Mercurial > repos > galaxyp > maxquant

comparison test-data/03/mqpar.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
children 2133b0be850a
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3:175e062b6a17 4:dcd39bcc7481
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta</fastaFilePath>
6 <identifierParseRule>^&gt;.*\|(.*)\|.*$</identifierParseRule>
7 <descriptionParseRule>^&gt;.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule>
8 <taxonomyParseRule/>
9 <variationParseRule/>
10 <modificationParseRule/>
11 <taxonomyId/>
12 </FastaFileInfo>
13 </fastaFiles>
14 <fastaFilesProteogenomics>
15 </fastaFilesProteogenomics>
16 <fastaFilesFirstSearch>
17 </fastaFilesFirstSearch>
18 <fixedSearchFolder/>
19 <andromedaCacheSize>350000</andromedaCacheSize>
20 <advancedRatios>True</advancedRatios>
21 <pvalThres>0.005</pvalThres>
22 <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
24 <rtShift>False</rtShift>
25 <separateLfq>False</separateLfq>
26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
27 <lfqRequireMsms>True</lfqRequireMsms>
28 <decoyMode>revert</decoyMode>
29 <boxCarMode>all</boxCarMode>
30 <includeContaminants>True</includeContaminants>
31 <maxPeptideMass>4600</maxPeptideMass>
32 <epsilonMutationScore>True</epsilonMutationScore>
33 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
34 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
35 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
36 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
37 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
38 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
39 <secondPeptide>True</secondPeptide>
40 <matchBetweenRuns>False</matchBetweenRuns>
41 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
42 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
43 <dependentPeptides>False</dependentPeptides>
44 <dependentPeptideFdr>0</dependentPeptideFdr>
45 <dependentPeptideMassBin>0</dependentPeptideMassBin>
46 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
47 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
48 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
49 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
50 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
51 <msmsConnection>False</msmsConnection>
52 <ibaq>True</ibaq>
53 <top3>False</top3>
54 <independentEnzymes>False</independentEnzymes>
55 <useDeltaScore>False</useDeltaScore>
56 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
57 <taxonomyLevel>Species</taxonomyLevel>
58 <avalon>False</avalon>
59 <nModColumns>3</nModColumns>
60 <ibaqLogFit>False</ibaqLogFit>
61 <razorProteinFdr>True</razorProteinFdr>
62 <deNovoSequencing>False</deNovoSequencing>
63 <deNovoVarMods>True</deNovoVarMods>
64 <massDifferenceSearch>False</massDifferenceSearch>
65 <isotopeCalc>False</isotopeCalc>
66 <writePeptidesForSpectrumFile/>
67 <intensityPredictionsFile>
68 </intensityPredictionsFile>
69 <minPepLen>7</minPepLen>
70 <psmFdrCrosslink>0.01</psmFdrCrosslink>
71 <peptideFdr>0.01</peptideFdr>
72 <proteinFdr>0.01</proteinFdr>
73 <siteFdr>0.01</siteFdr>
74 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
75 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
76 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
77 <minPeptides>1</minPeptides>
78 <minRazorPeptides>1</minRazorPeptides>
79 <minUniquePeptides>1</minUniquePeptides>
80 <useCounterparts>False</useCounterparts>
81 <advancedSiteIntensities>True</advancedSiteIntensities>
82 <customProteinQuantification>False</customProteinQuantification>
83 <customProteinQuantificationFile/>
84 <minRatioCount>2</minRatioCount>
85 <restrictProteinQuantification>True</restrictProteinQuantification>
86 <restrictMods>
87 <string>Oxidation (M)</string>
88 <string>Acetyl (Protein N-term)</string>
89 </restrictMods>
90 <matchingTimeWindow>0</matchingTimeWindow>
91 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
92 <alignmentTimeWindow>0</alignmentTimeWindow>
93 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
94 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
95 <compositionPrediction>0</compositionPrediction>
96 <quantMode>1</quantMode>
97 <massDifferenceMods>
98 </massDifferenceMods>
99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
100 <writeMsScansTable>False</writeMsScansTable>
101 <writeMsmsScansTable>True</writeMsmsScansTable>
102 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
103 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
104 <writeMs3ScansTable>True</writeMs3ScansTable>
105 <writeAllPeptidesTable>True</writeAllPeptidesTable>
106 <writeMzRangeTable>True</writeMzRangeTable>
107 <writeMzTab>False</writeMzTab>
108 <disableMd5>False</disableMd5>
109 <cacheBinInds>True</cacheBinInds>
110 <etdIncludeB>False</etdIncludeB>
111 <ms2PrecursorShift>0</ms2PrecursorShift>
112 <complementaryIonPpm>20</complementaryIonPpm>
113 <variationParseRule/>
114 <variationMode>none</variationMode>
115 <useSeriesReporters>False</useSeriesReporters>
116 <name>session1</name>
117 <maxQuantVersion>1.6.10.43</maxQuantVersion>
118 <tempFolder/>
119 <pluginFolder/>
120 <numThreads>1</numThreads>
121 <emailAddress/>
122 <smtpHost/>
123 <emailFromAddress/>
124 <fixedCombinedFolder/>
125 <fullMinMz>-1.79589544172745E+308</fullMinMz>
126 <fullMaxMz>1.79589544172745E+308</fullMaxMz>
127 <sendEmail>False</sendEmail>
128 <ionCountIntensities>False</ionCountIntensities>
129 <verboseColumnHeaders>False</verboseColumnHeaders>
130 <calcPeakProperties>False</calcPeakProperties>
131 <showCentroidMassDifferences>False</showCentroidMassDifferences>
132 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
133 <useDotNetCore>False</useDotNetCore>
134 <filePaths>
135 <string>D:\shared\dglaetzer\maxquant_tool\test3\BSA_min_22.mzXML</string>
136 </filePaths>
137 <experiments>
138 <string>BSA_min_22.mzxml</string>
139 </experiments>
140 <fractions>
141 <short>32767</short>
142 </fractions>
143 <ptms>
144 <boolean>False</boolean>
145 </ptms>
146 <paramGroupIndices>
147 <int>0</int>
148 </paramGroupIndices>
149 <referenceChannel>
150 <string/>
151 </referenceChannel>
152 <intensPred>False</intensPred>
153 <intensPredModelReTrain>False</intensPredModelReTrain>
154 <parameterGroups>
155 <parameterGroup>
156 <msInstrument>0</msInstrument>
157 <maxCharge>7</maxCharge>
158 <minPeakLen>2</minPeakLen>
159 <diaMinPeakLen>2</diaMinPeakLen>
160 <useMs1Centroids>False</useMs1Centroids>
161 <useMs2Centroids>False</useMs2Centroids>
162 <cutPeaks>True</cutPeaks>
163 <gapScans>1</gapScans>
164 <minTime>NaN</minTime>
165 <maxTime>NaN</maxTime>
166 <matchType>MatchFromAndTo</matchType>
167 <intensityDetermination>0</intensityDetermination>
168 <centroidMatchTol>8</centroidMatchTol>
169 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
170 <centroidHalfWidth>35</centroidHalfWidth>
171 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
172 <valleyFactor>1.4</valleyFactor>
173 <isotopeValleyFactor>1.2</isotopeValleyFactor>
174 <advancedPeakSplitting>False</advancedPeakSplitting>
175 <intensityThreshold>0</intensityThreshold>
176 <labelMods>
177 <string/>
178 </labelMods>
179 <lcmsRunType>Standard</lcmsRunType>
180 <reQuantify>False</reQuantify>
181 <lfqMode>1</lfqMode>
182 <lfqSkipNorm>True</lfqSkipNorm>
183 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
184 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
185 <lfqMaxFeatures>100000</lfqMaxFeatures>
186 <neucodeMaxPpm>0</neucodeMaxPpm>
187 <neucodeResolution>0</neucodeResolution>
188 <neucodeResolutionInMda>False</neucodeResolutionInMda>
189 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
190 <fastLfq>True</fastLfq>
191 <lfqRestrictFeatures>False</lfqRestrictFeatures>
192 <lfqMinRatioCount>2</lfqMinRatioCount>
193 <maxLabeledAa>0</maxLabeledAa>
194 <maxNmods>5</maxNmods>
195 <maxMissedCleavages>1</maxMissedCleavages>
196 <multiplicity>1</multiplicity>
197 <enzymeMode>0</enzymeMode>
198 <complementaryReporterType>0</complementaryReporterType>
199 <reporterNormalization>0</reporterNormalization>
200 <neucodeIntensityMode>0</neucodeIntensityMode>
201 <fixedModifications>
202 <string>Carbamidomethyl (C)</string>
203 </fixedModifications>
204 <enzymes>
205 <string>Trypsin/P</string>
206 </enzymes>
207 <enzymesFirstSearch>
208 </enzymesFirstSearch>
209 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
210 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
211 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
212 <variableModifications>
213 <string>Oxidation (M)</string>
214 </variableModifications>
215 <useMultiModification>False</useMultiModification>
216 <multiModifications>
217 </multiModifications>
218 <isobaricLabels>
219 </isobaricLabels>
220 <neucodeLabels>
221 </neucodeLabels>
222 <variableModificationsFirstSearch>
223 </variableModificationsFirstSearch>
224 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
225 <additionalVariableModifications>
226 </additionalVariableModifications>
227 <additionalVariableModificationProteins>
228 </additionalVariableModificationProteins>
229 <doMassFiltering>True</doMassFiltering>
230 <firstSearchTol>20</firstSearchTol>
231 <mainSearchTol>4.5</mainSearchTol>
232 <searchTolInPpm>True</searchTolInPpm>
233 <isotopeMatchTol>2</isotopeMatchTol>
234 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
235 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
236 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
237 <checkMassDeficit>True</checkMassDeficit>
238 <recalibrationInPpm>True</recalibrationInPpm>
239 <intensityDependentCalibration>False</intensityDependentCalibration>
240 <minScoreForCalibration>70</minScoreForCalibration>
241 <matchLibraryFile>False</matchLibraryFile>
242 <libraryFile/>
243 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
244 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
245 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
246 <reporterMassTolerance>NaN</reporterMassTolerance>
247 <reporterPif>NaN</reporterPif>
248 <filterPif>False</filterPif>
249 <reporterFraction>NaN</reporterFraction>
250 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
251 <timsHalfWidth>0</timsHalfWidth>
252 <timsStep>0</timsStep>
253 <timsResolution>0</timsResolution>
254 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
255 <timsRemovePrecursor>True</timsRemovePrecursor>
256 <timsIsobaricLabels>False</timsIsobaricLabels>
257 <timsCollapseMsms>True</timsCollapseMsms>
258 <crosslinkSearch>False</crosslinkSearch>
259 <crossLinker/>
260 <minMatchXl>0</minMatchXl>
261 <minPairedPepLenXl>6</minPairedPepLenXl>
262 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
263 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
264 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
265 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
266 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
267 <crosslinkModifications>
268 </crosslinkModifications>
269 <crosslinkFastaFiles>
270 </crosslinkFastaFiles>
271 <crosslinkSites>
272 </crosslinkSites>
273 <crosslinkNetworkFiles>
274 </crosslinkNetworkFiles>
275 <crosslinkMode/>
276 <peakRefinement>False</peakRefinement>
277 <isobaricSumOverWindow>True</isobaricSumOverWindow>
278 <isobaricWeightExponent>0.75</isobaricWeightExponent>
279 <diaLibraryType>0</diaLibraryType>
280 <diaLibraryPath/>
281 <diaPeptidePaths>
282 </diaPeptidePaths>
283 <diaEvidencePaths>
284 </diaEvidencePaths>
285 <diaMsmsPaths>
286 </diaMsmsPaths>
287 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
288 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
289 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
290 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
291 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
292 <diaScoreN>7</diaScoreN>
293 <diaMinScore>2.99</diaMinScore>
294 <diaPrecursorQuant>False</diaPrecursorQuant>
295 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
296 </parameterGroup>
297 </parameterGroups>
298 <msmsParamsArray>
299 <msmsParams>
300 <Name>FTMS</Name>
301 <MatchTolerance>20</MatchTolerance>
302 <MatchToleranceInPpm>True</MatchToleranceInPpm>
303 <DeisotopeTolerance>7</DeisotopeTolerance>
304 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
305 <DeNovoTolerance>10</DeNovoTolerance>
306 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
307 <Deisotope>True</Deisotope>
308 <Topx>12</Topx>
309 <TopxInterval>100</TopxInterval>
310 <HigherCharges>True</HigherCharges>
311 <IncludeWater>True</IncludeWater>
312 <IncludeAmmonia>True</IncludeAmmonia>
313 <DependentLosses>True</DependentLosses>
314 <Recalibration>False</Recalibration>
315 </msmsParams>
316 <msmsParams>
317 <Name>ITMS</Name>
318 <MatchTolerance>0.5</MatchTolerance>
319 <MatchToleranceInPpm>False</MatchToleranceInPpm>
320 <DeisotopeTolerance>0.15</DeisotopeTolerance>
321 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
322 <DeNovoTolerance>0.25</DeNovoTolerance>
323 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
324 <Deisotope>False</Deisotope>
325 <Topx>8</Topx>
326 <TopxInterval>100</TopxInterval>
327 <HigherCharges>True</HigherCharges>
328 <IncludeWater>True</IncludeWater>
329 <IncludeAmmonia>True</IncludeAmmonia>
330 <DependentLosses>True</DependentLosses>
331 <Recalibration>False</Recalibration>
332 </msmsParams>
333 <msmsParams>
334 <Name>TOF</Name>
335 <MatchTolerance>40</MatchTolerance>
336 <MatchToleranceInPpm>True</MatchToleranceInPpm>
337 <DeisotopeTolerance>0.01</DeisotopeTolerance>
338 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
339 <DeNovoTolerance>0.02</DeNovoTolerance>
340 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
341 <Deisotope>True</Deisotope>
342 <Topx>10</Topx>
343 <TopxInterval>100</TopxInterval>
344 <HigherCharges>True</HigherCharges>
345 <IncludeWater>True</IncludeWater>
346 <IncludeAmmonia>True</IncludeAmmonia>
347 <DependentLosses>True</DependentLosses>
348 <Recalibration>False</Recalibration>
349 </msmsParams>
350 <msmsParams>
351 <Name>Unknown</Name>
352 <MatchTolerance>20</MatchTolerance>
353 <MatchToleranceInPpm>True</MatchToleranceInPpm>
354 <DeisotopeTolerance>7</DeisotopeTolerance>
355 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
356 <DeNovoTolerance>10</DeNovoTolerance>
357 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
358 <Deisotope>True</Deisotope>
359 <Topx>12</Topx>
360 <TopxInterval>100</TopxInterval>
361 <HigherCharges>True</HigherCharges>
362 <IncludeWater>True</IncludeWater>
363 <IncludeAmmonia>True</IncludeAmmonia>
364 <DependentLosses>True</DependentLosses>
365 <Recalibration>False</Recalibration>
366 </msmsParams>
367 </msmsParamsArray>
368 <fragmentationParamsArray>
369 <fragmentationParams>
370 <Name>CID</Name>
371 <Connected>False</Connected>
372 <ConnectedScore0>1</ConnectedScore0>
373 <ConnectedScore1>1</ConnectedScore1>
374 <ConnectedScore2>1</ConnectedScore2>
375 <InternalFragments>False</InternalFragments>
376 <InternalFragmentWeight>1</InternalFragmentWeight>
377 <InternalFragmentAas>KRH</InternalFragmentAas>
378 </fragmentationParams>
379 <fragmentationParams>
380 <Name>HCD</Name>
381 <Connected>False</Connected>
382 <ConnectedScore0>1</ConnectedScore0>
383 <ConnectedScore1>1</ConnectedScore1>
384 <ConnectedScore2>1</ConnectedScore2>
385 <InternalFragments>False</InternalFragments>
386 <InternalFragmentWeight>1</InternalFragmentWeight>
387 <InternalFragmentAas>KRH</InternalFragmentAas>
388 </fragmentationParams>
389 <fragmentationParams>
390 <Name>ETD</Name>
391 <Connected>False</Connected>
392 <ConnectedScore0>1</ConnectedScore0>
393 <ConnectedScore1>1</ConnectedScore1>
394 <ConnectedScore2>1</ConnectedScore2>
395 <InternalFragments>False</InternalFragments>
396 <InternalFragmentWeight>1</InternalFragmentWeight>
397 <InternalFragmentAas>KRH</InternalFragmentAas>
398 </fragmentationParams>
399 <fragmentationParams>
400 <Name>PQD</Name>
401 <Connected>False</Connected>
402 <ConnectedScore0>1</ConnectedScore0>
403 <ConnectedScore1>1</ConnectedScore1>
404 <ConnectedScore2>1</ConnectedScore2>
405 <InternalFragments>False</InternalFragments>
406 <InternalFragmentWeight>1</InternalFragmentWeight>
407 <InternalFragmentAas>KRH</InternalFragmentAas>
408 </fragmentationParams>
409 <fragmentationParams>
410 <Name>ETHCD</Name>
411 <Connected>False</Connected>
412 <ConnectedScore0>1</ConnectedScore0>
413 <ConnectedScore1>1</ConnectedScore1>
414 <ConnectedScore2>1</ConnectedScore2>
415 <InternalFragments>False</InternalFragments>
416 <InternalFragmentWeight>1</InternalFragmentWeight>
417 <InternalFragmentAas>KRH</InternalFragmentAas>
418 </fragmentationParams>
419 <fragmentationParams>
420 <Name>ETCID</Name>
421 <Connected>False</Connected>
422 <ConnectedScore0>1</ConnectedScore0>
423 <ConnectedScore1>1</ConnectedScore1>
424 <ConnectedScore2>1</ConnectedScore2>
425 <InternalFragments>False</InternalFragments>
426 <InternalFragmentWeight>1</InternalFragmentWeight>
427 <InternalFragmentAas>KRH</InternalFragmentAas>
428 </fragmentationParams>
429 <fragmentationParams>
430 <Name>UVPD</Name>
431 <Connected>False</Connected>
432 <ConnectedScore0>1</ConnectedScore0>
433 <ConnectedScore1>1</ConnectedScore1>
434 <ConnectedScore2>1</ConnectedScore2>
435 <InternalFragments>False</InternalFragments>
436 <InternalFragmentWeight>1</InternalFragmentWeight>
437 <InternalFragmentAas>KRH</InternalFragmentAas>
438 </fragmentationParams>
439 <fragmentationParams>
440 <Name>Unknown</Name>
441 <Connected>False</Connected>
442 <ConnectedScore0>1</ConnectedScore0>
443 <ConnectedScore1>1</ConnectedScore1>
444 <ConnectedScore2>1</ConnectedScore2>
445 <InternalFragments>False</InternalFragments>
446 <InternalFragmentWeight>1</InternalFragmentWeight>
447 <InternalFragmentAas>KRH</InternalFragmentAas>
448 </fragmentationParams>
449 </fragmentationParamsArray>
450 </MaxQuantParams>
451