Mercurial > repos > pravs > msms_extractor
diff MSMS_Extractor.xml @ 2:aa944e3a353c draft
planemo upload
author | pravs |
---|---|
date | Thu, 03 Aug 2017 13:53:09 -0400 |
parents | f444e529363d |
children | e7c63cfef363 |
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--- a/MSMS_Extractor.xml Thu Feb 16 11:56:45 2017 -0500 +++ b/MSMS_Extractor.xml Thu Aug 03 13:53:09 2017 -0400 @@ -1,11 +1,11 @@ -<tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0"> - <description>Removes scans with identified PSMs from the mzML file(s).</description> +<tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.1.0"> + <description>Extract scans based on PSM report from the mzML file(s).</description> <requirements> <requirement type="package" version="3.0.9016">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]}]]></command> + <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> @@ -13,6 +13,17 @@ <param name="psmreportfile" type="data" format="tabular"> <label>Input PSM Report File</label> </param> + + <conditional name="removeretain"> + <param name="doremoveretain" type="boolean" truevalue="retain" falsevalue="remove" label="Remove or Retain the given Scans" help="Retain=Yes; Remove=No (default)" /> + <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> @@ -21,6 +32,16 @@ <help> -MSMS_Extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and removes it from the mzML file. +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>