </when> <when value="retain"> <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="false" /> </when> </conditional> </inputs> <outputs> <data format="mzml" name="output" label="${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>