Mercurial > repos > galaxyp > maxquant_mqpar

comparison test-data/txt/mqpar.xml @ 4:9cb7dcc07dae draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
author galaxyp
date Fri, 19 Feb 2021 21:25:06 +0000
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3:2d67fb758956 4:9cb7dcc07dae
1 <?xml version="1.0" ?>
2 <MaxQuantParams>
3 <fastaFiles>
4 <FastaFileInfo>
5 <fastaFilePath>/mnt/galaxy/data/003/dataset_3981.dat</fastaFilePath>
6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
7 <descriptionParseRule>&gt;(.*)</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>False</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>0</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>2</numThreads>
121 <emailAddress/>
122 <smtpHost/>
123 <emailFromAddress/>
124 <fixedCombinedFolder/>
125 <fullMinMz>-1.79769313486232E+308</fullMinMz>
126 <fullMaxMz>1.79769313486232E+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>/mnt/galaxy/tmp/job_working_directory/003/3118/working/BSA_min_21.mzXML</string>
136 <string>/mnt/galaxy/tmp/job_working_directory/003/3118/working/BSA_min_22.mzxml</string>
137 </filePaths>
138 <experiments>
139 <string/>
140 <string/>
141 </experiments>
142 <fractions>
143 <short>32767</short>
144 <short>32767</short>
145 </fractions>
146 <ptms>
147 <boolean>False</boolean>
148 <boolean>False</boolean>
149 </ptms>
150 <paramGroupIndices>
151 <int>0</int>
152 <int>0</int>
153 </paramGroupIndices>
154 <referenceChannel>
155 <string/>
156 <string/>
157 </referenceChannel>
158 <intensPred>False</intensPred>
159 <intensPredModelReTrain>False</intensPredModelReTrain>
160 <parameterGroups>
161 <parameterGroup>
162 <msInstrument>0</msInstrument>
163 <maxCharge>7</maxCharge>
164 <minPeakLen>2</minPeakLen>
165 <diaMinPeakLen>2</diaMinPeakLen>
166 <useMs1Centroids>False</useMs1Centroids>
167 <useMs2Centroids>False</useMs2Centroids>
168 <cutPeaks>True</cutPeaks>
169 <gapScans>1</gapScans>
170 <minTime>NaN</minTime>
171 <maxTime>NaN</maxTime>
172 <matchType>MatchFromAndTo</matchType>
173 <intensityDetermination>0</intensityDetermination>
174 <centroidMatchTol>8</centroidMatchTol>
175 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
176 <centroidHalfWidth>35</centroidHalfWidth>
177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
178 <valleyFactor>1.4</valleyFactor>
179 <isotopeValleyFactor>1.2</isotopeValleyFactor>
180 <advancedPeakSplitting>False</advancedPeakSplitting>
181 <intensityThreshold>0</intensityThreshold>
182 <labelMods>
183 <string/>
184 </labelMods>
185 <lcmsRunType>Standard</lcmsRunType>
186 <reQuantify>False</reQuantify>
187 <lfqMode>0</lfqMode>
188 <lfqSkipNorm>False</lfqSkipNorm>
189 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
190 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
191 <lfqMaxFeatures>100000</lfqMaxFeatures>
192 <neucodeMaxPpm>0</neucodeMaxPpm>
193 <neucodeResolution>0</neucodeResolution>
194 <neucodeResolutionInMda>False</neucodeResolutionInMda>
195 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
196 <fastLfq>True</fastLfq>
197 <lfqRestrictFeatures>False</lfqRestrictFeatures>
198 <lfqMinRatioCount>2</lfqMinRatioCount>
199 <maxLabeledAa>0</maxLabeledAa>
200 <maxNmods>5</maxNmods>
201 <maxMissedCleavages>0</maxMissedCleavages>
202 <multiplicity>1</multiplicity>
203 <enzymeMode>0</enzymeMode>
204 <complementaryReporterType>0</complementaryReporterType>
205 <reporterNormalization>0</reporterNormalization>
206 <neucodeIntensityMode>0</neucodeIntensityMode>
207 <fixedModifications>
208 <string>Carbamidomethyl (C)</string>
209 </fixedModifications>
210 <enzymes>
211 <string>Trypsin/P</string>
212 </enzymes>
213 <enzymesFirstSearch>
214 </enzymesFirstSearch>
215 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
216 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
217 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
218 <variableModifications>
219 <string>Oxidation (M)</string>
220 <string>Acetyl (Protein N-term)</string>
221 </variableModifications>
222 <useMultiModification>False</useMultiModification>
223 <multiModifications>
224 </multiModifications>
225 <isobaricLabels>
226 </isobaricLabels>
227 <neucodeLabels>
228 </neucodeLabels>
229 <variableModificationsFirstSearch>
230 </variableModificationsFirstSearch>
231 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
232 <additionalVariableModifications>
233 </additionalVariableModifications>
234 <additionalVariableModificationProteins>
235 </additionalVariableModificationProteins>
236 <doMassFiltering>True</doMassFiltering>
237 <firstSearchTol>20</firstSearchTol>
238 <mainSearchTol>4.5</mainSearchTol>
239 <searchTolInPpm>True</searchTolInPpm>
240 <isotopeMatchTol>2</isotopeMatchTol>
241 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
242 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
243 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
244 <checkMassDeficit>True</checkMassDeficit>
245 <recalibrationInPpm>True</recalibrationInPpm>
246 <intensityDependentCalibration>False</intensityDependentCalibration>
247 <minScoreForCalibration>70</minScoreForCalibration>
248 <matchLibraryFile>False</matchLibraryFile>
249 <libraryFile/>
250 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
251 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
252 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
253 <reporterMassTolerance>NaN</reporterMassTolerance>
254 <reporterPif>NaN</reporterPif>
255 <filterPif>False</filterPif>
256 <reporterFraction>NaN</reporterFraction>
257 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
258 <timsHalfWidth>0</timsHalfWidth>
259 <timsStep>0</timsStep>
260 <timsResolution>0</timsResolution>
261 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
262 <timsRemovePrecursor>True</timsRemovePrecursor>
263 <timsIsobaricLabels>False</timsIsobaricLabels>
264 <timsCollapseMsms>True</timsCollapseMsms>
265 <crosslinkSearch>False</crosslinkSearch>
266 <crossLinker/>
267 <minMatchXl>0</minMatchXl>
268 <minPairedPepLenXl>6</minPairedPepLenXl>
269 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
270 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
271 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
272 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
273 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
274 <crosslinkModifications>
275 </crosslinkModifications>
276 <crosslinkFastaFiles>
277 </crosslinkFastaFiles>
278 <crosslinkSites>
279 </crosslinkSites>
280 <crosslinkNetworkFiles>
281 </crosslinkNetworkFiles>
282 <crosslinkMode/>
283 <peakRefinement>False</peakRefinement>
284 <isobaricSumOverWindow>True</isobaricSumOverWindow>
285 <isobaricWeightExponent>0.75</isobaricWeightExponent>
286 <diaLibraryType>0</diaLibraryType>
287 <diaLibraryPath/>
288 <diaPeptidePaths>
289 </diaPeptidePaths>
290 <diaEvidencePaths>
291 </diaEvidencePaths>
292 <diaMsmsPaths>
293 </diaMsmsPaths>
294 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
295 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
296 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
297 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
298 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
299 <diaScoreN>7</diaScoreN>
300 <diaMinScore>2.99</diaMinScore>
301 <diaPrecursorQuant>False</diaPrecursorQuant>
302 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
303 </parameterGroup>
304 </parameterGroups>
305 <msmsParamsArray>
306 <msmsParams>
307 <Name>FTMS</Name>
308 <MatchTolerance>20</MatchTolerance>
309 <MatchToleranceInPpm>True</MatchToleranceInPpm>
310 <DeisotopeTolerance>7</DeisotopeTolerance>
311 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
312 <DeNovoTolerance>10</DeNovoTolerance>
313 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
314 <Deisotope>True</Deisotope>
315 <Topx>12</Topx>
316 <TopxInterval>100</TopxInterval>
317 <HigherCharges>True</HigherCharges>
318 <IncludeWater>True</IncludeWater>
319 <IncludeAmmonia>True</IncludeAmmonia>
320 <DependentLosses>True</DependentLosses>
321 <Recalibration>False</Recalibration>
322 </msmsParams>
323 <msmsParams>
324 <Name>ITMS</Name>
325 <MatchTolerance>0.5</MatchTolerance>
326 <MatchToleranceInPpm>False</MatchToleranceInPpm>
327 <DeisotopeTolerance>0.15</DeisotopeTolerance>
328 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
329 <DeNovoTolerance>0.25</DeNovoTolerance>
330 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
331 <Deisotope>False</Deisotope>
332 <Topx>8</Topx>
333 <TopxInterval>100</TopxInterval>
334 <HigherCharges>True</HigherCharges>
335 <IncludeWater>True</IncludeWater>
336 <IncludeAmmonia>True</IncludeAmmonia>
337 <DependentLosses>True</DependentLosses>
338 <Recalibration>False</Recalibration>
339 </msmsParams>
340 <msmsParams>
341 <Name>TOF</Name>
342 <MatchTolerance>40</MatchTolerance>
343 <MatchToleranceInPpm>True</MatchToleranceInPpm>
344 <DeisotopeTolerance>0.01</DeisotopeTolerance>
345 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
346 <DeNovoTolerance>0.02</DeNovoTolerance>
347 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
348 <Deisotope>True</Deisotope>
349 <Topx>10</Topx>
350 <TopxInterval>100</TopxInterval>
351 <HigherCharges>True</HigherCharges>
352 <IncludeWater>True</IncludeWater>
353 <IncludeAmmonia>True</IncludeAmmonia>
354 <DependentLosses>True</DependentLosses>
355 <Recalibration>False</Recalibration>
356 </msmsParams>
357 <msmsParams>
358 <Name>Unknown</Name>
359 <MatchTolerance>20</MatchTolerance>
360 <MatchToleranceInPpm>True</MatchToleranceInPpm>
361 <DeisotopeTolerance>7</DeisotopeTolerance>
362 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
363 <DeNovoTolerance>10</DeNovoTolerance>
364 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
365 <Deisotope>True</Deisotope>
366 <Topx>12</Topx>
367 <TopxInterval>100</TopxInterval>
368 <HigherCharges>True</HigherCharges>
369 <IncludeWater>True</IncludeWater>
370 <IncludeAmmonia>True</IncludeAmmonia>
371 <DependentLosses>True</DependentLosses>
372 <Recalibration>False</Recalibration>
373 </msmsParams>
374 </msmsParamsArray>
375 <fragmentationParamsArray>
376 <fragmentationParams>
377 <Name>CID</Name>
378 <Connected>False</Connected>
379 <ConnectedScore0>1</ConnectedScore0>
380 <ConnectedScore1>1</ConnectedScore1>
381 <ConnectedScore2>1</ConnectedScore2>
382 <InternalFragments>False</InternalFragments>
383 <InternalFragmentWeight>1</InternalFragmentWeight>
384 <InternalFragmentAas>KRH</InternalFragmentAas>
385 </fragmentationParams>
386 <fragmentationParams>
387 <Name>HCD</Name>
388 <Connected>False</Connected>
389 <ConnectedScore0>1</ConnectedScore0>
390 <ConnectedScore1>1</ConnectedScore1>
391 <ConnectedScore2>1</ConnectedScore2>
392 <InternalFragments>False</InternalFragments>
393 <InternalFragmentWeight>1</InternalFragmentWeight>
394 <InternalFragmentAas>KRH</InternalFragmentAas>
395 </fragmentationParams>
396 <fragmentationParams>
397 <Name>ETD</Name>
398 <Connected>False</Connected>
399 <ConnectedScore0>1</ConnectedScore0>
400 <ConnectedScore1>1</ConnectedScore1>
401 <ConnectedScore2>1</ConnectedScore2>
402 <InternalFragments>False</InternalFragments>
403 <InternalFragmentWeight>1</InternalFragmentWeight>
404 <InternalFragmentAas>KRH</InternalFragmentAas>
405 </fragmentationParams>
406 <fragmentationParams>
407 <Name>PQD</Name>
408 <Connected>False</Connected>
409 <ConnectedScore0>1</ConnectedScore0>
410 <ConnectedScore1>1</ConnectedScore1>
411 <ConnectedScore2>1</ConnectedScore2>
412 <InternalFragments>False</InternalFragments>
413 <InternalFragmentWeight>1</InternalFragmentWeight>
414 <InternalFragmentAas>KRH</InternalFragmentAas>
415 </fragmentationParams>
416 <fragmentationParams>
417 <Name>ETHCD</Name>
418 <Connected>False</Connected>
419 <ConnectedScore0>1</ConnectedScore0>
420 <ConnectedScore1>1</ConnectedScore1>
421 <ConnectedScore2>1</ConnectedScore2>
422 <InternalFragments>False</InternalFragments>
423 <InternalFragmentWeight>1</InternalFragmentWeight>
424 <InternalFragmentAas>KRH</InternalFragmentAas>
425 </fragmentationParams>
426 <fragmentationParams>
427 <Name>ETCID</Name>
428 <Connected>False</Connected>
429 <ConnectedScore0>1</ConnectedScore0>
430 <ConnectedScore1>1</ConnectedScore1>
431 <ConnectedScore2>1</ConnectedScore2>
432 <InternalFragments>False</InternalFragments>
433 <InternalFragmentWeight>1</InternalFragmentWeight>
434 <InternalFragmentAas>KRH</InternalFragmentAas>
435 </fragmentationParams>
436 <fragmentationParams>
437 <Name>UVPD</Name>
438 <Connected>False</Connected>
439 <ConnectedScore0>1</ConnectedScore0>
440 <ConnectedScore1>1</ConnectedScore1>
441 <ConnectedScore2>1</ConnectedScore2>
442 <InternalFragments>False</InternalFragments>
443 <InternalFragmentWeight>1</InternalFragmentWeight>
444 <InternalFragmentAas>KRH</InternalFragmentAas>
445 </fragmentationParams>
446 <fragmentationParams>
447 <Name>Unknown</Name>
448 <Connected>False</Connected>
449 <ConnectedScore0>1</ConnectedScore0>
450 <ConnectedScore1>1</ConnectedScore1>
451 <ConnectedScore2>1</ConnectedScore2>
452 <InternalFragments>False</InternalFragments>
453 <InternalFragmentWeight>1</InternalFragmentWeight>
454 <InternalFragmentAas>KRH</InternalFragmentAas>
455 </fragmentationParams>
456 </fragmentationParamsArray>
457 </MaxQuantParams>
458