Mercurial > repos > galaxyp > maxquant
comparison test-data/03/mqpar.xml @ 12:0839f84def5e draft
"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 | d253b379322b |
| children | 837224ad1694 |
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| 11:d72c96ad9a16 | 12:0839f84def5e |
|---|---|
| 1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
| 2 <MaxQuantParams> | 2 <MaxQuantParams> |
| 3 <fastaFiles> | 3 <fastaFiles> |
| 4 <FastaFileInfo> | 4 <FastaFileInfo> |
| 5 <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath> | 5 <fastaFilePath>/tmp/tmpwu9ns_ue/files/b/7/c/dataset_b7c3a34e-122e-456d-90ed-78fe5ab2ef9a.dat</fastaFilePath> |
| 6 <identifierParseRule>^>.*\|(.*)\|.*$</identifierParseRule> | 6 <identifierParseRule>^>.*\|(.*)\|.*$</identifierParseRule> |
| 7 <descriptionParseRule>^>.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule> | 7 <descriptionParseRule>^>.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule> |
| 8 <taxonomyParseRule/> | 8 <taxonomyParseRule/> |
| 9 <variationParseRule/> | 9 <variationParseRule/> |
| 10 <modificationParseRule/> | 10 <modificationParseRule/> |
| 17 </fastaFilesFirstSearch> | 17 </fastaFilesFirstSearch> |
| 18 <fixedSearchFolder/> | 18 <fixedSearchFolder/> |
| 19 <andromedaCacheSize>350000</andromedaCacheSize> | 19 <andromedaCacheSize>350000</andromedaCacheSize> |
| 20 <advancedRatios>True</advancedRatios> | 20 <advancedRatios>True</advancedRatios> |
| 21 <pvalThres>0.005</pvalThres> | 21 <pvalThres>0.005</pvalThres> |
| 22 <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification> | |
| 23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios> | |
| 24 <rtShift>False</rtShift> | 22 <rtShift>False</rtShift> |
| 25 <separateLfq>False</separateLfq> | 23 <separateLfq>False</separateLfq> |
| 26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> | 24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> |
| 27 <lfqRequireMsms>True</lfqRequireMsms> | 25 <lfqRequireMsms>True</lfqRequireMsms> |
| 28 <decoyMode>revert</decoyMode> | 26 <decoyMode>revert</decoyMode> |
| 46 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> | 44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns> |
| 47 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> | 45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment> |
| 48 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> | 46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup> |
| 49 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> | 47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions> |
| 50 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> | 48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference> |
| 51 <msmsConnection>False</msmsConnection> | |
| 52 <ibaq>True</ibaq> | 49 <ibaq>True</ibaq> |
| 53 <top3>False</top3> | 50 <top3>False</top3> |
| 54 <independentEnzymes>False</independentEnzymes> | 51 <independentEnzymes>False</independentEnzymes> |
| 55 <useDeltaScore>False</useDeltaScore> | 52 <useDeltaScore>False</useDeltaScore> |
| 56 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> | 53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy> |
| 98 </massDifferenceMods> | 95 </massDifferenceMods> |
| 99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> | 96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations> |
| 100 <writeMsScansTable>False</writeMsScansTable> | 97 <writeMsScansTable>False</writeMsScansTable> |
| 101 <writeMsmsScansTable>True</writeMsmsScansTable> | 98 <writeMsmsScansTable>True</writeMsmsScansTable> |
| 102 <writePasefMsmsScansTable>True</writePasefMsmsScansTable> | 99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable> |
| 103 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable> | 100 <writeAccumulatedPasefMsmsScansTable>False</writeAccumulatedPasefMsmsScansTable> |
| 104 <writeMs3ScansTable>True</writeMs3ScansTable> | 101 <writeMs3ScansTable>True</writeMs3ScansTable> |
| 105 <writeAllPeptidesTable>True</writeAllPeptidesTable> | 102 <writeAllPeptidesTable>True</writeAllPeptidesTable> |
| 106 <writeMzRangeTable>True</writeMzRangeTable> | 103 <writeMzRangeTable>True</writeMzRangeTable> |
| 104 <writeDiaFragmentTable>False</writeDiaFragmentTable> | |
| 107 <writeMzTab>False</writeMzTab> | 105 <writeMzTab>False</writeMzTab> |
| 108 <disableMd5>False</disableMd5> | 106 <disableMd5>False</disableMd5> |
| 109 <cacheBinInds>True</cacheBinInds> | 107 <cacheBinInds>True</cacheBinInds> |
| 110 <etdIncludeB>False</etdIncludeB> | 108 <etdIncludeB>False</etdIncludeB> |
| 111 <ms2PrecursorShift>0</ms2PrecursorShift> | 109 <ms2PrecursorShift>0</ms2PrecursorShift> |
| 112 <complementaryIonPpm>20</complementaryIonPpm> | 110 <complementaryIonPpm>20</complementaryIonPpm> |
| 113 <variationParseRule/> | 111 <variationParseRule/> |
| 114 <variationMode>none</variationMode> | 112 <variationMode>none</variationMode> |
| 115 <useSeriesReporters>False</useSeriesReporters> | 113 <useSeriesReporters>False</useSeriesReporters> |
| 116 <name>session1</name> | 114 <name>templateSession</name> |
| 117 <maxQuantVersion>1.6.10.43</maxQuantVersion> | 115 <maxQuantVersion>1.6.17.0</maxQuantVersion> |
| 118 <tempFolder/> | |
| 119 <pluginFolder/> | 116 <pluginFolder/> |
| 120 <numThreads>1</numThreads> | 117 <numThreads>1</numThreads> |
| 118 <batchSize>1</batchSize> | |
| 121 <emailAddress/> | 119 <emailAddress/> |
| 122 <smtpHost/> | 120 <smtpHost/> |
| 123 <emailFromAddress/> | 121 <emailFromAddress/> |
| 124 <fixedCombinedFolder/> | 122 <fixedCombinedFolder/> |
| 125 <fullMinMz>-1.79589544172745E+308</fullMinMz> | 123 <fullMinMz>-1.79769313486232E+308</fullMinMz> |
| 126 <fullMaxMz>1.79589544172745E+308</fullMaxMz> | 124 <fullMaxMz>1.79769313486232E+308</fullMaxMz> |
| 127 <sendEmail>False</sendEmail> | 125 <sendEmail>False</sendEmail> |
| 128 <ionCountIntensities>False</ionCountIntensities> | 126 <ionCountIntensities>False</ionCountIntensities> |
| 129 <verboseColumnHeaders>False</verboseColumnHeaders> | 127 <verboseColumnHeaders>False</verboseColumnHeaders> |
| 130 <calcPeakProperties>False</calcPeakProperties> | 128 <calcPeakProperties>False</calcPeakProperties> |
| 131 <showCentroidMassDifferences>False</showCentroidMassDifferences> | 129 <showCentroidMassDifferences>False</showCentroidMassDifferences> |
| 132 <showIsotopeMassDifferences>False</showIsotopeMassDifferences> | 130 <showIsotopeMassDifferences>False</showIsotopeMassDifferences> |
| 133 <useDotNetCore>False</useDotNetCore> | 131 <useDotNetCore>True</useDotNetCore> |
| 132 <profilePerformance>False</profilePerformance> | |
| 134 <filePaths> | 133 <filePaths> |
| 135 <string>D:\shared\dglaetzer\maxquant_tool\test3\BSA_min_22.mzXML</string> | 134 <string>/tmp/tmpwu9ns_ue/job_working_directory/000/6/working/BSA_min_22.mzxml</string> |
| 136 </filePaths> | 135 </filePaths> |
| 137 <experiments> | 136 <experiments> |
| 138 <string>BSA_min_22.mzxml</string> | 137 <string>BSA_min_22.mzxml</string> |
| 139 </experiments> | 138 </experiments> |
| 140 <fractions> | 139 <fractions> |
| 149 <referenceChannel> | 148 <referenceChannel> |
| 150 <string/> | 149 <string/> |
| 151 </referenceChannel> | 150 </referenceChannel> |
| 152 <intensPred>False</intensPred> | 151 <intensPred>False</intensPred> |
| 153 <intensPredModelReTrain>False</intensPredModelReTrain> | 152 <intensPredModelReTrain>False</intensPredModelReTrain> |
| 153 <lfqTopNPeptides>0</lfqTopNPeptides> | |
| 154 <parameterGroups> | 154 <parameterGroups> |
| 155 <parameterGroup> | 155 <parameterGroup> |
| 156 <msInstrument>0</msInstrument> | 156 <msInstrument>0</msInstrument> |
| 157 <maxCharge>7</maxCharge> | 157 <maxCharge>7</maxCharge> |
| 158 <minPeakLen>2</minPeakLen> | 158 <minPeakLen>2</minPeakLen> |
| 159 <diaMinPeakLen>2</diaMinPeakLen> | 159 <diaMinPeakLen>1</diaMinPeakLen> |
| 160 <useMs1Centroids>False</useMs1Centroids> | 160 <useMs1Centroids>False</useMs1Centroids> |
| 161 <useMs2Centroids>False</useMs2Centroids> | 161 <useMs2Centroids>False</useMs2Centroids> |
| 162 <cutPeaks>True</cutPeaks> | 162 <cutPeaks>True</cutPeaks> |
| 163 <gapScans>1</gapScans> | 163 <gapScans>1</gapScans> |
| 164 <minTime>NaN</minTime> | 164 <minTime>NaN</minTime> |
| 170 <centroidHalfWidth>35</centroidHalfWidth> | 170 <centroidHalfWidth>35</centroidHalfWidth> |
| 171 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> | 171 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> |
| 172 <valleyFactor>1.4</valleyFactor> | 172 <valleyFactor>1.4</valleyFactor> |
| 173 <isotopeValleyFactor>1.2</isotopeValleyFactor> | 173 <isotopeValleyFactor>1.2</isotopeValleyFactor> |
| 174 <advancedPeakSplitting>False</advancedPeakSplitting> | 174 <advancedPeakSplitting>False</advancedPeakSplitting> |
| 175 <intensityThreshold>0</intensityThreshold> | 175 <intensityThresholdMs1>0</intensityThresholdMs1> |
| 176 <intensityThresholdMs2>0</intensityThresholdMs2> | |
| 176 <labelMods> | 177 <labelMods> |
| 177 <string/> | 178 <string/> |
| 178 </labelMods> | 179 </labelMods> |
| 179 <lcmsRunType>Standard</lcmsRunType> | 180 <lcmsRunType>Standard</lcmsRunType> |
| 180 <reQuantify>False</reQuantify> | 181 <reQuantify>False</reQuantify> |
| 181 <lfqMode>1</lfqMode> | 182 <lfqMode>1</lfqMode> |
| 182 <lfqSkipNorm>True</lfqSkipNorm> | 183 <lfqNormClusterSize>80</lfqNormClusterSize> |
| 183 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> | 184 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> |
| 184 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> | 185 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> |
| 185 <lfqMaxFeatures>100000</lfqMaxFeatures> | 186 <lfqMaxFeatures>100000</lfqMaxFeatures> |
| 186 <neucodeMaxPpm>0</neucodeMaxPpm> | 187 <neucodeMaxPpm>0</neucodeMaxPpm> |
| 187 <neucodeResolution>0</neucodeResolution> | 188 <neucodeResolution>0</neucodeResolution> |
| 253 <timsResolution>0</timsResolution> | 254 <timsResolution>0</timsResolution> |
| 254 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> | 255 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> |
| 255 <timsRemovePrecursor>True</timsRemovePrecursor> | 256 <timsRemovePrecursor>True</timsRemovePrecursor> |
| 256 <timsIsobaricLabels>False</timsIsobaricLabels> | 257 <timsIsobaricLabels>False</timsIsobaricLabels> |
| 257 <timsCollapseMsms>True</timsCollapseMsms> | 258 <timsCollapseMsms>True</timsCollapseMsms> |
| 258 <crosslinkSearch>False</crosslinkSearch> | 259 <crossLinkingType>0</crossLinkingType> |
| 259 <crossLinker/> | 260 <crossLinker/> |
| 260 <minMatchXl>0</minMatchXl> | 261 <minMatchXl>0</minMatchXl> |
| 261 <minPairedPepLenXl>6</minPairedPepLenXl> | 262 <minPairedPepLenXl>6</minPairedPepLenXl> |
| 262 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> | 263 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> |
| 263 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> | 264 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> |
| 275 <crosslinkMode/> | 276 <crosslinkMode/> |
| 276 <peakRefinement>False</peakRefinement> | 277 <peakRefinement>False</peakRefinement> |
| 277 <isobaricSumOverWindow>True</isobaricSumOverWindow> | 278 <isobaricSumOverWindow>True</isobaricSumOverWindow> |
| 278 <isobaricWeightExponent>0.75</isobaricWeightExponent> | 279 <isobaricWeightExponent>0.75</isobaricWeightExponent> |
| 279 <diaLibraryType>0</diaLibraryType> | 280 <diaLibraryType>0</diaLibraryType> |
| 280 <diaLibraryPath/> | 281 <diaLibraryPaths> |
| 282 </diaLibraryPaths> | |
| 281 <diaPeptidePaths> | 283 <diaPeptidePaths> |
| 282 </diaPeptidePaths> | 284 </diaPeptidePaths> |
| 283 <diaEvidencePaths> | 285 <diaEvidencePaths> |
| 284 </diaEvidencePaths> | 286 </diaEvidencePaths> |
| 285 <diaMsmsPaths> | 287 <diaMsmsPaths> |
| 288 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> | 290 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> |
| 289 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> | 291 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> |
| 290 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> | 292 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> |
| 291 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> | 293 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> |
| 292 <diaScoreN>7</diaScoreN> | 294 <diaScoreN>7</diaScoreN> |
| 293 <diaMinScore>2.99</diaMinScore> | 295 <diaMinScore>1.99</diaMinScore> |
| 294 <diaPrecursorQuant>False</diaPrecursorQuant> | 296 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore> |
| 295 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> | 297 <diaXgBoostSubSample>0.9</diaXgBoostSubSample> |
| 298 <centroidPosition>0</centroidPosition> | |
| 299 <diaQuantMethod>7</diaQuantMethod> | |
| 300 <diaFeatureQuantMethod>2</diaFeatureQuantMethod> | |
| 301 <lfqNormType>0</lfqNormType> | |
| 302 <diaTopNForQuant>10</diaTopNForQuant> | |
| 303 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant> | |
| 304 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant> | |
| 305 <diaPrecursorFilterType>0</diaPrecursorFilterType> | |
| 306 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore> | |
| 307 <diaMinPrecursorScore>0.5</diaMinPrecursorScore> | |
| 308 <diaMinProfileCorrelation>0</diaMinProfileCorrelation> | |
| 309 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight> | |
| 310 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth> | |
| 311 <diaXgBoostEstimators>580</diaXgBoostEstimators> | |
| 312 <diaXgBoostGamma>0.9</diaXgBoostGamma> | |
| 313 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep> | |
| 314 <diaGlobalMl>True</diaGlobalMl> | |
| 315 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy> | |
| 316 <diaMassWindowFactor>3.3</diaMassWindowFactor> | |
| 317 <diaRtPrediction>False</diaRtPrediction> | |
| 318 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound> | |
| 319 <diaNoMl>False</diaNoMl> | |
| 320 <diaPermuteRt>False</diaPermuteRt> | |
| 321 <diaPermuteCcs>False</diaPermuteCcs> | |
| 322 <diaBackgroundSubtraction>False</diaBackgroundSubtraction> | |
| 323 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile> | |
| 324 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor> | |
| 325 <diaLfqWeightedMedian>False</diaLfqWeightedMedian> | |
| 296 </parameterGroup> | 326 </parameterGroup> |
| 297 </parameterGroups> | 327 </parameterGroups> |
| 298 <msmsParamsArray> | 328 <msmsParamsArray> |
| 299 <msmsParams> | 329 <msmsParams> |
| 300 <Name>FTMS</Name> | 330 <Name>FTMS</Name> |