| Previous changeset 8:153e9eb5f2ff (2014-01-31) Next changeset 10:f47b24cccf88 (2014-02-07) |
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Commit message:
Made converter more robust and added support for mzXML in xtandem interface |
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modified:
MassComb.jar masscomb_dbsearch_converter.xml masscomb_dbsearch_xtandem.xml |
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| diff -r 153e9eb5f2ff -r c317e0f939df MassComb.jar |
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| Binary file MassComb.jar has changed |
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| diff -r 153e9eb5f2ff -r c317e0f939df masscomb_dbsearch_converter.xml --- 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 |
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| @@ -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 ${on_string} "> @@ -73,7 +82,7 @@ .. class:: infomark -This tool translates X!Tandem and OMSSA results to mzIdentML format. +This tool translates X!Tandem, OMSSA or Proteome Discoverer peptide identification results to mzIdentML format. It uses the library at http://code.google.com/p/mzidentml-parsers/ ----- |
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| diff -r 153e9eb5f2ff -r c317e0f939df masscomb_dbsearch_xtandem.xml --- a/masscomb_dbsearch_xtandem.xml Fri Jan 31 12:06:57 2014 +0100 +++ b/masscomb_dbsearch_xtandem.xml Fri Feb 07 11:41:58 2014 +0100 |
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| @@ -26,7 +26,7 @@ <option value="fileSet">fileSet</option> </param> <when value="single"> - <param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/> + <param name="inputFile" type="data" format="mzml,mzxml" label="MS/MS input file (mzml or mzxml)"/> </when> <when value="fileSet"> <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/> @@ -214,6 +214,7 @@ <Files/> <Parameters> <Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/bin" type="Unknown" description=""/> + <Attribute attributeName="xtandemLocation_dev" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-13-09-01-1/bin/" type="Unknown" description=""/> <Attribute attributeName="database" value="${database}" type="Unknown" description=""/> <Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/> <Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/> |