Mercurial > repos > galaxyp > maxquant

diff test-data/06/mqpar.xml @ 12:0839f84def5e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
author galaxyp
date Sun, 20 Jun 2021 16:37:41 +0000
parents f522c08e900c
children 837224ad1694
line wrap: on
line diff
--- a/test-data/06/mqpar.xml	Tue Jun 15 07:55:59 2021 +0000
+++ b/test-data/06/mqpar.xml	Sun Jun 20 16:37:41 2021 +0000
@@ -2,7 +2,7 @@
 <MaxQuantParams>
 	<fastaFiles>
 		<FastaFileInfo>
-			<fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat</fastaFilePath>
+			<fastaFilePath>/tmp/tmpyzym30dx/files/b/9/7/dataset_b97123e2-9db4-407c-bd7f-b69d65fc32cc.dat</fastaFilePath>
 			<identifierParseRule>&gt;([^\s]*)</identifierParseRule>
 			<descriptionParseRule>&gt;(.*)</descriptionParseRule>
 			<taxonomyParseRule/>
@@ -19,8 +19,6 @@
 	<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>
@@ -48,7 +46,6 @@
 	<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
 	<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
 	<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
-	<msmsConnection>False</msmsConnection>
 	<ibaq>False</ibaq>
 	<top3>False</top3>
 	<independentEnzymes>False</independentEnzymes>
@@ -100,10 +97,11 @@
 	<writeMsScansTable>False</writeMsScansTable>
 	<writeMsmsScansTable>True</writeMsmsScansTable>
 	<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
-	<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
+	<writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable>
 	<writeMs3ScansTable>True</writeMs3ScansTable>
 	<writeAllPeptidesTable>True</writeAllPeptidesTable>
 	<writeMzRangeTable>True</writeMzRangeTable>
+	<writeDiaFragmentTable>False</writeDiaFragmentTable>
 	<writeMzTab>True</writeMzTab>
 	<disableMd5>False</disableMd5>
 	<cacheBinInds>True</cacheBinInds>
@@ -114,10 +112,10 @@
 	<variationMode>none</variationMode>
 	<useSeriesReporters>False</useSeriesReporters>
 	<name>templateSession</name>
-	<maxQuantVersion>1.6.10.43</maxQuantVersion>
-	<tempFolder/>
+	<maxQuantVersion>1.6.17.0</maxQuantVersion>
 	<pluginFolder/>
 	<numThreads>1</numThreads>
+	<batchSize>1</batchSize>
 	<emailAddress/>
 	<smtpHost/>
 	<emailFromAddress/>
@@ -130,10 +128,11 @@
 	<calcPeakProperties>False</calcPeakProperties>
 	<showCentroidMassDifferences>False</showCentroidMassDifferences>
 	<showIsotopeMassDifferences>False</showIsotopeMassDifferences>
-	<useDotNetCore>False</useDotNetCore>
+	<useDotNetCore>True</useDotNetCore>
+	<profilePerformance>False</profilePerformance>
 	<filePaths>
-		<string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_23.mzXML</string>
-		<string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_22.mzxml</string>
+		<string>/tmp/tmpyzym30dx/job_working_directory/000/11/working/BSA_min_23.mzXML</string>
+		<string>/tmp/tmpyzym30dx/job_working_directory/000/11/working/BSA_min_22.mzxml</string>
 	</filePaths>
 	<experiments>
 		<string>BSA_min_23.mzXML</string>
@@ -157,12 +156,13 @@
 	</referenceChannel>
 	<intensPred>False</intensPred>
 	<intensPredModelReTrain>False</intensPredModelReTrain>
+	<lfqTopNPeptides>0</lfqTopNPeptides>
 	<parameterGroups>
 		<parameterGroup>
 			<msInstrument>0</msInstrument>
 			<maxCharge>7</maxCharge>
 			<minPeakLen>2</minPeakLen>
-			<diaMinPeakLen>2</diaMinPeakLen>
+			<diaMinPeakLen>1</diaMinPeakLen>
 			<useMs1Centroids>False</useMs1Centroids>
 			<useMs2Centroids>False</useMs2Centroids>
 			<cutPeaks>True</cutPeaks>
@@ -178,14 +178,15 @@
 			<valleyFactor>1.4</valleyFactor>
 			<isotopeValleyFactor>1.2</isotopeValleyFactor>
 			<advancedPeakSplitting>False</advancedPeakSplitting>
-			<intensityThreshold>0</intensityThreshold>
+			<intensityThresholdMs1>0</intensityThresholdMs1>
+			<intensityThresholdMs2>0</intensityThresholdMs2>
 			<labelMods>
 				<string/>
 			</labelMods>
 			<lcmsRunType>Reporter ion MS3</lcmsRunType>
 			<reQuantify>False</reQuantify>
 			<lfqMode>0</lfqMode>
-			<lfqSkipNorm>False</lfqSkipNorm>
+			<lfqNormClusterSize>80</lfqNormClusterSize>
 			<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
 			<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
 			<lfqMaxFeatures>100000</lfqMaxFeatures>
@@ -277,7 +278,7 @@
 			<timsRemovePrecursor>True</timsRemovePrecursor>
 			<timsIsobaricLabels>False</timsIsobaricLabels>
 			<timsCollapseMsms>True</timsCollapseMsms>
-			<crosslinkSearch>False</crosslinkSearch>
+			<crossLinkingType>0</crossLinkingType>
 			<crossLinker/>
 			<minMatchXl>0</minMatchXl>
 			<minPairedPepLenXl>6</minPairedPepLenXl>
@@ -299,7 +300,8 @@
 			<isobaricSumOverWindow>True</isobaricSumOverWindow>
 			<isobaricWeightExponent>0.75</isobaricWeightExponent>
 			<diaLibraryType>0</diaLibraryType>
-			<diaLibraryPath/>
+			<diaLibraryPaths>
+         </diaLibraryPaths>
 			<diaPeptidePaths>
          </diaPeptidePaths>
 			<diaEvidencePaths>
@@ -312,15 +314,43 @@
 			<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
 			<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
 			<diaScoreN>7</diaScoreN>
-			<diaMinScore>2.99</diaMinScore>
-			<diaPrecursorQuant>False</diaPrecursorQuant>
-			<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
+			<diaMinScore>1.99</diaMinScore>
+			<diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
+			<diaXgBoostSubSample>0.9</diaXgBoostSubSample>
+			<centroidPosition>0</centroidPosition>
+			<diaQuantMethod>7</diaQuantMethod>
+			<diaFeatureQuantMethod>2</diaFeatureQuantMethod>
+			<lfqNormType>1</lfqNormType>
+			<diaTopNForQuant>10</diaTopNForQuant>
+			<diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
+			<diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
+			<diaPrecursorFilterType>0</diaPrecursorFilterType>
+			<diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
+			<diaMinPrecursorScore>0.5</diaMinPrecursorScore>
+			<diaMinProfileCorrelation>0</diaMinProfileCorrelation>
+			<diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
+			<diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
+			<diaXgBoostEstimators>580</diaXgBoostEstimators>
+			<diaXgBoostGamma>0.9</diaXgBoostGamma>
+			<diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
+			<diaGlobalMl>True</diaGlobalMl>
+			<diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
+			<diaMassWindowFactor>3.3</diaMassWindowFactor>
+			<diaRtPrediction>False</diaRtPrediction>
+			<diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
+			<diaNoMl>False</diaNoMl>
+			<diaPermuteRt>False</diaPermuteRt>
+			<diaPermuteCcs>False</diaPermuteCcs>
+			<diaBackgroundSubtraction>False</diaBackgroundSubtraction>
+			<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
+			<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
+			<diaLfqWeightedMedian>False</diaLfqWeightedMedian>
 		</parameterGroup>
 		<parameterGroup>
 			<msInstrument>0</msInstrument>
 			<maxCharge>7</maxCharge>
 			<minPeakLen>2</minPeakLen>
-			<diaMinPeakLen>2</diaMinPeakLen>
+			<diaMinPeakLen>1</diaMinPeakLen>
 			<useMs1Centroids>False</useMs1Centroids>
 			<useMs2Centroids>False</useMs2Centroids>
 			<cutPeaks>True</cutPeaks>
@@ -336,14 +366,15 @@
 			<valleyFactor>1.4</valleyFactor>
 			<isotopeValleyFactor>1.2</isotopeValleyFactor>
 			<advancedPeakSplitting>False</advancedPeakSplitting>
-			<intensityThreshold>0</intensityThreshold>
+			<intensityThresholdMs1>0</intensityThresholdMs1>
+			<intensityThresholdMs2>0</intensityThresholdMs2>
 			<labelMods>
 				<string/>
 			</labelMods>
 			<lcmsRunType>Reporter ion MS3</lcmsRunType>
 			<reQuantify>False</reQuantify>
 			<lfqMode>0</lfqMode>
-			<lfqSkipNorm>False</lfqSkipNorm>
+			<lfqNormClusterSize>80</lfqNormClusterSize>
 			<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
 			<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
 			<lfqMaxFeatures>100000</lfqMaxFeatures>
@@ -449,7 +480,7 @@
 			<timsRemovePrecursor>True</timsRemovePrecursor>
 			<timsIsobaricLabels>False</timsIsobaricLabels>
 			<timsCollapseMsms>True</timsCollapseMsms>
-			<crosslinkSearch>False</crosslinkSearch>
+			<crossLinkingType>0</crossLinkingType>
 			<crossLinker/>
 			<minMatchXl>0</minMatchXl>
 			<minPairedPepLenXl>6</minPairedPepLenXl>
@@ -471,7 +502,8 @@
 			<isobaricSumOverWindow>True</isobaricSumOverWindow>
 			<isobaricWeightExponent>0.75</isobaricWeightExponent>
 			<diaLibraryType>0</diaLibraryType>
-			<diaLibraryPath/>
+			<diaLibraryPaths>
+         </diaLibraryPaths>
 			<diaPeptidePaths>
          </diaPeptidePaths>
 			<diaEvidencePaths>
@@ -484,9 +516,37 @@
 			<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
 			<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
 			<diaScoreN>7</diaScoreN>
-			<diaMinScore>2.99</diaMinScore>
-			<diaPrecursorQuant>False</diaPrecursorQuant>
-			<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
+			<diaMinScore>1.99</diaMinScore>
+			<diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
+			<diaXgBoostSubSample>0.9</diaXgBoostSubSample>
+			<centroidPosition>0</centroidPosition>
+			<diaQuantMethod>7</diaQuantMethod>
+			<diaFeatureQuantMethod>2</diaFeatureQuantMethod>
+			<lfqNormType>1</lfqNormType>
+			<diaTopNForQuant>10</diaTopNForQuant>
+			<diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
+			<diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
+			<diaPrecursorFilterType>0</diaPrecursorFilterType>
+			<diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
+			<diaMinPrecursorScore>0.5</diaMinPrecursorScore>
+			<diaMinProfileCorrelation>0</diaMinProfileCorrelation>
+			<diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
+			<diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
+			<diaXgBoostEstimators>580</diaXgBoostEstimators>
+			<diaXgBoostGamma>0.9</diaXgBoostGamma>
+			<diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
+			<diaGlobalMl>True</diaGlobalMl>
+			<diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
+			<diaMassWindowFactor>3.3</diaMassWindowFactor>
+			<diaRtPrediction>False</diaRtPrediction>
+			<diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
+			<diaNoMl>False</diaNoMl>
+			<diaPermuteRt>False</diaPermuteRt>
+			<diaPermuteCcs>False</diaPermuteCcs>
+			<diaBackgroundSubtraction>False</diaBackgroundSubtraction>
+			<diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
+			<diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
+			<diaLfqWeightedMedian>False</diaLfqWeightedMedian>
 		</parameterGroup>
 	</parameterGroups>
 	<msmsParamsArray>