annotate test-data/04/mqpar.xml @ 6:2133b0be850a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"

<?xml version="1.0" ?>
<MaxQuantParams>
	<fastaFiles>
		<FastaFileInfo>
			<fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test2\bsa.fasta</fastaFilePath>
			<identifierParseRule>&gt;([^\s]*)</identifierParseRule>
			<descriptionParseRule>&gt;(.*)</descriptionParseRule>
			<taxonomyParseRule/>
			<variationParseRule/>
			<modificationParseRule/>
			<taxonomyId/>
		</FastaFileInfo>
	</fastaFiles>
	<fastaFilesProteogenomics>
   </fastaFilesProteogenomics>
	<fastaFilesFirstSearch>
   </fastaFilesFirstSearch>
	<fixedSearchFolder/>
	<andromedaCacheSize>350000</andromedaCacheSize>
	<advancedRatios>True</advancedRatios>
	<pvalThres>0.005</pvalThres>
	<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
	<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
	<rtShift>False</rtShift>
	<separateLfq>False</separateLfq>
	<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
	<lfqRequireMsms>True</lfqRequireMsms>
	<decoyMode>revert</decoyMode>
	<boxCarMode>all</boxCarMode>
	<includeContaminants>True</includeContaminants>
	<maxPeptideMass>4600</maxPeptideMass>
	<epsilonMutationScore>True</epsilonMutationScore>
	<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
	<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
	<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
	<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
	<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
	<minScoreModifiedPeptides>40</minScoreModifiedPeptides>
	<secondPeptide>True</secondPeptide>
	<matchBetweenRuns>False</matchBetweenRuns>
	<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
	<matchBetweenRunsFdr>False</matchBetweenRunsFdr>
	<dependentPeptides>False</dependentPeptides>
	<dependentPeptideFdr>0</dependentPeptideFdr>
	<dependentPeptideMassBin>0</dependentPeptideMassBin>
	<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
	<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
	<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
	<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
	<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
	<msmsConnection>False</msmsConnection>
	<ibaq>False</ibaq>
	<top3>False</top3>
	<independentEnzymes>False</independentEnzymes>
	<useDeltaScore>False</useDeltaScore>
	<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
	<taxonomyLevel>Species</taxonomyLevel>
	<avalon>False</avalon>
	<nModColumns>3</nModColumns>
	<ibaqLogFit>False</ibaqLogFit>
	<razorProteinFdr>True</razorProteinFdr>
	<deNovoSequencing>False</deNovoSequencing>
	<deNovoVarMods>True</deNovoVarMods>
	<massDifferenceSearch>False</massDifferenceSearch>
	<isotopeCalc>False</isotopeCalc>
	<writePeptidesForSpectrumFile/>
	<intensityPredictionsFile>
   </intensityPredictionsFile>
	<minPepLen>7</minPepLen>
	<psmFdrCrosslink>0.01</psmFdrCrosslink>
	<peptideFdr>0.01</peptideFdr>
	<proteinFdr>0.01</proteinFdr>
	<siteFdr>0.01</siteFdr>
	<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
	<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
	<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
	<minPeptides>1</minPeptides>
	<minRazorPeptides>1</minRazorPeptides>
	<minUniquePeptides>0</minUniquePeptides>
	<useCounterparts>True</useCounterparts>
	<advancedSiteIntensities>True</advancedSiteIntensities>
	<customProteinQuantification>False</customProteinQuantification>
	<customProteinQuantificationFile/>
	<minRatioCount>2</minRatioCount>
	<restrictProteinQuantification>True</restrictProteinQuantification>
	<restrictMods/>
	<matchingTimeWindow>0</matchingTimeWindow>
	<matchingIonMobilityWindow>0</matchingIonMobilityWindow>
	<alignmentTimeWindow>0</alignmentTimeWindow>
	<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
	<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
	<compositionPrediction>0</compositionPrediction>
	<quantMode>1</quantMode>
	<massDifferenceMods>
   </massDifferenceMods>
	<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
	<writeMsScansTable>False</writeMsScansTable>
	<writeMsmsScansTable>True</writeMsmsScansTable>
	<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
	<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
	<writeMs3ScansTable>True</writeMs3ScansTable>
	<writeAllPeptidesTable>True</writeAllPeptidesTable>
	<writeMzRangeTable>True</writeMzRangeTable>
	<writeMzTab>False</writeMzTab>
	<disableMd5>False</disableMd5>
	<cacheBinInds>True</cacheBinInds>
	<etdIncludeB>False</etdIncludeB>
	<ms2PrecursorShift>0</ms2PrecursorShift>
	<complementaryIonPpm>20</complementaryIonPpm>
	<variationParseRule/>
	<variationMode>none</variationMode>
	<useSeriesReporters>False</useSeriesReporters>
	<name>session1</name>
	<maxQuantVersion>1.6.10.43</maxQuantVersion>
	<tempFolder/>
	<pluginFolder/>
	<numThreads>1</numThreads>
	<emailAddress/>
	<smtpHost/>
	<emailFromAddress/>
	<fixedCombinedFolder/>
	<fullMinMz>-1.79589544172745E+308</fullMinMz>
	<fullMaxMz>1.79589544172745E+308</fullMaxMz>
	<sendEmail>False</sendEmail>
	<ionCountIntensities>False</ionCountIntensities>
	<verboseColumnHeaders>False</verboseColumnHeaders>
	<calcPeakProperties>False</calcPeakProperties>
	<showCentroidMassDifferences>False</showCentroidMassDifferences>
	<showIsotopeMassDifferences>False</showIsotopeMassDifferences>
	<useDotNetCore>False</useDotNetCore>
	<filePaths>
		<string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_22.mzXML</string>
		<string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_23.mzXML</string>
	</filePaths>
	<experiments>
		<string>e1</string>
		<string>e2</string>
	</experiments>
	<fractions>
		<short>1</short>
		<short>2</short>
	</fractions>
	<ptms>
		<boolean>False</boolean>
		<boolean>False</boolean>
	</ptms>
	<paramGroupIndices>
		<int>0</int>
		<int>0</int>
	</paramGroupIndices>
	<referenceChannel>
		<string/>
		<string/>
	</referenceChannel>
	<intensPred>False</intensPred>
	<intensPredModelReTrain>False</intensPredModelReTrain>
	<parameterGroups>
		<parameterGroup>
			<msInstrument>0</msInstrument>
			<maxCharge>7</maxCharge>
			<minPeakLen>2</minPeakLen>
			<diaMinPeakLen>2</diaMinPeakLen>
			<useMs1Centroids>False</useMs1Centroids>
			<useMs2Centroids>False</useMs2Centroids>
			<cutPeaks>True</cutPeaks>
			<gapScans>1</gapScans>
			<minTime>NaN</minTime>
			<maxTime>NaN</maxTime>
			<matchType>MatchFromAndTo</matchType>
			<intensityDetermination>0</intensityDetermination>
			<centroidMatchTol>8</centroidMatchTol>
			<centroidMatchTolInPpm>True</centroidMatchTolInPpm>
			<centroidHalfWidth>35</centroidHalfWidth>
			<centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
			<valleyFactor>1.4</valleyFactor>
			<isotopeValleyFactor>1.2</isotopeValleyFactor>
			<advancedPeakSplitting>False</advancedPeakSplitting>
			<intensityThreshold>0</intensityThreshold>
			<labelMods>
				<string>Arg6;Lys4</string>
				<string>Arg10;DimethLys8</string>
			</labelMods>
			<lcmsRunType>Standard</lcmsRunType>
			<reQuantify>False</reQuantify>
			<lfqMode>0</lfqMode>
			<lfqSkipNorm>False</lfqSkipNorm>
			<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
			<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
			<lfqMaxFeatures>100000</lfqMaxFeatures>
			<neucodeMaxPpm>0</neucodeMaxPpm>
			<neucodeResolution>0</neucodeResolution>
			<neucodeResolutionInMda>False</neucodeResolutionInMda>
			<neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
			<fastLfq>True</fastLfq>
			<lfqRestrictFeatures>False</lfqRestrictFeatures>
			<lfqMinRatioCount>2</lfqMinRatioCount>
			<maxLabeledAa>2</maxLabeledAa>
			<maxNmods>5</maxNmods>
			<maxMissedCleavages>2</maxMissedCleavages>
			<multiplicity>2</multiplicity>
			<enzymeMode>0</enzymeMode>
			<complementaryReporterType>0</complementaryReporterType>
			<reporterNormalization>0</reporterNormalization>
			<neucodeIntensityMode>0</neucodeIntensityMode>
			<fixedModifications>
				<string>Carbamidomethyl (C)</string>
			</fixedModifications>
			<enzymes>
				<string>Trypsin/P</string>
			</enzymes>
			<enzymesFirstSearch>
         </enzymesFirstSearch>
			<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
			<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
			<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
			<variableModifications>
				<string>Oxidation (M)</string>
			</variableModifications>
			<useMultiModification>False</useMultiModification>
			<multiModifications>
         </multiModifications>
			<isobaricLabels>
         </isobaricLabels>
			<neucodeLabels>
         </neucodeLabels>
			<variableModificationsFirstSearch>
         </variableModificationsFirstSearch>
			<hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
			<additionalVariableModifications>
         </additionalVariableModifications>
			<additionalVariableModificationProteins>
         </additionalVariableModificationProteins>
			<doMassFiltering>True</doMassFiltering>
			<firstSearchTol>20</firstSearchTol>
			<mainSearchTol>4.5</mainSearchTol>
			<searchTolInPpm>True</searchTolInPpm>
			<isotopeMatchTol>2</isotopeMatchTol>
			<isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
			<isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
			<theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
			<checkMassDeficit>True</checkMassDeficit>
			<recalibrationInPpm>True</recalibrationInPpm>
			<intensityDependentCalibration>False</intensityDependentCalibration>
			<minScoreForCalibration>70</minScoreForCalibration>
			<matchLibraryFile>False</matchLibraryFile>
			<libraryFile/>
			<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
			<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
			<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
			<reporterMassTolerance>NaN</reporterMassTolerance>
			<reporterPif>NaN</reporterPif>
			<filterPif>False</filterPif>
			<reporterFraction>NaN</reporterFraction>
			<reporterBasePeakRatio>NaN</reporterBasePeakRatio>
			<timsHalfWidth>0</timsHalfWidth>
			<timsStep>0</timsStep>
			<timsResolution>0</timsResolution>
			<timsMinMsmsIntensity>0</timsMinMsmsIntensity>
			<timsRemovePrecursor>True</timsRemovePrecursor>
			<timsIsobaricLabels>False</timsIsobaricLabels>
			<timsCollapseMsms>True</timsCollapseMsms>
			<crosslinkSearch>False</crosslinkSearch>
			<crossLinker/>
			<minMatchXl>0</minMatchXl>
			<minPairedPepLenXl>6</minPairedPepLenXl>
			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
			<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
			<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
			<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
			<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
			<crosslinkModifications>
         </crosslinkModifications>
			<crosslinkFastaFiles>
         </crosslinkFastaFiles>
			<crosslinkSites>
         </crosslinkSites>
			<crosslinkNetworkFiles>
         </crosslinkNetworkFiles>
			<crosslinkMode/>
			<peakRefinement>False</peakRefinement>
			<isobaricSumOverWindow>True</isobaricSumOverWindow>
			<isobaricWeightExponent>0.75</isobaricWeightExponent>
			<diaLibraryType>0</diaLibraryType>
			<diaLibraryPath/>
			<diaPeptidePaths>
         </diaPeptidePaths>
			<diaEvidencePaths>
         </diaEvidencePaths>
			<diaMsmsPaths>
         </diaMsmsPaths>
			<diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
			<diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
			<diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
			<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
			<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
			<diaScoreN>7</diaScoreN>
			<diaMinScore>2.99</diaMinScore>
			<diaPrecursorQuant>False</diaPrecursorQuant>
			<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
		</parameterGroup>
	</parameterGroups>
	<msmsParamsArray>
		<msmsParams>
			<Name>FTMS</Name>
			<MatchTolerance>20</MatchTolerance>
			<MatchToleranceInPpm>True</MatchToleranceInPpm>
			<DeisotopeTolerance>7</DeisotopeTolerance>
			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
			<DeNovoTolerance>10</DeNovoTolerance>
			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
			<Deisotope>True</Deisotope>
			<Topx>12</Topx>
			<TopxInterval>100</TopxInterval>
			<HigherCharges>True</HigherCharges>
			<IncludeWater>True</IncludeWater>
			<IncludeAmmonia>True</IncludeAmmonia>
			<DependentLosses>True</DependentLosses>
			<Recalibration>False</Recalibration>
		</msmsParams>
		<msmsParams>
			<Name>ITMS</Name>
			<MatchTolerance>0.5</MatchTolerance>
			<MatchToleranceInPpm>False</MatchToleranceInPpm>
			<DeisotopeTolerance>0.15</DeisotopeTolerance>
			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
			<DeNovoTolerance>0.25</DeNovoTolerance>
			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
			<Deisotope>False</Deisotope>
			<Topx>8</Topx>
			<TopxInterval>100</TopxInterval>
			<HigherCharges>True</HigherCharges>
			<IncludeWater>True</IncludeWater>
			<IncludeAmmonia>True</IncludeAmmonia>
			<DependentLosses>True</DependentLosses>
			<Recalibration>False</Recalibration>
		</msmsParams>
		<msmsParams>
			<Name>TOF</Name>
			<MatchTolerance>40</MatchTolerance>
			<MatchToleranceInPpm>True</MatchToleranceInPpm>
			<DeisotopeTolerance>0.01</DeisotopeTolerance>
			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
			<DeNovoTolerance>0.02</DeNovoTolerance>
			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
			<Deisotope>True</Deisotope>
			<Topx>10</Topx>
			<TopxInterval>100</TopxInterval>
			<HigherCharges>True</HigherCharges>
			<IncludeWater>True</IncludeWater>
			<IncludeAmmonia>True</IncludeAmmonia>
			<DependentLosses>True</DependentLosses>
			<Recalibration>False</Recalibration>
		</msmsParams>
		<msmsParams>
			<Name>Unknown</Name>
			<MatchTolerance>20</MatchTolerance>
			<MatchToleranceInPpm>True</MatchToleranceInPpm>
			<DeisotopeTolerance>7</DeisotopeTolerance>
			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
			<DeNovoTolerance>10</DeNovoTolerance>
			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
			<Deisotope>True</Deisotope>
			<Topx>12</Topx>
			<TopxInterval>100</TopxInterval>
			<HigherCharges>True</HigherCharges>
			<IncludeWater>True</IncludeWater>
			<IncludeAmmonia>True</IncludeAmmonia>
			<DependentLosses>True</DependentLosses>
			<Recalibration>False</Recalibration>
		</msmsParams>
	</msmsParamsArray>
	<fragmentationParamsArray>
		<fragmentationParams>
			<Name>CID</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
		<fragmentationParams>
			<Name>HCD</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
		<fragmentationParams>
			<Name>ETD</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
		<fragmentationParams>
			<Name>PQD</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
		<fragmentationParams>
			<Name>ETHCD</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
		<fragmentationParams>
			<Name>ETCID</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
		<fragmentationParams>
			<Name>UVPD</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
		<fragmentationParams>
			<Name>Unknown</Name>
			<Connected>False</Connected>
			<ConnectedScore0>1</ConnectedScore0>
			<ConnectedScore1>1</ConnectedScore1>
			<ConnectedScore2>1</ConnectedScore2>
			<InternalFragments>False</InternalFragments>
			<InternalFragmentWeight>1</InternalFragmentWeight>
			<InternalFragmentAas>KRH</InternalFragmentAas>
		</fragmentationParams>
	</fragmentationParamsArray>
</MaxQuantParams>