Mercurial > repos > galaxyp > maxquant

comparison test-data/01/mqpar.xml @ 11:057bf124c80e 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 16:36:56 +0000
parents f2f79f0be7d1
children 5d013f405259
comparison
equal deleted inserted replaced
10:68d8dcdbddb1 11:057bf124c80e
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/tmpyzym30dx/files/3/c/e/dataset_3cea3228-eaab-4e71-aba7-9ffa9900b54a.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>
104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
107 <writeMzTab>True</writeMzTab> 105 <writeMzTab>True</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>-1.79769313486232E+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>D:\shared\dglaetzer\maxquant_tool\test1\BSA_min_23.mzXML</string> 134 <string>/tmp/tmpyzym30dx/job_working_directory/000/3/working/BSA_min_23.mzXML</string>
136 </filePaths> 135 </filePaths>
137 <experiments> 136 <experiments>
138 <string>BSA_min_23.mzXML</string> 137 <string>BSA_min_23.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>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>
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>1</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>