Mercurial > repos > galaxyp > maxquant

comparison test-data/04/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 d253b379322b
children 8934bc76bb52
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>D:\shared\dglaetzer\maxquant_tool\test2\bsa.fasta</fastaFilePath> 5 <fastaFilePath>/tmp/tmpyzym30dx/files/a/5/9/dataset_a592c8b5-872b-4804-9f05-abeef0fda2f1.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>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\test2\BSA_min_22.mzXML</string> 134 <string>/tmp/tmpyzym30dx/job_working_directory/000/22/working/BSA_min_22.mzxml</string>
136 <string>D:\shared\dglaetzer\maxquant_tool\test2\BSA_min_23.mzXML</string> 135 <string>/tmp/tmpyzym30dx/job_working_directory/000/22/working/BSA_min_23.mzXML</string>
137 </filePaths> 136 </filePaths>
138 <experiments> 137 <experiments>
139 <string>e1</string> 138 <string>e1</string>
140 <string>e2</string> 139 <string>e2</string>
141 </experiments> 140 </experiments>
155 <string/> 154 <string/>
156 <string/> 155 <string/>
157 </referenceChannel> 156 </referenceChannel>
158 <intensPred>False</intensPred> 157 <intensPred>False</intensPred>
159 <intensPredModelReTrain>False</intensPredModelReTrain> 158 <intensPredModelReTrain>False</intensPredModelReTrain>
159 <lfqTopNPeptides>0</lfqTopNPeptides>
160 <parameterGroups> 160 <parameterGroups>
161 <parameterGroup> 161 <parameterGroup>
162 <msInstrument>0</msInstrument> 162 <msInstrument>0</msInstrument>
163 <maxCharge>7</maxCharge> 163 <maxCharge>7</maxCharge>
164 <minPeakLen>2</minPeakLen> 164 <minPeakLen>2</minPeakLen>
165 <diaMinPeakLen>2</diaMinPeakLen> 165 <diaMinPeakLen>1</diaMinPeakLen>
166 <useMs1Centroids>False</useMs1Centroids> 166 <useMs1Centroids>False</useMs1Centroids>
167 <useMs2Centroids>False</useMs2Centroids> 167 <useMs2Centroids>False</useMs2Centroids>
168 <cutPeaks>True</cutPeaks> 168 <cutPeaks>True</cutPeaks>
169 <gapScans>1</gapScans> 169 <gapScans>1</gapScans>
170 <minTime>NaN</minTime> 170 <minTime>NaN</minTime>
176 <centroidHalfWidth>35</centroidHalfWidth> 176 <centroidHalfWidth>35</centroidHalfWidth>
177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm> 177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
178 <valleyFactor>1.4</valleyFactor> 178 <valleyFactor>1.4</valleyFactor>
179 <isotopeValleyFactor>1.2</isotopeValleyFactor> 179 <isotopeValleyFactor>1.2</isotopeValleyFactor>
180 <advancedPeakSplitting>False</advancedPeakSplitting> 180 <advancedPeakSplitting>False</advancedPeakSplitting>
181 <intensityThreshold>0</intensityThreshold> 181 <intensityThresholdMs1>0</intensityThresholdMs1>
182 <intensityThresholdMs2>0</intensityThresholdMs2>
182 <labelMods> 183 <labelMods>
183 <string>Arg6;Lys4</string> 184 <string>Arg6;Lys4</string>
184 <string>Arg10;DimethLys8</string> 185 <string>Arg10;DimethLys8</string>
185 </labelMods> 186 </labelMods>
186 <lcmsRunType>Standard</lcmsRunType> 187 <lcmsRunType>Standard</lcmsRunType>
187 <reQuantify>False</reQuantify> 188 <reQuantify>False</reQuantify>
188 <lfqMode>0</lfqMode> 189 <lfqMode>0</lfqMode>
189 <lfqSkipNorm>False</lfqSkipNorm> 190 <lfqNormClusterSize>80</lfqNormClusterSize>
190 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode> 191 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
191 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode> 192 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
192 <lfqMaxFeatures>100000</lfqMaxFeatures> 193 <lfqMaxFeatures>100000</lfqMaxFeatures>
193 <neucodeMaxPpm>0</neucodeMaxPpm> 194 <neucodeMaxPpm>0</neucodeMaxPpm>
194 <neucodeResolution>0</neucodeResolution> 195 <neucodeResolution>0</neucodeResolution>
260 <timsResolution>0</timsResolution> 261 <timsResolution>0</timsResolution>
261 <timsMinMsmsIntensity>0</timsMinMsmsIntensity> 262 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
262 <timsRemovePrecursor>True</timsRemovePrecursor> 263 <timsRemovePrecursor>True</timsRemovePrecursor>
263 <timsIsobaricLabels>False</timsIsobaricLabels> 264 <timsIsobaricLabels>False</timsIsobaricLabels>
264 <timsCollapseMsms>True</timsCollapseMsms> 265 <timsCollapseMsms>True</timsCollapseMsms>
265 <crosslinkSearch>False</crosslinkSearch> 266 <crossLinkingType>0</crossLinkingType>
266 <crossLinker/> 267 <crossLinker/>
267 <minMatchXl>0</minMatchXl> 268 <minMatchXl>0</minMatchXl>
268 <minPairedPepLenXl>6</minPairedPepLenXl> 269 <minPairedPepLenXl>6</minPairedPepLenXl>
269 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 270 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
270 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 271 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
282 <crosslinkMode/> 283 <crosslinkMode/>
283 <peakRefinement>False</peakRefinement> 284 <peakRefinement>False</peakRefinement>
284 <isobaricSumOverWindow>True</isobaricSumOverWindow> 285 <isobaricSumOverWindow>True</isobaricSumOverWindow>
285 <isobaricWeightExponent>0.75</isobaricWeightExponent> 286 <isobaricWeightExponent>0.75</isobaricWeightExponent>
286 <diaLibraryType>0</diaLibraryType> 287 <diaLibraryType>0</diaLibraryType>
287 <diaLibraryPath/> 288 <diaLibraryPaths>
289 </diaLibraryPaths>
288 <diaPeptidePaths> 290 <diaPeptidePaths>
289 </diaPeptidePaths> 291 </diaPeptidePaths>
290 <diaEvidencePaths> 292 <diaEvidencePaths>
291 </diaEvidencePaths> 293 </diaEvidencePaths>
292 <diaMsmsPaths> 294 <diaMsmsPaths>
295 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm> 297 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
296 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering> 298 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
297 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering> 299 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
298 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering> 300 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
299 <diaScoreN>7</diaScoreN> 301 <diaScoreN>7</diaScoreN>
300 <diaMinScore>2.99</diaMinScore> 302 <diaMinScore>1.99</diaMinScore>
301 <diaPrecursorQuant>False</diaPrecursorQuant> 303 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
302 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant> 304 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
305 <centroidPosition>0</centroidPosition>
306 <diaQuantMethod>7</diaQuantMethod>
307 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
308 <lfqNormType>1</lfqNormType>
309 <diaTopNForQuant>10</diaTopNForQuant>
310 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
311 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
312 <diaPrecursorFilterType>0</diaPrecursorFilterType>
313 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
314 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
315 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
316 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
317 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
318 <diaXgBoostEstimators>580</diaXgBoostEstimators>
319 <diaXgBoostGamma>0.9</diaXgBoostGamma>
320 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
321 <diaGlobalMl>True</diaGlobalMl>
322 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
323 <diaMassWindowFactor>3.3</diaMassWindowFactor>
324 <diaRtPrediction>False</diaRtPrediction>
325 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
326 <diaNoMl>False</diaNoMl>
327 <diaPermuteRt>False</diaPermuteRt>
328 <diaPermuteCcs>False</diaPermuteCcs>
329 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
330 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
331 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
332 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
303 </parameterGroup> 333 </parameterGroup>
304 </parameterGroups> 334 </parameterGroups>
305 <msmsParamsArray> 335 <msmsParamsArray>
306 <msmsParams> 336 <msmsParams>
307 <Name>FTMS</Name> 337 <Name>FTMS</Name>