Mercurial > repos > galaxyp > maxquant

comparison test-data/template.xml @ 4:dcd39bcc7481 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 11:49:19 -0400
parents 8bac3cc5c5de
children 0839f84def5e
comparison
equal deleted inserted replaced
3:175e062b6a17 4:dcd39bcc7481
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> 2 <MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
3 <fastaFiles> 3 <fastaFiles>
4 <FastaFileInfo> 4 <FastaFileInfo>
5 <fastaFilePath></fastaFilePath> 5 <fastaFilePath>example.fasta</fastaFilePath>
6 <identifierParseRule>>(.*)</identifierParseRule> 6 <identifierParseRule>>(.*)</identifierParseRule>
7 <descriptionParseRule></descriptionParseRule> 7 <descriptionParseRule></descriptionParseRule>
8 <taxonomyParseRule></taxonomyParseRule> 8 <taxonomyParseRule></taxonomyParseRule>
9 <variationParseRule></variationParseRule> 9 <variationParseRule></variationParseRule>
10 <modificationParseRule></modificationParseRule> 10 <modificationParseRule></modificationParseRule>
86 <restrictMods> 86 <restrictMods>
87 <string>Oxidation (M)</string> 87 <string>Oxidation (M)</string>
88 <string>Acetyl (Protein N-term)</string> 88 <string>Acetyl (Protein N-term)</string>
89 </restrictMods> 89 </restrictMods>
90 <matchingTimeWindow>0</matchingTimeWindow> 90 <matchingTimeWindow>0</matchingTimeWindow>
91 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
91 <alignmentTimeWindow>0</alignmentTimeWindow> 92 <alignmentTimeWindow>0</alignmentTimeWindow>
92 <numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms> 93 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
93 <numberOfCandidatesMsms>15</numberOfCandidatesMsms> 94 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
94 <compositionPrediction>0</compositionPrediction> 95 <compositionPrediction>0</compositionPrediction>
95 <quantMode>1</quantMode> 96 <quantMode>1</quantMode>
96 <massDifferenceMods> 97 <massDifferenceMods>
97 </massDifferenceMods> 98 </massDifferenceMods>
105 <writeMzRangeTable>True</writeMzRangeTable> 106 <writeMzRangeTable>True</writeMzRangeTable>
106 <writeMzTab>False</writeMzTab> 107 <writeMzTab>False</writeMzTab>
107 <disableMd5>False</disableMd5> 108 <disableMd5>False</disableMd5>
108 <cacheBinInds>True</cacheBinInds> 109 <cacheBinInds>True</cacheBinInds>
109 <etdIncludeB>False</etdIncludeB> 110 <etdIncludeB>False</etdIncludeB>
110 <complementaryTmtCollapseNplets>True</complementaryTmtCollapseNplets>
111 <stackPeaks>False</stackPeaks>
112 <ms2PrecursorShift>0</ms2PrecursorShift> 111 <ms2PrecursorShift>0</ms2PrecursorShift>
113 <complementaryIonPpm>20</complementaryIonPpm> 112 <complementaryIonPpm>20</complementaryIonPpm>
114 <variationParseRule></variationParseRule> 113 <variationParseRule></variationParseRule>
115 <variationMode>none</variationMode> 114 <variationMode>none</variationMode>
116 <useSeriesReporters>False</useSeriesReporters> 115 <useSeriesReporters>False</useSeriesReporters>
117 <name>templateSession</name> 116 <name>templateSession</name>
118 <maxQuantVersion>1.6.3.4</maxQuantVersion> 117 <maxQuantVersion>1.6.10.43</maxQuantVersion>
119 <tempFolder></tempFolder> 118 <tempFolder></tempFolder>
120 <pluginFolder></pluginFolder> 119 <pluginFolder></pluginFolder>
121 <numThreads>1</numThreads> 120 <numThreads>1</numThreads>
122 <emailAddress></emailAddress> 121 <emailAddress></emailAddress>
123 <smtpHost></smtpHost> 122 <smtpHost></smtpHost>
148 <int>0</int> 147 <int>0</int>
149 </paramGroupIndices> 148 </paramGroupIndices>
150 <referenceChannel> 149 <referenceChannel>
151 <string></string> 150 <string></string>
152 </referenceChannel> 151 </referenceChannel>
152 <intensPred>False</intensPred>
153 <intensPredModelReTrain>False</intensPredModelReTrain>
153 <parameterGroups> 154 <parameterGroups>
154 <parameterGroup> 155 <parameterGroup>
155 <msInstrument>0</msInstrument> 156 <msInstrument>0</msInstrument>
156 <maxCharge>7</maxCharge> 157 <maxCharge>7</maxCharge>
157 <minPeakLen>2</minPeakLen> 158 <minPeakLen>2</minPeakLen>
159 <diaMinPeakLen>2</diaMinPeakLen>
158 <useMs1Centroids>False</useMs1Centroids> 160 <useMs1Centroids>False</useMs1Centroids>
159 <useMs2Centroids>False</useMs2Centroids> 161 <useMs2Centroids>False</useMs2Centroids>
160 <cutPeaks>True</cutPeaks> 162 <cutPeaks>True</cutPeaks>
161 <gapScans>1</gapScans> 163 <gapScans>1</gapScans>
162 <minTime>NaN</minTime> 164 <minTime>NaN</minTime>
261 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein> 263 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
262 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated> 264 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
263 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated> 265 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
264 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated> 266 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
265 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated> 267 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
266 <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta> 268 <crosslinkModifications>
267 <crosslinkCleaveModifications> 269 </crosslinkModifications>
268 </crosslinkCleaveModifications>
269 <crosslinkFastaFiles> 270 <crosslinkFastaFiles>
270 </crosslinkFastaFiles> 271 </crosslinkFastaFiles>
271 <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode> 272 <crosslinkSites>
273 </crosslinkSites>
274 <crosslinkNetworkFiles>
275 </crosslinkNetworkFiles>
276 <crosslinkMode></crosslinkMode>
272 <peakRefinement>False</peakRefinement> 277 <peakRefinement>False</peakRefinement>
273 <isobaricSumOverWindow>True</isobaricSumOverWindow> 278 <isobaricSumOverWindow>True</isobaricSumOverWindow>
279 <isobaricWeightExponent>0.75</isobaricWeightExponent>
280 <diaLibraryType>0</diaLibraryType>
281 <diaLibraryPath></diaLibraryPath>
282 <diaPeptidePaths>
283 </diaPeptidePaths>
284 <diaEvidencePaths>
285 </diaEvidencePaths>
286 <diaMsmsPaths>
287 </diaMsmsPaths>
288 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
289 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
290 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
291 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
292 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
293 <diaScoreN>7</diaScoreN>
294 <diaMinScore>2.99</diaMinScore>
295 <diaPrecursorQuant>False</diaPrecursorQuant>
296 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
274 </parameterGroup> 297 </parameterGroup>
275 </parameterGroups> 298 </parameterGroups>
276 <msmsParamsArray> 299 <msmsParamsArray>
277 <msmsParams> 300 <msmsParams>
278 <Name>FTMS</Name> 301 <Name>FTMS</Name>
325 <DependentLosses>True</DependentLosses> 348 <DependentLosses>True</DependentLosses>
326 <Recalibration>False</Recalibration> 349 <Recalibration>False</Recalibration>
327 </msmsParams> 350 </msmsParams>
328 <msmsParams> 351 <msmsParams>
329 <Name>Unknown</Name> 352 <Name>Unknown</Name>
330 <MatchTolerance>0.5</MatchTolerance> 353 <MatchTolerance>20</MatchTolerance>
331 <MatchToleranceInPpm>False</MatchToleranceInPpm> 354 <MatchToleranceInPpm>True</MatchToleranceInPpm>
332 <DeisotopeTolerance>0.15</DeisotopeTolerance> 355 <DeisotopeTolerance>7</DeisotopeTolerance>
333 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm> 356 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
334 <DeNovoTolerance>0.25</DeNovoTolerance> 357 <DeNovoTolerance>10</DeNovoTolerance>
335 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm> 358 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
336 <Deisotope>False</Deisotope> 359 <Deisotope>True</Deisotope>
337 <Topx>8</Topx> 360 <Topx>12</Topx>
338 <TopxInterval>100</TopxInterval> 361 <TopxInterval>100</TopxInterval>
339 <HigherCharges>True</HigherCharges> 362 <HigherCharges>True</HigherCharges>
340 <IncludeWater>True</IncludeWater> 363 <IncludeWater>True</IncludeWater>
341 <IncludeAmmonia>True</IncludeAmmonia> 364 <IncludeAmmonia>True</IncludeAmmonia>
342 <DependentLosses>True</DependentLosses> 365 <DependentLosses>True</DependentLosses>