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comparison MSMS_Extractor.xml @ 1:f444e529363d draft

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planemo upload
author pravs
date Thu, 16 Feb 2017 11:56:45 -0500
parents 093015b1b904
children aa944e3a353c
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0:093015b1b904 1:f444e529363d
1 1
2 <tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0"> 2 <tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0">
3 <description>Removes identified scans from the mzML file using PSM report.</description> 3 <description>Removes scans with identified PSMs from the mzML file(s).</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.0.9016">proteowizard</requirement> 5 <requirement type="package" version="3.0.9016">proteowizard</requirement>
6 <requirement type="package" version="3.4">pyteomics</requirement> 6 <requirement type="package" version="3.4">pyteomics</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]}]]></command> 8 <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]}]]></command>
19 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" /> 19 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
20 </outputs> 20 </outputs>
21 21
22 22
23 <help> 23 <help>
24 Testing to run MSMS_Extractor script in Galaxy 24 MSMS_Extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and removes it from the mzML file.
25 </help> 25 </help>
26 </tool> 26 </tool>