Mercurial > repos > galaxyp > maxquant

comparison test-data/07/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 d72c96ad9a16
children 837224ad1694
comparison
equal deleted inserted replaced
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>/tmp/tmpfqvn4g0u/files/5/b/8/dataset_5b803772-27b2-44fa-a4cf-8da6ee3cdfb8.dat</fastaFilePath> 5 <fastaFilePath>/tmp/tmpojxmxo_4/files/2/d/f/dataset_2df03e43-042c-483e-9a8a-ad29add25dbd.dat</fastaFilePath>
6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule> 6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
7 <descriptionParseRule>&gt;(.*)</descriptionParseRule> 7 <descriptionParseRule>&gt;(.*)</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>False</ibaq> 49 <ibaq>False</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>
107 <writeMzTab>True</writeMzTab> 104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
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>templateSession</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>-1.79769313486232E+308</fullMinMz> 123 <fullMinMz>-1.79769313486232E+308</fullMinMz>
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>/tmp/tmpfqvn4g0u/job_working_directory/000/3/working/ptxqc_test3.mzXML</string> 134 <string>/tmp/tmpojxmxo_4/job_working_directory/000/6/working/tmt_data.mzXML</string>
136 </filePaths> 135 </filePaths>
137 <experiments> 136 <experiments>
138 <string>ptxqc_test3.mzXML</string> 137 <string>tmt_data.mzXML</string>
139 </experiments> 138 </experiments>
140 <fractions> 139 <fractions>
141 <short>32767</short> 140 <short>32767</short>
142 </fractions> 141 </fractions>
143 <ptms> 142 <ptms>
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>Reporter ion MS2</lcmsRunType> 180 <lcmsRunType>Reporter ion MS2</lcmsRunType>
180 <reQuantify>False</reQuantify> 181 <reQuantify>False</reQuantify>
181 <lfqMode>0</lfqMode> 182 <lfqMode>0</lfqMode>
182 <lfqSkipNorm>False</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>
341 <timsResolution>0</timsResolution> 342 <timsResolution>0</timsResolution>
342 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> 343 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
343 <timsRemovePrecursor>True</timsRemovePrecursor> 344 <timsRemovePrecursor>True</timsRemovePrecursor>
344 <timsIsobaricLabels>False</timsIsobaricLabels> 345 <timsIsobaricLabels>False</timsIsobaricLabels>
345 <timsCollapseMsms>True</timsCollapseMsms> 346 <timsCollapseMsms>True</timsCollapseMsms>
346 <crosslinkSearch>False</crosslinkSearch> 347 <crossLinkingType>0</crossLinkingType>
347 <crossLinker/> 348 <crossLinker/>
348 <minMatchXl>0</minMatchXl> 349 <minMatchXl>0</minMatchXl>
349 <minPairedPepLenXl>6</minPairedPepLenXl> 350 <minPairedPepLenXl>6</minPairedPepLenXl>
350 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 351 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
351 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 352 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
363 <crosslinkMode/> 364 <crosslinkMode/>
364 <peakRefinement>False</peakRefinement> 365 <peakRefinement>False</peakRefinement>
365 <isobaricSumOverWindow>True</isobaricSumOverWindow> 366 <isobaricSumOverWindow>True</isobaricSumOverWindow>
366 <isobaricWeightExponent>0.75</isobaricWeightExponent> 367 <isobaricWeightExponent>0.75</isobaricWeightExponent>
367 <diaLibraryType>0</diaLibraryType> 368 <diaLibraryType>0</diaLibraryType>
368 <diaLibraryPath/> 369 <diaLibraryPaths>
370 </diaLibraryPaths>
369 <diaPeptidePaths> 371 <diaPeptidePaths>
370 </diaPeptidePaths> 372 </diaPeptidePaths>
371 <diaEvidencePaths> 373 <diaEvidencePaths>
372 </diaEvidencePaths> 374 </diaEvidencePaths>
373 <diaMsmsPaths> 375 <diaMsmsPaths>
376 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> 378 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
377 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> 379 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
378 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> 380 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
379 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> 381 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
380 <diaScoreN>7</diaScoreN> 382 <diaScoreN>7</diaScoreN>
381 <diaMinScore>2.99</diaMinScore> 383 <diaMinScore>1.99</diaMinScore>
382 <diaPrecursorQuant>False</diaPrecursorQuant> 384 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
383 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> 385 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
386 <centroidPosition>0</centroidPosition>
387 <diaQuantMethod>7</diaQuantMethod>
388 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
389 <lfqNormType>1</lfqNormType>
390 <diaTopNForQuant>10</diaTopNForQuant>
391 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
392 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
393 <diaPrecursorFilterType>0</diaPrecursorFilterType>
394 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
395 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
396 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
397 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
398 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
399 <diaXgBoostEstimators>580</diaXgBoostEstimators>
400 <diaXgBoostGamma>0.9</diaXgBoostGamma>
401 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
402 <diaGlobalMl>True</diaGlobalMl>
403 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
404 <diaMassWindowFactor>3.3</diaMassWindowFactor>
405 <diaRtPrediction>False</diaRtPrediction>
406 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
407 <diaNoMl>False</diaNoMl>
408 <diaPermuteRt>False</diaPermuteRt>
409 <diaPermuteCcs>False</diaPermuteCcs>
410 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
411 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
412 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
413 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
384 </parameterGroup> 414 </parameterGroup>
385 </parameterGroups> 415 </parameterGroups>
386 <msmsParamsArray> 416 <msmsParamsArray>
387 <msmsParams> 417 <msmsParams>
388 <Name>FTMS</Name> 418 <Name>FTMS</Name>