| Previous changeset 9:37d669de2828 (2021-02-19) Next changeset 11:d72c96ad9a16 (2021-06-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" |
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modified:
macros.xml maxquant.xml |
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added:
test-data/05/config.yml test-data/05/mqpar.xml test-data/06/config.yml test-data/06/mqpar.xml |
| b |
| diff -r 37d669de2828 -r f522c08e900c macros.xml --- a/macros.xml Fri Feb 19 21:24:41 2021 +0000 +++ b/macros.xml Fri Mar 12 08:41:06 2021 +0000 |
| b |
| @@ -65,7 +65,11 @@ cont_MYCO: - MYCOPLASMA - '1' + #if $search_opts.mbr.match_between_runs == 'True': + MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window} + #else: MQpar_MatchingTimeWindow_num: 0.0 + #end if MatchBetweenRuns_wA: auto MQpar_firstSearchTol_num: 20.0 firstSearch_outOfCalWarnSD_num: 2.0 |
| b |
| diff -r 37d669de2828 -r f522c08e900c maxquant.xml --- a/maxquant.xml Fri Feb 19 21:24:41 2021 +0000 +++ b/maxquant.xml Fri Mar 12 08:41:06 2021 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy3">\n+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy4">\n <macros>\n <xml name="output" token_format="tabular" token_label="default description" token_name="default">\n <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">\n@@ -89,7 +89,14 @@\n lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}\n lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}\n advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}\n- matchBetweenRuns: ${search_opts.match_between_runs}\n+ matchBetweenRuns: ${search_opts.mbr.match_between_runs}\n+ #if $search_opts.mbr.match_between_runs == \'True\':\n+ matchingTimeWindow: ${search_opts.mbr.matching_time_window}\n+ matchingIonMobilityWindow: ${search_opts.mbr.matching_ion_mobility_window}\n+ alignmentTimeWindow: ${search_opts.mbr.alignment_time_window}\n+ alignmentIonMobilityWindow: ${search_opts.mbr.alignment_ion_mobility_window}\n+ matchUnidentifiedFeatures: ${search_opts.mbr.match_unidentified_features}\n+ #end if\n includeContaminants: ${search_opts.incl_contaminants}\n minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length}\n maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length}\n@@ -223,7 +230,78 @@\n - [iodoTMT6plex-Cys130,\'\',0,0,0,0,True]\n - [iodoTMT6plex-Cys131,\'\',0,0,0,0,True]\n #end if\n- #end if \n+ #end if\n+ #if $pg.quant_method.select_quant_method == \'reporter_ion_ms3\':\n+ lcmsRunType: \'Reporter ion MS3\'\n+ reporterMassTolerance: 0.003\n+ #if $pg.quant_method.filter_by_pif.filter_pif == \'True\':\n+ reporterPif: ${pg.quant_method.filter_by_pif.reporter_pif}\n+ #else:\n+ reporterPif: 0\n+ #end if\n+ reporterFraction: 0\n+ reporterBasePeakRatio: 0\n+ filterPif: ${pg.quant_method.filter_by_pif.filter_pif}\n+ isobaricLabels:\n+ #if $pg.quant_method.iso_labels.labeling == \'custom\':\n+ #for $l in $pg.quant_method.iso_labels.iso_label:\n+ - [\'$l.internallabel\',\'$l.terminallabel\',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]\n+ #end for\n+ #end if\n+ #if $pg.quant_method.iso_labels.labeling == \'tmt2plex\':\n+ - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]\n+ - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]\n+ #end if\n+ #if $pg.quant_method.iso_labels.labeling == \'tmt6plex\':\n+ - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]\n+ - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]\n+ - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]\n+ - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]\n+ - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]\n+ - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]\n+ #end if\n+ #if $pg.quant_method.iso_labels.labeling == \'tmt8plex\':\n+ - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]\n+ - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]\n+ - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]\n+ - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]\n+ - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]\n+ - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]\n+ - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]\n+ - [TMT8plex-Lys131N,TMT8'..b'="select_quant_method" value="reporter_ion_ms3"/>\n+ <conditional name="iso_labels">\n+ <param name="labeling" value="itraq4plex"/>\n+ </conditional>\n+ <conditional name="filter_by_pif">\n+ <param name="filter_pif" value="True"/>\n+ <param name="reporter_pif" value="0.8"/> <!-- as filter_pif is True this value is used -->\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <param name="dry_run" value="True" />\n+ <param name="output" value="config,mqpar,mzTab" />\n+ <output name="config" file="06/config.yml" lines_diff="2">\n+ <assert_contents>\n+ <has_text_matching expression="lcmsRunType\\: \\\'Reporter ion MS3\\\'" />\n+ </assert_contents>\n+ </output>\n+ <output name="mqpar" file="06/mqpar.xml" lines_diff="6">\n+ <assert_contents>\n+ <has_text_matching expression=".lcmsRunType.Reporter ion MS3.\\/lcmsRunType." />\n+ </assert_contents>\n+ </output>\n+ </test>\n <!-- lfq, testing yaml conf file and mqpar.xml only -->\n <test expect_num_outputs="2">\n <param name="ftype" value=".mzxml" />\n@@ -654,6 +882,37 @@\n <output name="config" file="03/config.yml" lines_diff="2" />\n <output name="mqpar" file="03/mqpar.xml" lines_diff="10" />\n </test>\n+ <!-- Test for MBR -->\n+ <test expect_num_outputs="2">\n+ <param name="ftype" value=".mzxml" />\n+ <param name="fasta_files" value="bsa.fasta" />\n+ <param name="identifier_parse_rule" value="^>.*\\|(.*)\\|.*$" />\n+ <param name="description_parse_rule" value="^>.*\\|.*\\|[^ ]+ (.*) OS.*$" />\n+ <param name="min_unique_pep" value="1" />\n+ <param name="ibaq" value="True" />\n+ <param name="match_between_runs" value="True" />\n+ <param name="ibaqLogFit" value="False" />\n+ <repeat name="paramGroups">\n+ <param name="files" value="BSA_min_22"/>\n+ <param name="maxMissedCleavages" value="1"/>\n+ <param name="variableModifications" value="Oxidation (M)" />\n+ <conditional name="quant_method">\n+ <param name="select_quant_method" value="lfq" />\n+ </conditional>\n+ </repeat>\n+ <param name="dry_run" value="True" />\n+ <param name="output" value="config,mqpar" />\n+ <output name="config" file="05/config.yml" lines_diff="2">\n+ <assert_contents>\n+ <has_text_matching expression="matchBetweenRuns\\: True" />\n+ </assert_contents>\n+ </output>\n+ <output name="mqpar" file="05/mqpar.xml" lines_diff="4">\n+ <assert_contents>\n+ <has_text_matching expression=".matchBetweenRuns.True.\\/matchBetweenRuns." />\n+ </assert_contents>\n+ </output>\n+ </test>\n <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only -->\n <test expect_num_outputs="2">\n <param name="ftype" value=".mzxml" />\n@@ -744,7 +1003,7 @@\n \n - for two channels: choose options from light and heavy sections\n - for three channels: choose options from light, medium and heavy sections\n- - reporter ion ms2: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling\n+ - reporter ion ms2/ms3: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling\n - PTXQC quality control: quality control software creates an automatic quality control pdf report \n \n \n' |
| b |
| diff -r 37d669de2828 -r f522c08e900c test-data/05/config.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/05/config.yml Fri Mar 12 08:41:06 2021 +0000 |
| [ |
| @@ -0,0 +1,45 @@ + + fastaFiles: [/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat] + parseRules: + identifierParseRule: '^>.*\|(.*)\|.*$' + descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$' + minUniquePeptides: 1 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: False + ibaq: True + ibaqLogFit: False + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: True + matchingTimeWindow: 0.7 + matchingIonMobilityWindow: 0.05 + alignmentTimeWindow: 20 + alignmentIonMobilityWindow: 1 + matchUnidentifiedFeatures: False + includeContaminants: True + minPeptideLengthForUnspecificSearch: 8 + maxPeptideLengthForUnspecificSearch: 25 + decoyMode: revert + peptideFdr: 0.01 + proteinFdr: 0.01 + quantMode: 1 + restrictProteinQuantification: True + restrictMods: [Oxidation (M),Acetyl (Protein N-term)] + useCounterparts: True + paramGroups: + - files: ['BSA_min_22.mzxml'] + maxMissedCleavages: 1 + fixedModifications: [Carbamidomethyl (C)] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + enzymeMode: 0 + lfqMode: 1 + lfqSkipNorm: True + lfqMinEdgesPerNode: 3 + lfqAvEdgesPerNode: 6 + lfqMinRatioCount: 2 + \ No newline at end of file |
| b |
| diff -r 37d669de2828 -r f522c08e900c test-data/05/mqpar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/05/mqpar.xml Fri Mar 12 08:41:06 2021 +0000 |
| [ |
| b'@@ -0,0 +1,451 @@\n+<?xml version="1.0" ?>\n+<MaxQuantParams>\n+\t<fastaFiles>\n+\t\t<FastaFileInfo>\n+\t\t\t<fastaFilePath>/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat</fastaFilePath>\n+\t\t\t<identifierParseRule>^>.*\\|(.*)\\|.*$</identifierParseRule>\n+\t\t\t<descriptionParseRule>^>.*\\|.*\\|[^ ]+ (.*) OS.*$</descriptionParseRule>\n+\t\t\t<taxonomyParseRule/>\n+\t\t\t<variationParseRule/>\n+\t\t\t<modificationParseRule/>\n+\t\t\t<taxonomyId/>\n+\t\t</FastaFileInfo>\n+\t</fastaFiles>\n+\t<fastaFilesProteogenomics>\n+ </fastaFilesProteogenomics>\n+\t<fastaFilesFirstSearch>\n+ </fastaFilesFirstSearch>\n+\t<fixedSearchFolder/>\n+\t<andromedaCacheSize>350000</andromedaCacheSize>\n+\t<advancedRatios>True</advancedRatios>\n+\t<pvalThres>0.005</pvalThres>\n+\t<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>\n+\t<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>\n+\t<rtShift>False</rtShift>\n+\t<separateLfq>False</separateLfq>\n+\t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+\t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<decoyMode>revert</decoyMode>\n+\t<boxCarMode>all</boxCarMode>\n+\t<includeContaminants>True</includeContaminants>\n+\t<maxPeptideMass>4600</maxPeptideMass>\n+\t<epsilonMutationScore>True</epsilonMutationScore>\n+\t<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+\t<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+\t<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+\t<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+\t<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+\t<minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+\t<secondPeptide>True</secondPeptide>\n+\t<matchBetweenRuns>True</matchBetweenRuns>\n+\t<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+\t<matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+\t<dependentPeptides>False</dependentPeptides>\n+\t<dependentPeptideFdr>0</dependentPeptideFdr>\n+\t<dependentPeptideMassBin>0</dependentPeptideMassBin>\n+\t<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+\t<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+\t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+\t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+\t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+\t<msmsConnection>False</msmsConnection>\n+\t<ibaq>True</ibaq>\n+\t<top3>False</top3>\n+\t<independentEnzymes>False</independentEnzymes>\n+\t<useDeltaScore>False</useDeltaScore>\n+\t<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+\t<taxonomyLevel>Species</taxonomyLevel>\n+\t<avalon>False</avalon>\n+\t<nModColumns>3</nModColumns>\n+\t<ibaqLogFit>False</ibaqLogFit>\n+\t<razorProteinFdr>True</razorProteinFdr>\n+\t<deNovoSequencing>False</deNovoSequencing>\n+\t<deNovoVarMods>True</deNovoVarMods>\n+\t<massDifferenceSearch>False</massDifferenceSearch>\n+\t<isotopeCalc>False</isotopeCalc>\n+\t<writePeptidesForSpectrumFile/>\n+\t<intensityPredictionsFile>\n+ </intensityPredictionsFile>\n+\t<minPepLen>7</minPepLen>\n+\t<psmFdrCrosslink>0.01</psmFdrCrosslink>\n+\t<peptideFdr>0.01</peptideFdr>\n+\t<proteinFdr>0.01</proteinFdr>\n+\t<siteFdr>0.01</siteFdr>\n+\t<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\n+\t<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\n+\t<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+\t<minPeptides>1</minPeptides>\n+\t<minRazorPeptides>1</minRazorPeptides>\n+\t<minUniquePeptides>1</minUniquePeptides>\n+\t<useCounterparts>True</useCounterparts>\n+\t<advancedSiteIntensities>True</advancedSiteIntensities>\n+\t<customProteinQuantification>False</customProteinQuantification>\n+\t<customProteinQuantificationFile/>\n+\t<minRatioCount>2</minRatioCount>\n+\t<restrictProteinQuantification>True</restrictProteinQuantification>\n+\t<restrictMods>\n+\t\t<string>Oxidation (M)</string>\n+\t\t<string>Acetyl (Protein N-term)</string>\n+\t</restrictMods>\n+\t<matchingTimeWind'..b'<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t\t<msmsParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<MatchTolerance>20</MatchTolerance>\n+\t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n+\t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n+\t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n+\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n+\t\t\t<Deisotope>True</Deisotope>\n+\t\t\t<Topx>12</Topx>\n+\t\t\t<TopxInterval>100</TopxInterval>\n+\t\t\t<HigherCharges>True</HigherCharges>\n+\t\t\t<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t</msmsParamsArray>\n+\t<fragmentationParamsArray>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>CID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>HCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>PQD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETHCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETCID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>UVPD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t</fragmentationParamsArray>\n+</MaxQuantParams>\n+\n' |
| b |
| diff -r 37d669de2828 -r f522c08e900c test-data/06/config.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/06/config.yml Fri Mar 12 08:41:06 2021 +0000 |
| [ |
| @@ -0,0 +1,59 @@ + + fastaFiles: [/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat] + parseRules: + identifierParseRule: '>([^\s]*)' + descriptionParseRule: '>(.*)' + minUniquePeptides: 0 + minPepLen: 7 + maxPeptideMass: 4600 + calcPeakProperties: False + writeMzTab: True + separateLfq: False + lfqStabilizeLargeRatios: True + lfqRequireMsms: True + advancedSiteIntensities: True + matchBetweenRuns: False + includeContaminants: False + minPeptideLengthForUnspecificSearch: 7 + maxPeptideLengthForUnspecificSearch: 24 + decoyMode: randomize + peptideFdr: 0.5 + proteinFdr: 0.4 + quantMode: 0 + restrictProteinQuantification: True + restrictMods: [Pro5,Pro6] + useCounterparts: True + paramGroups: + - files: ['BSA_min_23.mzXML'] + maxMissedCleavages: 2 + fixedModifications: [] + variableModifications: [Oxidation (M)] + enzymes: [Trypsin/P] + enzymeMode: 0 + lcmsRunType: 'Reporter ion MS3' + reporterMassTolerance: 0.003 + reporterPif: 0 + reporterFraction: 0 + reporterBasePeakRatio: 0 + filterPif: False + isobaricLabels: + - ['TMT2plex-Lys126','TMT2plex-Nter126',0.0,0.0,6.7,3.0,True] + - ['TMT2plex-Lys127','TMT2plex-Nter127',0.0,0.0,0.0,0.0,True] + - files: ['BSA_min_22.mzxml'] + maxMissedCleavages: 2 + fixedModifications: [] + variableModifications: [] + enzymes: [] + enzymeMode: 0 + lcmsRunType: 'Reporter ion MS3' + reporterMassTolerance: 0.003 + reporterPif: 0.8 + reporterFraction: 0 + reporterBasePeakRatio: 0 + filterPif: True + isobaricLabels: + - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + \ No newline at end of file |
| b |
| diff -r 37d669de2828 -r f522c08e900c test-data/06/mqpar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/06/mqpar.xml Fri Mar 12 08:41:06 2021 +0000 |
| [ |
| b'@@ -0,0 +1,645 @@\n+<?xml version="1.0" ?>\n+<MaxQuantParams>\n+\t<fastaFiles>\n+\t\t<FastaFileInfo>\n+\t\t\t<fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat</fastaFilePath>\n+\t\t\t<identifierParseRule>>([^\\s]*)</identifierParseRule>\n+\t\t\t<descriptionParseRule>>(.*)</descriptionParseRule>\n+\t\t\t<taxonomyParseRule/>\n+\t\t\t<variationParseRule/>\n+\t\t\t<modificationParseRule/>\n+\t\t\t<taxonomyId/>\n+\t\t</FastaFileInfo>\n+\t</fastaFiles>\n+\t<fastaFilesProteogenomics>\n+ </fastaFilesProteogenomics>\n+\t<fastaFilesFirstSearch>\n+ </fastaFilesFirstSearch>\n+\t<fixedSearchFolder/>\n+\t<andromedaCacheSize>350000</andromedaCacheSize>\n+\t<advancedRatios>True</advancedRatios>\n+\t<pvalThres>0.005</pvalThres>\n+\t<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>\n+\t<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>\n+\t<rtShift>False</rtShift>\n+\t<separateLfq>False</separateLfq>\n+\t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+\t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<decoyMode>randomize</decoyMode>\n+\t<boxCarMode>all</boxCarMode>\n+\t<includeContaminants>False</includeContaminants>\n+\t<maxPeptideMass>4600</maxPeptideMass>\n+\t<epsilonMutationScore>True</epsilonMutationScore>\n+\t<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+\t<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+\t<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+\t<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+\t<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+\t<minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+\t<secondPeptide>True</secondPeptide>\n+\t<matchBetweenRuns>False</matchBetweenRuns>\n+\t<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+\t<matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+\t<dependentPeptides>False</dependentPeptides>\n+\t<dependentPeptideFdr>0</dependentPeptideFdr>\n+\t<dependentPeptideMassBin>0</dependentPeptideMassBin>\n+\t<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+\t<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+\t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+\t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+\t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+\t<msmsConnection>False</msmsConnection>\n+\t<ibaq>False</ibaq>\n+\t<top3>False</top3>\n+\t<independentEnzymes>False</independentEnzymes>\n+\t<useDeltaScore>False</useDeltaScore>\n+\t<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+\t<taxonomyLevel>Species</taxonomyLevel>\n+\t<avalon>False</avalon>\n+\t<nModColumns>3</nModColumns>\n+\t<ibaqLogFit>False</ibaqLogFit>\n+\t<razorProteinFdr>True</razorProteinFdr>\n+\t<deNovoSequencing>False</deNovoSequencing>\n+\t<deNovoVarMods>True</deNovoVarMods>\n+\t<massDifferenceSearch>False</massDifferenceSearch>\n+\t<isotopeCalc>False</isotopeCalc>\n+\t<writePeptidesForSpectrumFile/>\n+\t<intensityPredictionsFile>\n+ </intensityPredictionsFile>\n+\t<minPepLen>7</minPepLen>\n+\t<psmFdrCrosslink>0.01</psmFdrCrosslink>\n+\t<peptideFdr>0.5</peptideFdr>\n+\t<proteinFdr>0.4</proteinFdr>\n+\t<siteFdr>0.01</siteFdr>\n+\t<minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch>\n+\t<maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch>\n+\t<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+\t<minPeptides>1</minPeptides>\n+\t<minRazorPeptides>1</minRazorPeptides>\n+\t<minUniquePeptides>0</minUniquePeptides>\n+\t<useCounterparts>True</useCounterparts>\n+\t<advancedSiteIntensities>True</advancedSiteIntensities>\n+\t<customProteinQuantification>False</customProteinQuantification>\n+\t<customProteinQuantificationFile/>\n+\t<minRatioCount>2</minRatioCount>\n+\t<restrictProteinQuantification>True</restrictProteinQuantification>\n+\t<restrictMods>\n+\t\t<string>Pro5</string>\n+\t\t<string>Pro6</string>\n+\t</restrictMods>\n+\t<matchingTimeWindow>0</matchingTimeWindow>\n+\t<matchingIonMobilityWin'..b'<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t\t<msmsParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<MatchTolerance>20</MatchTolerance>\n+\t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n+\t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n+\t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n+\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n+\t\t\t<Deisotope>True</Deisotope>\n+\t\t\t<Topx>12</Topx>\n+\t\t\t<TopxInterval>100</TopxInterval>\n+\t\t\t<HigherCharges>True</HigherCharges>\n+\t\t\t<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t</msmsParamsArray>\n+\t<fragmentationParamsArray>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>CID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>HCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>PQD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETHCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETCID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>UVPD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t</fragmentationParamsArray>\n+</MaxQuantParams>\n+\n' |