Mercurial > repos > galaxyp > maxquant

annotate test-data/06/mqpar.xml @ 10:f522c08e900c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
author galaxyp
date Fri, 12 Mar 2021 08:41:06 +0000
parents
children 0839f84def5e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
1 <?xml version="1.0" ?>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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2 <MaxQuantParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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3 <fastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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4 <FastaFileInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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5 <fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat</fastaFilePath>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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6 <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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7 <descriptionParseRule>&gt;(.*)</descriptionParseRule>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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8 <taxonomyParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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9 <variationParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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10 <modificationParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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11 <taxonomyId/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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12 </FastaFileInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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13 </fastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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14 <fastaFilesProteogenomics>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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15 </fastaFilesProteogenomics>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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16 <fastaFilesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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17 </fastaFilesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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18 <fixedSearchFolder/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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19 <andromedaCacheSize>350000</andromedaCacheSize>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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20 <advancedRatios>True</advancedRatios>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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21 <pvalThres>0.005</pvalThres>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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22 <neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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23 <neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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24 <rtShift>False</rtShift>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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25 <separateLfq>False</separateLfq>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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26 <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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27 <lfqRequireMsms>True</lfqRequireMsms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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28 <decoyMode>randomize</decoyMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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29 <boxCarMode>all</boxCarMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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30 <includeContaminants>False</includeContaminants>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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31 <maxPeptideMass>4600</maxPeptideMass>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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32 <epsilonMutationScore>True</epsilonMutationScore>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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33 <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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34 <proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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35 <minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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36 <minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
37 <minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
38 <minScoreModifiedPeptides>40</minScoreModifiedPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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39 <secondPeptide>True</secondPeptide>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
40 <matchBetweenRuns>False</matchBetweenRuns>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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41 <matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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42 <matchBetweenRunsFdr>False</matchBetweenRunsFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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43 <dependentPeptides>False</dependentPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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44 <dependentPeptideFdr>0</dependentPeptideFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
45 <dependentPeptideMassBin>0</dependentPeptideMassBin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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diff changeset
46 <dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
47 <dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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48 <dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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49 <dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
50 <dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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51 <msmsConnection>False</msmsConnection>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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52 <ibaq>False</ibaq>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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53 <top3>False</top3>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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54 <independentEnzymes>False</independentEnzymes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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55 <useDeltaScore>False</useDeltaScore>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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56 <splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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57 <taxonomyLevel>Species</taxonomyLevel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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58 <avalon>False</avalon>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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59 <nModColumns>3</nModColumns>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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60 <ibaqLogFit>False</ibaqLogFit>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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61 <razorProteinFdr>True</razorProteinFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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62 <deNovoSequencing>False</deNovoSequencing>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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63 <deNovoVarMods>True</deNovoVarMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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64 <massDifferenceSearch>False</massDifferenceSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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65 <isotopeCalc>False</isotopeCalc>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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66 <writePeptidesForSpectrumFile/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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67 <intensityPredictionsFile>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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68 </intensityPredictionsFile>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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69 <minPepLen>7</minPepLen>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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70 <psmFdrCrosslink>0.01</psmFdrCrosslink>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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71 <peptideFdr>0.5</peptideFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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72 <proteinFdr>0.4</proteinFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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73 <siteFdr>0.01</siteFdr>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
74 <minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
75 <maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
76 <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
77 <minPeptides>1</minPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
78 <minRazorPeptides>1</minRazorPeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
79 <minUniquePeptides>0</minUniquePeptides>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
80 <useCounterparts>True</useCounterparts>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
81 <advancedSiteIntensities>True</advancedSiteIntensities>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
82 <customProteinQuantification>False</customProteinQuantification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
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diff changeset
83 <customProteinQuantificationFile/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
84 <minRatioCount>2</minRatioCount>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
85 <restrictProteinQuantification>True</restrictProteinQuantification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
86 <restrictMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
87 <string>Pro5</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
88 <string>Pro6</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
89 </restrictMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
90 <matchingTimeWindow>0</matchingTimeWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
91 <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
92 <alignmentTimeWindow>0</alignmentTimeWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
93 <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
94 <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
95 <compositionPrediction>0</compositionPrediction>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
96 <quantMode>0</quantMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
97 <massDifferenceMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
98 </massDifferenceMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
99 <mainSearchMaxCombinations>200</mainSearchMaxCombinations>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
100 <writeMsScansTable>False</writeMsScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
101 <writeMsmsScansTable>True</writeMsmsScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
102 <writePasefMsmsScansTable>True</writePasefMsmsScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
103 <writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
104 <writeMs3ScansTable>True</writeMs3ScansTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
105 <writeAllPeptidesTable>True</writeAllPeptidesTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
106 <writeMzRangeTable>True</writeMzRangeTable>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
107 <writeMzTab>True</writeMzTab>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
108 <disableMd5>False</disableMd5>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
109 <cacheBinInds>True</cacheBinInds>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
110 <etdIncludeB>False</etdIncludeB>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
111 <ms2PrecursorShift>0</ms2PrecursorShift>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
112 <complementaryIonPpm>20</complementaryIonPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
113 <variationParseRule/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
114 <variationMode>none</variationMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
115 <useSeriesReporters>False</useSeriesReporters>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
116 <name>templateSession</name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
117 <maxQuantVersion>1.6.10.43</maxQuantVersion>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
118 <tempFolder/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
119 <pluginFolder/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
120 <numThreads>1</numThreads>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
121 <emailAddress/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
122 <smtpHost/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
123 <emailFromAddress/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
124 <fixedCombinedFolder/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
125 <fullMinMz>-1.79769313486232E+308</fullMinMz>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
126 <fullMaxMz>1.79769313486232E+308</fullMaxMz>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
127 <sendEmail>False</sendEmail>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
128 <ionCountIntensities>False</ionCountIntensities>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
129 <verboseColumnHeaders>False</verboseColumnHeaders>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
130 <calcPeakProperties>False</calcPeakProperties>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
131 <showCentroidMassDifferences>False</showCentroidMassDifferences>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
132 <showIsotopeMassDifferences>False</showIsotopeMassDifferences>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
133 <useDotNetCore>False</useDotNetCore>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
134 <filePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
135 <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_23.mzXML</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
136 <string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_22.mzxml</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
137 </filePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
138 <experiments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
139 <string>BSA_min_23.mzXML</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
140 <string>BSA_min_22.mzxml</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
141 </experiments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
142 <fractions>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
143 <short>32767</short>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
144 <short>32767</short>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
145 </fractions>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
146 <ptms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
147 <boolean>False</boolean>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
148 <boolean>False</boolean>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
149 </ptms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
150 <paramGroupIndices>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
151 <int>0</int>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
152 <int>1</int>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
153 </paramGroupIndices>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
154 <referenceChannel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
155 <string/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
156 <string/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
157 </referenceChannel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
158 <intensPred>False</intensPred>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
159 <intensPredModelReTrain>False</intensPredModelReTrain>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
160 <parameterGroups>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
161 <parameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
162 <msInstrument>0</msInstrument>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
163 <maxCharge>7</maxCharge>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
164 <minPeakLen>2</minPeakLen>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
165 <diaMinPeakLen>2</diaMinPeakLen>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
166 <useMs1Centroids>False</useMs1Centroids>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
167 <useMs2Centroids>False</useMs2Centroids>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
168 <cutPeaks>True</cutPeaks>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
169 <gapScans>1</gapScans>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
170 <minTime>NaN</minTime>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
171 <maxTime>NaN</maxTime>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
172 <matchType>MatchFromAndTo</matchType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
173 <intensityDetermination>0</intensityDetermination>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
174 <centroidMatchTol>8</centroidMatchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
175 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
176 <centroidHalfWidth>35</centroidHalfWidth>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
177 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
178 <valleyFactor>1.4</valleyFactor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
179 <isotopeValleyFactor>1.2</isotopeValleyFactor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
180 <advancedPeakSplitting>False</advancedPeakSplitting>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
181 <intensityThreshold>0</intensityThreshold>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
182 <labelMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
183 <string/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
184 </labelMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
185 <lcmsRunType>Reporter ion MS3</lcmsRunType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
186 <reQuantify>False</reQuantify>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
187 <lfqMode>0</lfqMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
188 <lfqSkipNorm>False</lfqSkipNorm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
189 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
190 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
191 <lfqMaxFeatures>100000</lfqMaxFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
192 <neucodeMaxPpm>0</neucodeMaxPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
193 <neucodeResolution>0</neucodeResolution>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
194 <neucodeResolutionInMda>False</neucodeResolutionInMda>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
195 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
196 <fastLfq>True</fastLfq>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
197 <lfqRestrictFeatures>False</lfqRestrictFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
198 <lfqMinRatioCount>2</lfqMinRatioCount>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
199 <maxLabeledAa>0</maxLabeledAa>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
200 <maxNmods>5</maxNmods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
201 <maxMissedCleavages>2</maxMissedCleavages>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
202 <multiplicity>1</multiplicity>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
203 <enzymeMode>0</enzymeMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
204 <complementaryReporterType>0</complementaryReporterType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
205 <reporterNormalization>0</reporterNormalization>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
206 <neucodeIntensityMode>0</neucodeIntensityMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
207 <fixedModifications/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
208 <enzymes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
209 <string>Trypsin/P</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
210 </enzymes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
211 <enzymesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
212 </enzymesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
213 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
214 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
215 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
216 <variableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
217 <string>Oxidation (M)</string>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
218 </variableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
219 <useMultiModification>False</useMultiModification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
220 <multiModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
221 </multiModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
222 <isobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
223 <IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
224 <internalLabel>TMT2plex-Lys126</internalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
225 <terminalLabel>TMT2plex-Nter126</terminalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
226 <correctionFactorM2>0</correctionFactorM2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
227 <correctionFactorM1>0</correctionFactorM1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
228 <correctionFactorP1>6.7</correctionFactorP1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
229 <correctionFactorP2>3</correctionFactorP2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
230 <tmtLike>True</tmtLike>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
231 </IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
232 <IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
233 <internalLabel>TMT2plex-Lys127</internalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
234 <terminalLabel>TMT2plex-Nter127</terminalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
235 <correctionFactorM2>0</correctionFactorM2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
236 <correctionFactorM1>0</correctionFactorM1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
237 <correctionFactorP1>0</correctionFactorP1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
238 <correctionFactorP2>0</correctionFactorP2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
239 <tmtLike>True</tmtLike>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
240 </IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
241 </isobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
242 <neucodeLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
243 </neucodeLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
244 <variableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
245 </variableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
246 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
247 <additionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
248 </additionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
249 <additionalVariableModificationProteins>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
250 </additionalVariableModificationProteins>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
251 <doMassFiltering>True</doMassFiltering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
252 <firstSearchTol>20</firstSearchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
253 <mainSearchTol>4.5</mainSearchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
254 <searchTolInPpm>True</searchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
255 <isotopeMatchTol>2</isotopeMatchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
256 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
257 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
258 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
259 <checkMassDeficit>True</checkMassDeficit>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
260 <recalibrationInPpm>True</recalibrationInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
261 <intensityDependentCalibration>False</intensityDependentCalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
262 <minScoreForCalibration>70</minScoreForCalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
263 <matchLibraryFile>False</matchLibraryFile>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
264 <libraryFile/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
265 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
266 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
267 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
268 <reporterMassTolerance>0.003</reporterMassTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
269 <reporterPif>0</reporterPif>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
270 <filterPif>False</filterPif>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
271 <reporterFraction>0</reporterFraction>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
272 <reporterBasePeakRatio>0</reporterBasePeakRatio>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
273 <timsHalfWidth>0</timsHalfWidth>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
274 <timsStep>0</timsStep>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
275 <timsResolution>0</timsResolution>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
276 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
277 <timsRemovePrecursor>True</timsRemovePrecursor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
278 <timsIsobaricLabels>False</timsIsobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
279 <timsCollapseMsms>True</timsCollapseMsms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
280 <crosslinkSearch>False</crosslinkSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
281 <crossLinker/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
282 <minMatchXl>0</minMatchXl>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
283 <minPairedPepLenXl>6</minPairedPepLenXl>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
284 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
285 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
286 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
287 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
288 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
289 <crosslinkModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
290 </crosslinkModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
291 <crosslinkFastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
292 </crosslinkFastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
293 <crosslinkSites>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
294 </crosslinkSites>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
295 <crosslinkNetworkFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
296 </crosslinkNetworkFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
297 <crosslinkMode/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
298 <peakRefinement>False</peakRefinement>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
299 <isobaricSumOverWindow>True</isobaricSumOverWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
300 <isobaricWeightExponent>0.75</isobaricWeightExponent>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
301 <diaLibraryType>0</diaLibraryType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
302 <diaLibraryPath/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
303 <diaPeptidePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
304 </diaPeptidePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
305 <diaEvidencePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
306 </diaEvidencePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
307 <diaMsmsPaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
308 </diaMsmsPaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
309 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
310 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
311 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
312 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
313 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
314 <diaScoreN>7</diaScoreN>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
315 <diaMinScore>2.99</diaMinScore>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
316 <diaPrecursorQuant>False</diaPrecursorQuant>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
317 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
318 </parameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
319 <parameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
320 <msInstrument>0</msInstrument>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
321 <maxCharge>7</maxCharge>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
322 <minPeakLen>2</minPeakLen>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
323 <diaMinPeakLen>2</diaMinPeakLen>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
324 <useMs1Centroids>False</useMs1Centroids>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
325 <useMs2Centroids>False</useMs2Centroids>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
326 <cutPeaks>True</cutPeaks>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
327 <gapScans>1</gapScans>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
328 <minTime>NaN</minTime>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
329 <maxTime>NaN</maxTime>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
330 <matchType>MatchFromAndTo</matchType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
331 <intensityDetermination>0</intensityDetermination>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
332 <centroidMatchTol>8</centroidMatchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
333 <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
334 <centroidHalfWidth>35</centroidHalfWidth>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
335 <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
336 <valleyFactor>1.4</valleyFactor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
337 <isotopeValleyFactor>1.2</isotopeValleyFactor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
338 <advancedPeakSplitting>False</advancedPeakSplitting>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
339 <intensityThreshold>0</intensityThreshold>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
340 <labelMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
341 <string/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
342 </labelMods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
343 <lcmsRunType>Reporter ion MS3</lcmsRunType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
344 <reQuantify>False</reQuantify>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
345 <lfqMode>0</lfqMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
346 <lfqSkipNorm>False</lfqSkipNorm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
347 <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
348 <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
349 <lfqMaxFeatures>100000</lfqMaxFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
350 <neucodeMaxPpm>0</neucodeMaxPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
351 <neucodeResolution>0</neucodeResolution>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
352 <neucodeResolutionInMda>False</neucodeResolutionInMda>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
353 <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
354 <fastLfq>True</fastLfq>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
355 <lfqRestrictFeatures>False</lfqRestrictFeatures>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
356 <lfqMinRatioCount>2</lfqMinRatioCount>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
357 <maxLabeledAa>0</maxLabeledAa>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
358 <maxNmods>5</maxNmods>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
359 <maxMissedCleavages>2</maxMissedCleavages>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
360 <multiplicity>1</multiplicity>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
361 <enzymeMode>0</enzymeMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
362 <complementaryReporterType>0</complementaryReporterType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
363 <reporterNormalization>0</reporterNormalization>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
364 <neucodeIntensityMode>0</neucodeIntensityMode>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
365 <fixedModifications/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
366 <enzymes/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
367 <enzymesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
368 </enzymesFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
369 <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
370 <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
371 <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
372 <variableModifications/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
373 <useMultiModification>False</useMultiModification>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
374 <multiModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
375 </multiModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
376 <isobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
377 <IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
378 <internalLabel>iTRAQ4plex-Lys114</internalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
379 <terminalLabel>iTRAQ4plex-Nter114</terminalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
380 <correctionFactorM2>0</correctionFactorM2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
381 <correctionFactorM1>0</correctionFactorM1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
382 <correctionFactorP1>0</correctionFactorP1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
383 <correctionFactorP2>0</correctionFactorP2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
384 <tmtLike>False</tmtLike>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
385 </IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
386 <IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
387 <internalLabel>iTRAQ4plex-Lys115</internalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
388 <terminalLabel>iTRAQ4plex-Nter115</terminalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
389 <correctionFactorM2>0</correctionFactorM2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
390 <correctionFactorM1>0</correctionFactorM1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
391 <correctionFactorP1>0</correctionFactorP1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
392 <correctionFactorP2>0</correctionFactorP2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
393 <tmtLike>False</tmtLike>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
394 </IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
395 <IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
396 <internalLabel>iTRAQ4plex-Lys116</internalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
397 <terminalLabel>iTRAQ4plex-Nter116</terminalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
398 <correctionFactorM2>0</correctionFactorM2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
399 <correctionFactorM1>0</correctionFactorM1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
400 <correctionFactorP1>0</correctionFactorP1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
401 <correctionFactorP2>0</correctionFactorP2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
402 <tmtLike>False</tmtLike>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
403 </IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
404 <IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
405 <internalLabel>iTRAQ4plex-Lys117</internalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
406 <terminalLabel>iTRAQ4plex-Nter117</terminalLabel>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
407 <correctionFactorM2>0</correctionFactorM2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
408 <correctionFactorM1>0</correctionFactorM1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
409 <correctionFactorP1>0</correctionFactorP1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
410 <correctionFactorP2>0</correctionFactorP2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
411 <tmtLike>False</tmtLike>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
412 </IsobaricLabelInfo>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
413 </isobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
414 <neucodeLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
415 </neucodeLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
416 <variableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
417 </variableModificationsFirstSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
418 <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
419 <additionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
420 </additionalVariableModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
421 <additionalVariableModificationProteins>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
422 </additionalVariableModificationProteins>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
423 <doMassFiltering>True</doMassFiltering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
424 <firstSearchTol>20</firstSearchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
425 <mainSearchTol>4.5</mainSearchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
426 <searchTolInPpm>True</searchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
427 <isotopeMatchTol>2</isotopeMatchTol>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
428 <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
429 <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
430 <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
431 <checkMassDeficit>True</checkMassDeficit>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
432 <recalibrationInPpm>True</recalibrationInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
433 <intensityDependentCalibration>False</intensityDependentCalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
434 <minScoreForCalibration>70</minScoreForCalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
435 <matchLibraryFile>False</matchLibraryFile>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
436 <libraryFile/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
437 <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
438 <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
439 <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
440 <reporterMassTolerance>0.003</reporterMassTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
441 <reporterPif>0.8</reporterPif>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
442 <filterPif>True</filterPif>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
443 <reporterFraction>0</reporterFraction>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
444 <reporterBasePeakRatio>0</reporterBasePeakRatio>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
445 <timsHalfWidth>0</timsHalfWidth>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
446 <timsStep>0</timsStep>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
447 <timsResolution>0</timsResolution>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
448 <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
449 <timsRemovePrecursor>True</timsRemovePrecursor>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
450 <timsIsobaricLabels>False</timsIsobaricLabels>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
451 <timsCollapseMsms>True</timsCollapseMsms>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
452 <crosslinkSearch>False</crosslinkSearch>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
453 <crossLinker/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
454 <minMatchXl>0</minMatchXl>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
455 <minPairedPepLenXl>6</minPairedPepLenXl>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
456 <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
457 <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
458 <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
459 <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
460 <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
461 <crosslinkModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
462 </crosslinkModifications>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
463 <crosslinkFastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
464 </crosslinkFastaFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
465 <crosslinkSites>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
466 </crosslinkSites>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
467 <crosslinkNetworkFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
468 </crosslinkNetworkFiles>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
469 <crosslinkMode/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
470 <peakRefinement>False</peakRefinement>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
471 <isobaricSumOverWindow>True</isobaricSumOverWindow>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
472 <isobaricWeightExponent>0.75</isobaricWeightExponent>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
473 <diaLibraryType>0</diaLibraryType>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
474 <diaLibraryPath/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
475 <diaPeptidePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
476 </diaPeptidePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
477 <diaEvidencePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
478 </diaEvidencePaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
479 <diaMsmsPaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
480 </diaMsmsPaths>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
481 <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
482 <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
483 <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
484 <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
485 <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
486 <diaScoreN>7</diaScoreN>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
487 <diaMinScore>2.99</diaMinScore>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
488 <diaPrecursorQuant>False</diaPrecursorQuant>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
489 <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
490 </parameterGroup>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
491 </parameterGroups>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
492 <msmsParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
493 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
494 <Name>FTMS</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
495 <MatchTolerance>20</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
496 <MatchToleranceInPpm>True</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
497 <DeisotopeTolerance>7</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
498 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
499 <DeNovoTolerance>10</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
500 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
501 <Deisotope>True</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
502 <Topx>12</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
503 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
504 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
505 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
506 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
507 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
508 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
509 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
510 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
511 <Name>ITMS</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
512 <MatchTolerance>0.5</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
513 <MatchToleranceInPpm>False</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
514 <DeisotopeTolerance>0.15</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
515 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
516 <DeNovoTolerance>0.25</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
517 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
518 <Deisotope>False</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
519 <Topx>8</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
520 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
521 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
522 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
523 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
524 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
525 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
526 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
527 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
528 <Name>TOF</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
529 <MatchTolerance>40</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
530 <MatchToleranceInPpm>True</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
531 <DeisotopeTolerance>0.01</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
532 <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
533 <DeNovoTolerance>0.02</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
534 <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
535 <Deisotope>True</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
536 <Topx>10</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
537 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
538 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
539 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
540 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
541 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
542 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
543 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
544 <msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
545 <Name>Unknown</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
546 <MatchTolerance>20</MatchTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
547 <MatchToleranceInPpm>True</MatchToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
548 <DeisotopeTolerance>7</DeisotopeTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
549 <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
550 <DeNovoTolerance>10</DeNovoTolerance>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
551 <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
552 <Deisotope>True</Deisotope>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
553 <Topx>12</Topx>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
554 <TopxInterval>100</TopxInterval>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
555 <HigherCharges>True</HigherCharges>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
556 <IncludeWater>True</IncludeWater>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
557 <IncludeAmmonia>True</IncludeAmmonia>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
558 <DependentLosses>True</DependentLosses>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
559 <Recalibration>False</Recalibration>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
560 </msmsParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
561 </msmsParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
562 <fragmentationParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
563 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
564 <Name>CID</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
565 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
566 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
567 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
568 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
569 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
570 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
571 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
572 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
573 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
574 <Name>HCD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
575 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
576 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
577 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
578 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
579 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
580 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
581 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
582 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
583 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
584 <Name>ETD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
585 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
586 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
587 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
588 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
589 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
590 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
591 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
592 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
593 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
594 <Name>PQD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
595 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
596 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
597 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
598 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
599 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
600 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
601 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
602 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
603 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
604 <Name>ETHCD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
605 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
606 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
607 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
608 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
609 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
610 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
611 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
612 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
613 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
614 <Name>ETCID</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
615 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
616 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
617 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
618 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
619 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
620 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
621 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
622 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
623 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
624 <Name>UVPD</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
625 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
626 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
627 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
628 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
629 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
630 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
631 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
632 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
633 <fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
634 <Name>Unknown</Name>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
635 <Connected>False</Connected>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
636 <ConnectedScore0>1</ConnectedScore0>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
637 <ConnectedScore1>1</ConnectedScore1>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
638 <ConnectedScore2>1</ConnectedScore2>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
639 <InternalFragments>False</InternalFragments>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
640 <InternalFragmentWeight>1</InternalFragmentWeight>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
641 <InternalFragmentAas>KRH</InternalFragmentAas>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
642 </fragmentationParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
643 </fragmentationParamsArray>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
644 </MaxQuantParams>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents:
diff changeset
645