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

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"

--- a/test-data/template.xml	Thu Aug 15 08:09:00 2019 -0400
+++ b/test-data/template.xml	Sat Apr 11 11:49:19 2020 -0400
@@ -2,7 +2,7 @@
 <MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <fastaFiles>
       <FastaFileInfo>
-         <fastaFilePath></fastaFilePath>
+         <fastaFilePath>example.fasta</fastaFilePath>
          <identifierParseRule>>(.*)</identifierParseRule>
          <descriptionParseRule></descriptionParseRule>
          <taxonomyParseRule></taxonomyParseRule>
@@ -88,8 +88,9 @@
       <string>Acetyl (Protein N-term)</string>
    </restrictMods>
    <matchingTimeWindow>0</matchingTimeWindow>
+   <matchingIonMobilityWindow>0</matchingIonMobilityWindow>
    <alignmentTimeWindow>0</alignmentTimeWindow>
-   <numberOfCandidatesMultiplexedMsms>25</numberOfCandidatesMultiplexedMsms>
+   <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
    <numberOfCandidatesMsms>15</numberOfCandidatesMsms>
    <compositionPrediction>0</compositionPrediction>
    <quantMode>1</quantMode>
@@ -107,15 +108,13 @@
    <disableMd5>False</disableMd5>
    <cacheBinInds>True</cacheBinInds>
    <etdIncludeB>False</etdIncludeB>
-   <complementaryTmtCollapseNplets>True</complementaryTmtCollapseNplets>
-   <stackPeaks>False</stackPeaks>
    <ms2PrecursorShift>0</ms2PrecursorShift>
    <complementaryIonPpm>20</complementaryIonPpm>
    <variationParseRule></variationParseRule>
    <variationMode>none</variationMode>
    <useSeriesReporters>False</useSeriesReporters>
    <name>templateSession</name>
-   <maxQuantVersion>1.6.3.4</maxQuantVersion>
+   <maxQuantVersion>1.6.10.43</maxQuantVersion>
    <tempFolder></tempFolder>
    <pluginFolder></pluginFolder>
    <numThreads>1</numThreads>
@@ -150,11 +149,14 @@
    <referenceChannel>
       <string></string>
    </referenceChannel>
+   <intensPred>False</intensPred>
+   <intensPredModelReTrain>False</intensPredModelReTrain>
    <parameterGroups>
       <parameterGroup>
          <msInstrument>0</msInstrument>
          <maxCharge>7</maxCharge>
          <minPeakLen>2</minPeakLen>
+         <diaMinPeakLen>2</diaMinPeakLen>
          <useMs1Centroids>False</useMs1Centroids>
          <useMs2Centroids>False</useMs2Centroids>
          <cutPeaks>True</cutPeaks>
@@ -263,14 +265,35 @@
          <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
          <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
          <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
-         <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta>
-         <crosslinkCleaveModifications>
-         </crosslinkCleaveModifications>
+         <crosslinkModifications>
+         </crosslinkModifications>
          <crosslinkFastaFiles>
          </crosslinkFastaFiles>
-         <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
+         <crosslinkSites>
+         </crosslinkSites>
+         <crosslinkNetworkFiles>
+         </crosslinkNetworkFiles>
+         <crosslinkMode></crosslinkMode>
          <peakRefinement>False</peakRefinement>
          <isobaricSumOverWindow>True</isobaricSumOverWindow>
+         <isobaricWeightExponent>0.75</isobaricWeightExponent>
+         <diaLibraryType>0</diaLibraryType>
+         <diaLibraryPath></diaLibraryPath>
+         <diaPeptidePaths>
+         </diaPeptidePaths>
+         <diaEvidencePaths>
+         </diaEvidencePaths>
+         <diaMsmsPaths>
+         </diaMsmsPaths>
+         <diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
+         <diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
+         <diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
+         <diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
+         <diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
+         <diaScoreN>7</diaScoreN>
+         <diaMinScore>2.99</diaMinScore>
+         <diaPrecursorQuant>False</diaPrecursorQuant>
+         <diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
       </parameterGroup>
    </parameterGroups>
    <msmsParamsArray>
@@ -327,14 +350,14 @@
       </msmsParams>
       <msmsParams>
          <Name>Unknown</Name>
-         <MatchTolerance>0.5</MatchTolerance>
-         <MatchToleranceInPpm>False</MatchToleranceInPpm>
-         <DeisotopeTolerance>0.15</DeisotopeTolerance>
-         <DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
-         <DeNovoTolerance>0.25</DeNovoTolerance>
-         <DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
-         <Deisotope>False</Deisotope>
-         <Topx>8</Topx>
+         <MatchTolerance>20</MatchTolerance>
+         <MatchToleranceInPpm>True</MatchToleranceInPpm>
+         <DeisotopeTolerance>7</DeisotopeTolerance>
+         <DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
+         <DeNovoTolerance>10</DeNovoTolerance>
+         <DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
+         <Deisotope>True</Deisotope>
+         <Topx>12</Topx>
          <TopxInterval>100</TopxInterval>
          <HigherCharges>True</HigherCharges>
          <IncludeWater>True</IncludeWater>