Mercurial > repos > galaxyp > maxquant

annotate test-data/mqpar/mqpar.xml @ 21:8934bc76bb52 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
author galaxyp
date Mon, 19 Jun 2023 17:02:17 +0000
parents 97a7f34fcb6a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
1 <?xml version="1.0" ?>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
2 <MaxQuantParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
3 <fastaFiles>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
4 <FastaFileInfo>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
5 <fastaFilePath>bsa.fasta</fastaFilePath>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
7 <descriptionParseRule>&gt;(.*)</descriptionParseRule>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
8 <taxonomyParseRule/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
9 <variationParseRule/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
10 <modificationParseRule/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
11 <taxonomyId/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
12 </FastaFileInfo>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
13 </fastaFiles>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
14 <fastaFilesProteogenomics>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
15 </fastaFilesProteogenomics>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
16 <fastaFilesFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
17 </fastaFilesFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
18 <fixedSearchFolder/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
19 <andromedaCacheSize>350000</andromedaCacheSize>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
20 <advancedRatios>True</advancedRatios>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
21 <pvalThres>0.005</pvalThres>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
22 <rtShift>False</rtShift>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
23 <separateLfq>False</separateLfq>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
24 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
25 <lfqRequireMsms>True</lfqRequireMsms>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
26 <decoyMode>revert</decoyMode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
27 <boxCarMode>all</boxCarMode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
28 <includeContaminants>True</includeContaminants>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
29 <maxPeptideMass>4600</maxPeptideMass>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
30 <epsilonMutationScore>True</epsilonMutationScore>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
31 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
32 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
33 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
34 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
35 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
36 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
37 <secondPeptide>True</secondPeptide>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
38 <matchBetweenRuns>False</matchBetweenRuns>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
39 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
40 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
41 <dependentPeptides>False</dependentPeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
42 <dependentPeptideFdr>0</dependentPeptideFdr>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
43 <dependentPeptideMassBin>0</dependentPeptideMassBin>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
44 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
45 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
46 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
47 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
48 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
49 <ibaq>False</ibaq>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
50 <top3>False</top3>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
51 <independentEnzymes>False</independentEnzymes>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
52 <useDeltaScore>False</useDeltaScore>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
53 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
54 <taxonomyLevel>Species</taxonomyLevel>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
55 <avalon>False</avalon>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
56 <nModColumns>3</nModColumns>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
57 <ibaqLogFit>False</ibaqLogFit>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
58 <razorProteinFdr>True</razorProteinFdr>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
59 <deNovoSequencing>False</deNovoSequencing>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
60 <deNovoVarMods>True</deNovoVarMods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
61 <massDifferenceSearch>False</massDifferenceSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
62 <isotopeCalc>False</isotopeCalc>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
63 <writePeptidesForSpectrumFile/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
64 <intensityPredictionsFile>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
65 </intensityPredictionsFile>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
66 <minPepLen>7</minPepLen>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
67 <psmFdrCrosslink>0.01</psmFdrCrosslink>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
68 <peptideFdr>0.01</peptideFdr>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
69 <proteinFdr>0.01</proteinFdr>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
70 <siteFdr>0.01</siteFdr>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
71 <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
72 <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
73 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
74 <minPeptides>1</minPeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
75 <minRazorPeptides>1</minRazorPeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
76 <minUniquePeptides>0</minUniquePeptides>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
77 <useCounterparts>False</useCounterparts>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
78 <advancedSiteIntensities>True</advancedSiteIntensities>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
79 <customProteinQuantification>False</customProteinQuantification>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
80 <customProteinQuantificationFile/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
81 <minRatioCount>2</minRatioCount>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
82 <restrictProteinQuantification>True</restrictProteinQuantification>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
83 <restrictMods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
84 <string>Oxidation (M)</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
85 <string>Acetyl (Protein N-term)</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
86 </restrictMods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
87 <matchingTimeWindow>0</matchingTimeWindow>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
88 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
89 <alignmentTimeWindow>0</alignmentTimeWindow>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
90 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
91 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
92 <compositionPrediction>0</compositionPrediction>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
93 <quantMode>1</quantMode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
94 <massDifferenceMods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
95 </massDifferenceMods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
96 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
97 <writeMsScansTable>False</writeMsScansTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
98 <writeMsmsScansTable>True</writeMsmsScansTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
99 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
100 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
101 <writeMs3ScansTable>True</writeMs3ScansTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
102 <writeAllPeptidesTable>True</writeAllPeptidesTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
103 <writeMzRangeTable>True</writeMzRangeTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
104 <writeDiaFragmentTable>False</writeDiaFragmentTable>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
105 <writeMzTab>False</writeMzTab>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
106 <disableMd5>False</disableMd5>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
107 <cacheBinInds>True</cacheBinInds>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
108 <etdIncludeB>False</etdIncludeB>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
109 <ms2PrecursorShift>0</ms2PrecursorShift>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
110 <complementaryIonPpm>20</complementaryIonPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
111 <variationParseRule/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
112 <variationMode>none</variationMode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
113 <useSeriesReporters>False</useSeriesReporters>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
114 <name>session1</name>
21
8934bc76bb52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
galaxyp
parents: 15
diff changeset
115 <maxQuantVersion>2.0.3.0</maxQuantVersion>
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
116 <pluginFolder/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
117 <numThreads>1</numThreads>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
118 <emailAddress/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
119 <smtpHost/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
120 <emailFromAddress/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
121 <fixedCombinedFolder/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
122 <fullMinMz>-1.79769313486232E+308</fullMinMz>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
123 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
124 <sendEmail>False</sendEmail>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
125 <ionCountIntensities>False</ionCountIntensities>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
126 <verboseColumnHeaders>False</verboseColumnHeaders>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
127 <calcPeakProperties>False</calcPeakProperties>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
128 <showCentroidMassDifferences>False</showCentroidMassDifferences>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
129 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
130 <useDotNetCore>True</useDotNetCore>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
131 <profilePerformance>False</profilePerformance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
132 <filePaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
133 <string>BSA_min_21.mzXML</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
134 <string>BSA_min_22.mzxml</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
135 </filePaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
136 <experiments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
137 <string/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
138 <string/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
139 </experiments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
140 <fractions>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
141 <short>32767</short>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
142 <short>32767</short>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
143 </fractions>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
144 <ptms>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
145 <boolean>False</boolean>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
146 <boolean>False</boolean>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
147 </ptms>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
148 <paramGroupIndices>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
149 <int>0</int>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
150 <int>0</int>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
151 </paramGroupIndices>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
152 <referenceChannel>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
153 <string/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
154 <string/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
155 </referenceChannel>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
156 <intensPred>False</intensPred>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
157 <intensPredModelReTrain>False</intensPredModelReTrain>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
158 <parameterGroups>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
159 <parameterGroup>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
160 <msInstrument>0</msInstrument>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
161 <maxCharge>7</maxCharge>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
162 <minPeakLen>2</minPeakLen>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
163 <diaMinPeakLen>2</diaMinPeakLen>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
164 <useMs1Centroids>False</useMs1Centroids>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
165 <useMs2Centroids>False</useMs2Centroids>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
166 <cutPeaks>True</cutPeaks>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
167 <gapScans>1</gapScans>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
168 <minTime>NaN</minTime>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
169 <maxTime>NaN</maxTime>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
170 <matchType>MatchFromAndTo</matchType>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
171 <intensityDetermination>0</intensityDetermination>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
172 <centroidMatchTol>8</centroidMatchTol>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
173 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
174 <centroidHalfWidth>35</centroidHalfWidth>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
175 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
176 <valleyFactor>1.4</valleyFactor>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
177 <isotopeValleyFactor>1.2</isotopeValleyFactor>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
178 <advancedPeakSplitting>False</advancedPeakSplitting>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
179 <intensityThresholdMs1>0</intensityThresholdMs1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
180 <intensityThresholdMs2>0</intensityThresholdMs2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
181 <labelMods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
182 <string/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
183 </labelMods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
184 <lcmsRunType>Standard</lcmsRunType>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
185 <reQuantify>False</reQuantify>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
186 <lfqMode>0</lfqMode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
187 <lfqSkipNorm>False</lfqSkipNorm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
188 <lfqNormClusterSize>80</lfqNormClusterSize>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
189 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
190 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
191 <lfqMaxFeatures>100000</lfqMaxFeatures>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
192 <neucodeMaxPpm>0</neucodeMaxPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
193 <neucodeResolution>0</neucodeResolution>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
194 <neucodeResolutionInMda>False</neucodeResolutionInMda>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
195 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
196 <fastLfq>True</fastLfq>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
197 <lfqRestrictFeatures>False</lfqRestrictFeatures>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
198 <lfqMinRatioCount>2</lfqMinRatioCount>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
199 <maxLabeledAa>0</maxLabeledAa>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
200 <maxNmods>5</maxNmods>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
201 <maxMissedCleavages>0</maxMissedCleavages>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
202 <multiplicity>1</multiplicity>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
203 <enzymeMode>0</enzymeMode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
204 <complementaryReporterType>0</complementaryReporterType>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
205 <reporterNormalization>0</reporterNormalization>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
206 <neucodeIntensityMode>0</neucodeIntensityMode>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
207 <fixedModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
208 <string>Carbamidomethyl (C)</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
209 </fixedModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
210 <enzymes>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
211 <string>Trypsin/P</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
212 </enzymes>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
213 <enzymesFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
214 </enzymesFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
215 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
216 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
217 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
218 <variableModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
219 <string>Oxidation (M)</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
220 <string>Acetyl (Protein N-term)</string>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
221 </variableModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
222 <useMultiModification>False</useMultiModification>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
223 <multiModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
224 </multiModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
225 <isobaricLabels>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
226 </isobaricLabels>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
227 <neucodeLabels>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
228 </neucodeLabels>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
229 <variableModificationsFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
230 </variableModificationsFirstSearch>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
231 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
232 <additionalVariableModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
233 </additionalVariableModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
234 <additionalVariableModificationProteins>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
235 </additionalVariableModificationProteins>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
236 <doMassFiltering>True</doMassFiltering>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
237 <firstSearchTol>20</firstSearchTol>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
238 <mainSearchTol>4.5</mainSearchTol>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
239 <searchTolInPpm>True</searchTolInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
240 <isotopeMatchTol>2</isotopeMatchTol>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
241 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
242 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
243 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
244 <checkMassDeficit>True</checkMassDeficit>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
245 <recalibrationInPpm>True</recalibrationInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
246 <intensityDependentCalibration>False</intensityDependentCalibration>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
247 <minScoreForCalibration>70</minScoreForCalibration>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
248 <matchLibraryFile>False</matchLibraryFile>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
249 <libraryFile/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
250 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
251 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
252 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
253 <reporterMassTolerance>NaN</reporterMassTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
254 <reporterPif>NaN</reporterPif>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
255 <filterPif>False</filterPif>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
256 <reporterFraction>NaN</reporterFraction>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
257 <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
258 <timsHalfWidth>0</timsHalfWidth>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
259 <timsStep>0</timsStep>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
260 <timsResolution>0</timsResolution>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
261 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
262 <timsRemovePrecursor>True</timsRemovePrecursor>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
263 <timsIsobaricLabels>False</timsIsobaricLabels>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
264 <timsCollapseMsms>True</timsCollapseMsms>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
265 <crossLinkingType>0</crossLinkingType>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
266 <crossLinker/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
267 <minMatchXl>0</minMatchXl>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
268 <minPairedPepLenXl>6</minPairedPepLenXl>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
269 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
270 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
271 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
272 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
273 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
274 <crosslinkModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
275 </crosslinkModifications>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
276 <crosslinkFastaFiles>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
277 </crosslinkFastaFiles>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
278 <crosslinkSites>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
279 </crosslinkSites>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
280 <crosslinkNetworkFiles>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
281 </crosslinkNetworkFiles>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
282 <crosslinkMode/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
283 <peakRefinement>False</peakRefinement>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
284 <isobaricSumOverWindow>True</isobaricSumOverWindow>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
285 <isobaricWeightExponent>0.75</isobaricWeightExponent>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
286 <diaLibraryType>0</diaLibraryType>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
287 <diaLibraryPath/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
288 <diaPeptidePaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
289 </diaPeptidePaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
290 <diaEvidencePaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
291 </diaEvidencePaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
292 <diaMsmsPaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
293 </diaMsmsPaths>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
294 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
295 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
296 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
297 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
298 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
299 <diaScoreN>7</diaScoreN>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
300 <diaMinScore>2.99</diaMinScore>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
301 <diaXgBoostBaseScore>0.4</diaXgBoostBaseScore>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
302 <diaXgBoostSubSample>0.9</diaXgBoostSubSample>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
303 <centroidPosition>0</centroidPosition>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
304 <diaQuantMethod>7</diaQuantMethod>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
305 <diaFeatureQuantMethod>2</diaFeatureQuantMethod>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
306 <lfqNormType>1</lfqNormType>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
307 <diaTopNForQuant>10</diaTopNForQuant>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
308 <diaMinMsmsIntensityForQuant>0</diaMinMsmsIntensityForQuant>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
309 <diaTopMsmsIntensityQuantileForQuant>0.85</diaTopMsmsIntensityQuantileForQuant>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
310 <diaPrecursorFilterType>0</diaPrecursorFilterType>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
311 <diaMinFragmentOverlapScore>1</diaMinFragmentOverlapScore>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
312 <diaMinPrecursorScore>0.5</diaMinPrecursorScore>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
313 <diaMinProfileCorrelation>0</diaMinProfileCorrelation>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
314 <diaXgBoostMinChildWeight>9</diaXgBoostMinChildWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
315 <diaXgBoostMaximumTreeDepth>12</diaXgBoostMaximumTreeDepth>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
316 <diaXgBoostEstimators>580</diaXgBoostEstimators>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
317 <diaXgBoostGamma>0.9</diaXgBoostGamma>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
318 <diaXgBoostMaxDeltaStep>3</diaXgBoostMaxDeltaStep>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
319 <diaGlobalMl>True</diaGlobalMl>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
320 <diaAdaptiveMassAccuracy>False</diaAdaptiveMassAccuracy>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
321 <diaMassWindowFactor>3.3</diaMassWindowFactor>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
322 <diaRtPrediction>False</diaRtPrediction>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
323 <diaRtPredictionSecondRound>False</diaRtPredictionSecondRound>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
324 <diaNoMl>False</diaNoMl>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
325 <diaPermuteRt>False</diaPermuteRt>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
326 <diaPermuteCcs>False</diaPermuteCcs>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
327 <diaBackgroundSubtraction>False</diaBackgroundSubtraction>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
328 <diaBackgroundSubtractionQuantile>0.5</diaBackgroundSubtractionQuantile>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
329 <diaBackgroundSubtractionFactor>4</diaBackgroundSubtractionFactor>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
330 <diaLfqWeightedMedian>False</diaLfqWeightedMedian>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
331 </parameterGroup>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
332 </parameterGroups>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
333 <msmsParamsArray>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
334 <msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
335 <Name>FTMS</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
336 <MatchTolerance>20</MatchTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
337 <MatchToleranceInPpm>True</MatchToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
338 <DeisotopeTolerance>7</DeisotopeTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
339 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
340 <DeNovoTolerance>10</DeNovoTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
341 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
342 <Deisotope>True</Deisotope>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
343 <Topx>12</Topx>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
344 <TopxInterval>100</TopxInterval>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
345 <HigherCharges>True</HigherCharges>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
346 <IncludeWater>True</IncludeWater>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
347 <IncludeAmmonia>True</IncludeAmmonia>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
348 <DependentLosses>True</DependentLosses>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
349 <Recalibration>False</Recalibration>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
350 </msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
351 <msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
352 <Name>ITMS</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
353 <MatchTolerance>0.5</MatchTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
354 <MatchToleranceInPpm>False</MatchToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
355 <DeisotopeTolerance>0.15</DeisotopeTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
356 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
357 <DeNovoTolerance>0.25</DeNovoTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
358 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
359 <Deisotope>False</Deisotope>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
360 <Topx>8</Topx>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
361 <TopxInterval>100</TopxInterval>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
362 <HigherCharges>True</HigherCharges>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
363 <IncludeWater>True</IncludeWater>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
364 <IncludeAmmonia>True</IncludeAmmonia>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
365 <DependentLosses>True</DependentLosses>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
366 <Recalibration>False</Recalibration>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
367 </msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
368 <msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
369 <Name>TOF</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
370 <MatchTolerance>40</MatchTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
371 <MatchToleranceInPpm>True</MatchToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
372 <DeisotopeTolerance>0.01</DeisotopeTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
373 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
374 <DeNovoTolerance>0.02</DeNovoTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
375 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
376 <Deisotope>True</Deisotope>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
377 <Topx>10</Topx>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
378 <TopxInterval>100</TopxInterval>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
379 <HigherCharges>True</HigherCharges>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
380 <IncludeWater>True</IncludeWater>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
381 <IncludeAmmonia>True</IncludeAmmonia>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
382 <DependentLosses>True</DependentLosses>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
383 <Recalibration>False</Recalibration>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
384 </msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
385 <msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
386 <Name>Unknown</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
387 <MatchTolerance>20</MatchTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
388 <MatchToleranceInPpm>True</MatchToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
389 <DeisotopeTolerance>7</DeisotopeTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
390 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
391 <DeNovoTolerance>10</DeNovoTolerance>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
392 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
393 <Deisotope>True</Deisotope>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
394 <Topx>12</Topx>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
395 <TopxInterval>100</TopxInterval>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
396 <HigherCharges>True</HigherCharges>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
397 <IncludeWater>True</IncludeWater>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
398 <IncludeAmmonia>True</IncludeAmmonia>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
399 <DependentLosses>True</DependentLosses>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
400 <Recalibration>False</Recalibration>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
401 </msmsParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
402 </msmsParamsArray>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
403 <fragmentationParamsArray>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
404 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
405 <Name>CID</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
406 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
407 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
408 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
409 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
410 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
411 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
412 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
413 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
414 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
415 <Name>HCD</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
416 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
417 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
418 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
419 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
420 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
421 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
422 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
423 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
424 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
425 <Name>ETD</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
426 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
427 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
428 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
429 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
430 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
431 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
432 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
433 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
434 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
435 <Name>PQD</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
436 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
437 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
438 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
439 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
440 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
441 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
442 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
443 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
444 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
445 <Name>ETHCD</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
446 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
447 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
448 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
449 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
450 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
451 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
452 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
453 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
454 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
455 <Name>ETCID</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
456 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
457 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
458 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
459 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
460 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
461 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
462 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
463 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
464 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
465 <Name>UVPD</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
466 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
467 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
468 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
469 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
470 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
471 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
472 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
473 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
474 <fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
475 <Name>Unknown</Name>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
476 <Connected>False</Connected>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
477 <ConnectedScore0>1</ConnectedScore0>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
478 <ConnectedScore1>1</ConnectedScore1>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
479 <ConnectedScore2>1</ConnectedScore2>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
480 <InternalFragments>False</InternalFragments>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
481 <InternalFragmentWeight>1</InternalFragmentWeight>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
482 <InternalFragmentAas>KRH</InternalFragmentAas>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
483 </fragmentationParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
484 </fragmentationParamsArray>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
485 </MaxQuantParams>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents:
diff changeset
486