Mercurial > repos > pieterlukasse > prims_masscomb
diff masscomb_dbsearch_converter.xml @ 9:c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
author | pieter.lukasse@wur.nl |
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date | Fri, 07 Feb 2014 11:41:58 +0100 |
parents | d6001e8d7441 |
children | 1a6fa343b981 |
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--- a/masscomb_dbsearch_converter.xml Fri Jan 31 12:06:57 2014 +0100 +++ b/masscomb_dbsearch_converter.xml Fri Feb 07 11:41:58 2014 +0100 @@ -14,6 +14,7 @@ -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero #end if -inputFile $fileType.inputFormatType.inputFile + -outputMsMsFragmentationData $outputMsMsFragmentationData -outputFile $outputFile </command> <inputs> @@ -27,6 +28,7 @@ <param name="inputFormat" type="select" label="inputFormat"> <option value="xtandem">X!Tandem</option> <option value="omssa">OMSSA</option> + <option value="proteomediscoverer_pepxml">Proteome Discoverer (pepxml) [beta]</option> </param> <when value="xtandem"> <param name="inputFile" type="data" format="bioml,xml" label="MS/MS search results" help="Note: the spectra index values in the resulting file will only be reliable for when X!Tandem has executed on MzML data"/> @@ -38,6 +40,9 @@ <when value="omssa"> <param name="inputFile" type="data" format="omx" label="MS/MS search results"/> </when> + <when value="proteomediscoverer_pepxml"> + <param name="inputFile" type="data" format="pepxml" label="MS/MS search results (pepxml)"/> + </when> </conditional> </when> <when value="fileSet"> @@ -59,6 +64,10 @@ </conditional> </when> </conditional> + <param name="outputMsMsFragmentationData" type="boolean" checked="false" + label="Output MS/MS fragmentation data" + help="NB: this will add to the output also the fragment ions related to each peptide identification"/> + </inputs> <outputs> <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} "> @@ -73,7 +82,7 @@ .. class:: infomark -This tool translates X!Tandem and OMSSA results to mzIdentML format. +This tool translates X!Tandem, OMSSA or Proteome Discoverer peptide identification results to mzIdentML format. It uses the library at http://code.google.com/p/mzidentml-parsers/ -----