Mercurial > repos > galaxyp > maxquant

diff test-data/06/mqpar.xml @ 21:8934bc76bb52 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
author galaxyp
date Mon, 19 Jun 2023 17:02:17 +0000
parents 837224ad1694
children
line wrap: on
line diff
--- a/test-data/06/mqpar.xml	Tue Jan 31 18:14:40 2023 +0000
+++ b/test-data/06/mqpar.xml	Mon Jun 19 17:02:17 2023 +0000
@@ -23,6 +23,7 @@
 	<separateLfq>False</separateLfq>
 	<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
 	<lfqRequireMsms>True</lfqRequireMsms>
+	<lfqBayesQuant>False</lfqBayesQuant>
 	<decoyMode>randomize</decoyMode>
 	<boxCarMode>all</boxCarMode>
 	<includeContaminants>False</includeContaminants>
@@ -55,9 +56,22 @@
 	<avalon>False</avalon>
 	<nModColumns>3</nModColumns>
 	<ibaqLogFit>False</ibaqLogFit>
+	<ibaqChargeNormalization>False</ibaqChargeNormalization>
 	<razorProteinFdr>True</razorProteinFdr>
 	<deNovoSequencing>False</deNovoSequencing>
-	<deNovoVarMods>True</deNovoVarMods>
+	<deNovoVarMods>False</deNovoVarMods>
+	<deNovoCompleteSequence>False</deNovoCompleteSequence>
+	<deNovoCalibratedMasses>False</deNovoCalibratedMasses>
+	<deNovoMaxIterations>0</deNovoMaxIterations>
+	<deNovoProteaseReward>0</deNovoProteaseReward>
+	<deNovoProteaseRewardTof>0</deNovoProteaseRewardTof>
+	<deNovoAgPenalty>0</deNovoAgPenalty>
+	<deNovoGgPenalty>0</deNovoGgPenalty>
+	<deNovoUseComplementScore>True</deNovoUseComplementScore>
+	<deNovoUseProteaseScore>True</deNovoUseProteaseScore>
+	<deNovoUseWaterLossScore>True</deNovoUseWaterLossScore>
+	<deNovoUseAmmoniaLossScore>True</deNovoUseAmmoniaLossScore>
+	<deNovoUseA2Score>True</deNovoUseA2Score>
 	<massDifferenceSearch>False</massDifferenceSearch>
 	<isotopeCalc>False</isotopeCalc>
 	<writePeptidesForSpectrumFile/>
@@ -97,11 +111,12 @@
 	<writeMsScansTable>False</writeMsScansTable>
 	<writeMsmsScansTable>True</writeMsmsScansTable>
 	<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
-	<writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>
+	<writeAccumulatedMsmsScansTable>True</writeAccumulatedMsmsScansTable>
 	<writeMs3ScansTable>True</writeMs3ScansTable>
 	<writeAllPeptidesTable>True</writeAllPeptidesTable>
 	<writeMzRangeTable>True</writeMzRangeTable>
 	<writeDiaFragmentTable>False</writeDiaFragmentTable>
+	<writeDiaFragmentQuantTable>False</writeDiaFragmentQuantTable>
 	<writeMzTab>True</writeMzTab>
 	<disableMd5>False</disableMd5>
 	<cacheBinInds>True</cacheBinInds>
@@ -112,10 +127,9 @@
 	<variationMode>none</variationMode>
 	<useSeriesReporters>False</useSeriesReporters>
 	<name>templateSession</name>
-	<maxQuantVersion>1.6.17.0</maxQuantVersion>
+	<maxQuantVersion>2.0.3.0</maxQuantVersion>
 	<pluginFolder/>
-	<numThreads>2</numThreads>
-	<batchSize>1</batchSize>
+	<numThreads>1</numThreads>
 	<emailAddress/>
 	<smtpHost/>
 	<emailFromAddress/>
@@ -157,6 +171,11 @@
 	<intensPred>False</intensPred>
 	<intensPredModelReTrain>False</intensPredModelReTrain>
 	<lfqTopNPeptides>0</lfqTopNPeptides>
+	<diaJoinPrecChargesForLfq>False</diaJoinPrecChargesForLfq>
+	<diaFragChargesForQuant>1</diaFragChargesForQuant>
+	<timsRearrangeSpectra>False</timsRearrangeSpectra>
+	<gridSpacing>0.5</gridSpacing>
+	<proteinGroupingFile/>
 	<parameterGroups>
 		<parameterGroup>
 			<msInstrument>0</msInstrument>
@@ -280,9 +299,16 @@
 			<timsCollapseMsms>True</timsCollapseMsms>
 			<crossLinkingType>0</crossLinkingType>
 			<crossLinker/>
-			<minMatchXl>0</minMatchXl>
+			<minMatchXl>3</minMatchXl>
 			<minPairedPepLenXl>6</minPairedPepLenXl>
+			<minScore_Dipeptide>40</minScore_Dipeptide>
+			<minScore_Monopeptide>0</minScore_Monopeptide>
+			<minScore_PartialCross>10</minScore_PartialCross>
 			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
+			<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
+			<isHybridPrecDetermination>False</isHybridPrecDetermination>
+			<topXcross>3</topXcross>
+			<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
 			<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
 			<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
 			<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
@@ -299,6 +325,7 @@
 			<peakRefinement>False</peakRefinement>
 			<isobaricSumOverWindow>True</isobaricSumOverWindow>
 			<isobaricWeightExponent>0.75</isobaricWeightExponent>
+			<collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
 			<diaLibraryType>0</diaLibraryType>
 			<diaLibraryPaths>
          </diaLibraryPaths>
@@ -345,6 +372,12 @@
 			<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
 			<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
 			<diaLfqWeightedMedian>False</diaLfqWeightedMedian>
+			<diaTransferQvalue>0.3</diaTransferQvalue>
+			<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
+			<diaMinPeaksForRecal>5</diaMinPeaksForRecal>
+			<diaUseFragIntensForMl>False</diaUseFragIntensForMl>
+			<diaUseFragMassesForMl>False</diaUseFragMassesForMl>
+			<diaMaxTrainInstances>1000000</diaMaxTrainInstances>
 		</parameterGroup>
 		<parameterGroup>
 			<msInstrument>0</msInstrument>
@@ -482,9 +515,16 @@
 			<timsCollapseMsms>True</timsCollapseMsms>
 			<crossLinkingType>0</crossLinkingType>
 			<crossLinker/>
-			<minMatchXl>0</minMatchXl>
+			<minMatchXl>3</minMatchXl>
 			<minPairedPepLenXl>6</minPairedPepLenXl>
+			<minScore_Dipeptide>40</minScore_Dipeptide>
+			<minScore_Monopeptide>0</minScore_Monopeptide>
+			<minScore_PartialCross>10</minScore_PartialCross>
 			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
+			<crosslinkIntensityBasedPrecursor>True</crosslinkIntensityBasedPrecursor>
+			<isHybridPrecDetermination>False</isHybridPrecDetermination>
+			<topXcross>3</topXcross>
+			<doesSeparateInterIntraProteinCross>False</doesSeparateInterIntraProteinCross>
 			<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
 			<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
 			<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
@@ -501,6 +541,7 @@
 			<peakRefinement>False</peakRefinement>
 			<isobaricSumOverWindow>True</isobaricSumOverWindow>
 			<isobaricWeightExponent>0.75</isobaricWeightExponent>
+			<collapseMsmsOnIsotopePatterns>False</collapseMsmsOnIsotopePatterns>
 			<diaLibraryType>0</diaLibraryType>
 			<diaLibraryPaths>
          </diaLibraryPaths>
@@ -547,6 +588,12 @@
 			<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
 			<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
 			<diaLfqWeightedMedian>False</diaLfqWeightedMedian>
+			<diaTransferQvalue>0.3</diaTransferQvalue>
+			<diaOnlyIsosForRecal>True</diaOnlyIsosForRecal>
+			<diaMinPeaksForRecal>5</diaMinPeaksForRecal>
+			<diaUseFragIntensForMl>False</diaUseFragIntensForMl>
+			<diaUseFragMassesForMl>False</diaUseFragMassesForMl>
+			<diaMaxTrainInstances>1000000</diaMaxTrainInstances>
 		</parameterGroup>
 	</parameterGroups>
 	<msmsParamsArray>
@@ -556,7 +603,7 @@
 			<MatchToleranceInPpm>True</MatchToleranceInPpm>
 			<DeisotopeTolerance>7</DeisotopeTolerance>
 			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
-			<DeNovoTolerance>10</DeNovoTolerance>
+			<DeNovoTolerance>25</DeNovoTolerance>
 			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
 			<Deisotope>True</Deisotope>
 			<Topx>12</Topx>
@@ -573,7 +620,7 @@
 			<MatchToleranceInPpm>False</MatchToleranceInPpm>
 			<DeisotopeTolerance>0.15</DeisotopeTolerance>
 			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
-			<DeNovoTolerance>0.25</DeNovoTolerance>
+			<DeNovoTolerance>0.5</DeNovoTolerance>
 			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
 			<Deisotope>False</Deisotope>
 			<Topx>8</Topx>
@@ -590,8 +637,8 @@
 			<MatchToleranceInPpm>True</MatchToleranceInPpm>
 			<DeisotopeTolerance>0.01</DeisotopeTolerance>
 			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
-			<DeNovoTolerance>0.02</DeNovoTolerance>
-			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+			<DeNovoTolerance>25</DeNovoTolerance>
+			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
 			<Deisotope>True</Deisotope>
 			<Topx>10</Topx>
 			<TopxInterval>100</TopxInterval>
@@ -607,7 +654,7 @@
 			<MatchToleranceInPpm>True</MatchToleranceInPpm>
 			<DeisotopeTolerance>7</DeisotopeTolerance>
 			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
-			<DeNovoTolerance>10</DeNovoTolerance>
+			<DeNovoTolerance>25</DeNovoTolerance>
 			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
 			<Deisotope>True</Deisotope>
 			<Topx>12</Topx>