| Previous changeset 5:7f432d87c82c (2020-04-15) Next changeset 7:d253b379322b (2020-06-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" |
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modified:
maxquant.xml mqparam.py test-data/01/combined/txt/parameters.txt test-data/01/config.yml test-data/01/mqpar.xml test-data/02/config.yml test-data/02/mqpar.xml test-data/03/config.yml test-data/03/mqpar.xml test-data/04/config.yml test-data/04/mqpar.xml |
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| diff -r 7f432d87c82c -r 2133b0be850a maxquant.xml --- a/maxquant.xml Wed Apr 15 11:17:42 2020 -0400 +++ b/maxquant.xml Wed May 06 13:35:51 2020 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="maxquant" name="MaxQuant" version="@VERSION@">\n+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1">\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@@ -81,15 +81,26 @@\n calcPeakProperties: ${search_opts.calc_peak_properties}\n #set writeMzTab = "mzTab" in $output_opts.output\n writeMzTab: $writeMzTab\n- #if $lfq_opts.do_ibaq.ibaq == \'True\':\n- ibaq: ${lfq_opts.do_ibaq.ibaq}\n- ibaqLogFit: ${lfq_opts.do_ibaq.ibaqLogFit}\n+ #if $protein_quant.lfq_opts.do_ibaq.ibaq == \'True\':\n+ ibaq: ${protein_quant.lfq_opts.do_ibaq.ibaq}\n+ ibaqLogFit: ${protein_quant.lfq_opts.do_ibaq.ibaqLogFit}\n #end if\n- separateLfq: ${lfq_opts.separateLfq}\n- lfqStabilizeLargeRatios: ${lfq_opts.lfqStabilizeLargeRatios}\n- lfqRequireMsms: ${lfq_opts.lfqRequireMsms}\n- advancedSiteIntensities: ${lfq_opts.advancedSiteIntensities}\n+ separateLfq: ${protein_quant.lfq_opts.separateLfq}\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+ includeContaminants: ${search_opts.incl_contaminants}\n+ quantMode: ${protein_quant.peptides_for_quantification}\n+ restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot}\n+ #if $protein_quant.only_unmod_prot.unmod_prot == \'True\':\n+ #if $protein_quant.only_unmod_prot.mods_used_prot_quant:\n+ restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}]\n+ #else:\n+ restrictMods: []\n+ #end if\n+ useCounterparts: $protein_quant.only_unmod_prot.discard_unmod_cpart_peptides\n+ #end if\n paramGroups:\n #for $pg in $paramGroups:\n #set names = [re.sub(\'@SUBSTITUTION_RX@\', \'_\', str($n.element_identifier)) for $n in $pg.files]\n@@ -111,6 +122,7 @@\n #else:\n enzymes: []\n #end if\n+ enzymeMode: ${pg.digestion_mode}\n #if $pg.quant_method.select_quant_method == \'silac\':\n labelMods:\n #if $pg.quant_method.light_labels:\n@@ -139,9 +151,10 @@\n #if $pg.quant_method.select_quant_method == \'reporter_ion_ms2\':\n lcmsRunType: \'Reporter ion MS2\'\n reporterMassTolerance: 0.003\n- reporterPif: 0\n+ reporterPif: ${pg.quant_method.reporter_pif}\n reporterFraction: 0\n reporterBasePeakRatio: 0\n+ filterPif: ${pg.quant_method.filter_pif}\n isobaricLabels:\n #if $pg.quant_method.iso_labels.labeling == \'custom\':\n #for $l in $pg.quant_method.iso_labels.iso_label:\n@@ -216,7 +229,7 @@\n </param>\n <param format="fasta" multiple="true" name="fasta_files"\n type="data" label="FASTA files"\n- help="Specify one or more FASTA databases." />\n+ help="Specify one or more FASTA databases."/>\n <param name="identifier_parse_rule" type="text"\n label="identifier parse rule" value="^>.*\\|(.*)\\|.*$">\n <sanitizer>\n@@ -239,49 +252,133 @@\n <section name="search_opts" title="Search Options" expanded="true">\n <param format="tabular" name="template" type="data" optional="true"\n label="Specify an experimental design template (if needed). For detailed\n- '..b'falsevalue="False" \n- help="Large protein ratios will get an admixture of the total protein intensity ratio as described in the MaxLFQ paper"/>\n-\t <param name="lfqRequireMsms" type="boolean" checked="true"\n-\t\t label="Require MS/MS for LFQ comparisons"\n-\t\t truevalue="True" falsevalue="False" \n- help="Requires for each pari-wise peptide intensity comparison that at least one of two peptides has been identified by MS/MS"/>\n-\t <conditional name="do_ibaq">\n- <param name="ibaq" type="select" label="iBAQ (calculates absolute protein abundances by normalizing to copy number and not protein mass)">\n- <option value="False">No</option>\n- <option value="True">Yes</option>\n-\t\t</param>\n- <when value="True">\n- <param name="ibaqLogFit" type="boolean" checked="true"\n- label="Logarithmic fit"\n- truevalue="True" falsevalue="False" />\n- </when>\n- <when value="False">\n- </when>\n-\t </conditional>\n-\t <param name="advancedSiteIntensities" type="boolean" checked="true"\n-\t\t label="Advanced site intensities"\n-\t\t truevalue="True" falsevalue="False" />\n- </section>\n+ <expand macro="ptxqc-opts"/>\n \n- <expand macro="ptxqc-opts"/>\n <section title="Output Options" name="output_opts" expanded="true">\n <param name="dry_run" type="boolean" checked="false"\n-\t label="Only create config files? (i.e. for testing)"\n-\t truevalue="True" falsevalue="" /> \n+ label="Only create config files? (i.e. for testing)"\n+ truevalue="True" falsevalue=""/>\n <param type="select" name="output" label="Select the desired outputs."\n multiple="true" optional="false">\n <option value="proteinGroups">Protein Groups</option>\n@@ -430,6 +504,7 @@\n \n <tests>\n <!-- functional test with small mzXML file, no quantitation methods -->\n+ <!-- Disable this test when initally testing as it takes avery long tome to run -->\n <test expect_num_outputs="15">\n <param name="ftype" value=".mzxml" />\n <param name="fasta_files" value="bsa.fasta" />\n@@ -464,6 +539,14 @@\n <param name="fasta_files" value="bsa.fasta" />\n <param name="identifier_parse_rule" value=">([^\\s]*)" />\n <param name="description_parse_rule" value=">(.*)" />\n+ <param name="incl_contaminants" value="False" /> <!-- non-default value -->\n+ <section name="protein_quant">\n+ <param name="peptides_for_quantification" value="0"/><!-- non-default value -->\n+ <conditional name="only_unmod_prot">\n+ <param name="unmod_prot" value="True"/>\n+ <param name="mods_used_prot_quant" value="Pro5,Pro6"/>\n+ </conditional>\n+ </section>\n <repeat name="paramGroups">\n <param name="files" value="BSA_min_23.mzXML"/>\n <param name="variableModifications" value="Oxidation (M)" />\n@@ -485,6 +568,8 @@\n <param name="tmtlike" value="True" />\n </repeat>\n </conditional>\n+ <param name="filter_pif" value="False" />\n+ <param name="reporter_pif" value="0.6" />\n </conditional>\n </repeat>\n <repeat name="paramGroups">\n@@ -497,6 +582,8 @@\n <conditional name="iso_labels">\n <param name="labeling" value="itraq4plex" />\n </conditional>\n+ <param name="filter_pif" value="True" />\n+ <param name="reporter_pif" value="0.8" />\n </conditional>\n </repeat>\n <param name="dry_run" value="True" />\n' |
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| diff -r 7f432d87c82c -r 2133b0be850a mqparam.py --- a/mqparam.py Wed Apr 15 11:17:42 2020 -0400 +++ b/mqparam.py Wed May 06 13:35:51 2020 -0400 |
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| @@ -308,6 +308,23 @@ .format(key)) node.text = str(value) + def set_list_param(self, key, values): + """Set a list parameter. + Args: + key: (string) XML tag of the parameter + values: the lit of values of the parameter XML node + Returns: + None + """ + node = self._root.find(key) + if node is None: + raise ValueError('Element {} not found in parameter file' + .format(key)) + node.clear() + node.tag = key + for e in values: + et_add_child(node, name='string', text=e) + def _from_yaml(self, conf): """Read a yaml config file. Args: @@ -317,6 +334,7 @@ """ with open(conf) as f: conf_dict = yaml.safe_load(f.read()) + paramGroups = conf_dict.pop('paramGroups') self.add_infiles([pg.pop('files') for pg in paramGroups]) for i, pg in enumerate(paramGroups): @@ -339,7 +357,10 @@ else: raise Exception('No fasta files provided.') for key in conf_dict: - self.set_simple_param(key, conf_dict[key]) + if key in ['restrictMods']: + self.set_list_param(key, conf_dict[key]) + else: + self.set_simple_param(key, conf_dict[key]) def write(self, mqpar_out): """Write pretty formatted xml parameter file. |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/01/combined/txt/parameters.txt --- a/test-data/01/combined/txt/parameters.txt Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/01/combined/txt/parameters.txt Wed May 06 13:35:51 2020 -0400 |
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| @@ -18,9 +18,9 @@ Min. razor peptides 1 Min. peptides 1 Use only unmodified peptides and True -Modifications included in protein quantification Oxidation (M);Acetyl (Protein N-term) +Modifications included in protein quantification Peptides used for protein quantification Razor -Discard unmodified counterpart peptides True +Discard unmodified counterpart peptides False Label min. ratio count 2 Use delta score False iBAQ False |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/01/config.yml --- a/test-data/01/config.yml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/01/config.yml Wed May 06 13:35:51 2020 -0400 |
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| @@ -13,10 +13,16 @@ lfqRequireMsms: True advancedSiteIntensities: True matchBetweenRuns: False + includeContaminants: True + quantMode: 1 + restrictProteinQuantification: True + restrictMods: [] + useCounterparts: True paramGroups: - files: ['BSA_min_23.mzXML'] maxMissedCleavages: 1 fixedModifications: [Carbamidomethyl (C)] variableModifications: [Oxidation (M)] enzymes: [Trypsin/P] + enzymeMode: 0 \ No newline at end of file |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/01/mqpar.xml --- a/test-data/01/mqpar.xml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/01/mqpar.xml Wed May 06 13:35:51 2020 -0400 |
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| @@ -77,16 +77,13 @@ <minPeptides>1</minPeptides> <minRazorPeptides>1</minRazorPeptides> <minUniquePeptides>0</minUniquePeptides> - <useCounterparts>False</useCounterparts> + <useCounterparts>True</useCounterparts> <advancedSiteIntensities>True</advancedSiteIntensities> <customProteinQuantification>False</customProteinQuantification> <customProteinQuantificationFile/> <minRatioCount>2</minRatioCount> <restrictProteinQuantification>True</restrictProteinQuantification> - <restrictMods> - <string>Oxidation (M)</string> - <string>Acetyl (Protein N-term)</string> - </restrictMods> + <restrictMods/> <matchingTimeWindow>0</matchingTimeWindow> <matchingIonMobilityWindow>0</matchingIonMobilityWindow> <alignmentTimeWindow>0</alignmentTimeWindow> |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/02/config.yml --- a/test-data/02/config.yml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/02/config.yml Wed May 06 13:35:51 2020 -0400 |
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| @@ -13,17 +13,24 @@ lfqRequireMsms: True advancedSiteIntensities: True matchBetweenRuns: False + includeContaminants: False + 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 MS2' reporterMassTolerance: 0.003 - reporterPif: 0 + reporterPif: 0.6 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] @@ -32,11 +39,13 @@ fixedModifications: [] variableModifications: [] enzymes: [] + enzymeMode: 0 lcmsRunType: 'Reporter ion MS2' reporterMassTolerance: 0.003 - reporterPif: 0 + 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] |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/02/mqpar.xml --- a/test-data/02/mqpar.xml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/02/mqpar.xml Wed May 06 13:35:51 2020 -0400 |
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| @@ -27,7 +27,7 @@ <lfqRequireMsms>True</lfqRequireMsms> <decoyMode>revert</decoyMode> <boxCarMode>all</boxCarMode> - <includeContaminants>True</includeContaminants> + <includeContaminants>False</includeContaminants> <maxPeptideMass>4600</maxPeptideMass> <epsilonMutationScore>True</epsilonMutationScore> <mutatedPeptidesSeparately>True</mutatedPeptidesSeparately> @@ -77,15 +77,15 @@ <minPeptides>1</minPeptides> <minRazorPeptides>1</minRazorPeptides> <minUniquePeptides>0</minUniquePeptides> - <useCounterparts>False</useCounterparts> + <useCounterparts>True</useCounterparts> <advancedSiteIntensities>True</advancedSiteIntensities> <customProteinQuantification>False</customProteinQuantification> <customProteinQuantificationFile/> <minRatioCount>2</minRatioCount> <restrictProteinQuantification>True</restrictProteinQuantification> <restrictMods> - <string>Oxidation (M)</string> - <string>Acetyl (Protein N-term)</string> + <string>Pro5</string> + <string>Pro6</string> </restrictMods> <matchingTimeWindow>0</matchingTimeWindow> <matchingIonMobilityWindow>0</matchingIonMobilityWindow> @@ -93,7 +93,7 @@ <alignmentIonMobilityWindow>0</alignmentIonMobilityWindow> <numberOfCandidatesMsms>15</numberOfCandidatesMsms> <compositionPrediction>0</compositionPrediction> - <quantMode>1</quantMode> + <quantMode>0</quantMode> <massDifferenceMods> </massDifferenceMods> <mainSearchMaxCombinations>200</mainSearchMaxCombinations> @@ -267,7 +267,7 @@ <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> <matchLabelTimeTolMin>0</matchLabelTimeTolMin> <reporterMassTolerance>0.003</reporterMassTolerance> - <reporterPif>0</reporterPif> + <reporterPif>0.6</reporterPif> <filterPif>False</filterPif> <reporterFraction>0</reporterFraction> <reporterBasePeakRatio>0</reporterBasePeakRatio> @@ -442,8 +442,8 @@ <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> <matchLabelTimeTolMin>0</matchLabelTimeTolMin> <reporterMassTolerance>0.003</reporterMassTolerance> - <reporterPif>0</reporterPif> - <filterPif>False</filterPif> + <reporterPif>0.8</reporterPif> + <filterPif>True</filterPif> <reporterFraction>0</reporterFraction> <reporterBasePeakRatio>0</reporterBasePeakRatio> <timsHalfWidth>0</timsHalfWidth> |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/03/config.yml --- a/test-data/03/config.yml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/03/config.yml Wed May 06 13:35:51 2020 -0400 |
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| @@ -15,12 +15,18 @@ lfqRequireMsms: True advancedSiteIntensities: True matchBetweenRuns: False + includeContaminants: True + quantMode: 1 + restrictProteinQuantification: True + restrictMods: [] + 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 |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/03/mqpar.xml --- a/test-data/03/mqpar.xml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/03/mqpar.xml Wed May 06 13:35:51 2020 -0400 |
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| @@ -77,16 +77,13 @@ <minPeptides>1</minPeptides> <minRazorPeptides>1</minRazorPeptides> <minUniquePeptides>1</minUniquePeptides> - <useCounterparts>False</useCounterparts> + <useCounterparts>True</useCounterparts> <advancedSiteIntensities>True</advancedSiteIntensities> <customProteinQuantification>False</customProteinQuantification> <customProteinQuantificationFile/> <minRatioCount>2</minRatioCount> <restrictProteinQuantification>True</restrictProteinQuantification> - <restrictMods> - <string>Oxidation (M)</string> - <string>Acetyl (Protein N-term)</string> - </restrictMods> + <restrictMods/> <matchingTimeWindow>0</matchingTimeWindow> <matchingIonMobilityWindow>0</matchingIonMobilityWindow> <alignmentTimeWindow>0</alignmentTimeWindow> |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/04/config.yml --- a/test-data/04/config.yml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/04/config.yml Wed May 06 13:35:51 2020 -0400 |
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| @@ -13,12 +13,18 @@ lfqRequireMsms: True advancedSiteIntensities: True matchBetweenRuns: False + includeContaminants: True + quantMode: 1 + restrictProteinQuantification: True + restrictMods: [] + useCounterparts: True paramGroups: - files: ['BSA_min_23.mzXML', 'BSA_min_22.mzxml'] maxMissedCleavages: 2 fixedModifications: [Carbamidomethyl (C)] variableModifications: [Oxidation (M)] enzymes: [Trypsin/P] + enzymeMode: 0 labelMods: - [Arg6,Lys4] - [] |
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| diff -r 7f432d87c82c -r 2133b0be850a test-data/04/mqpar.xml --- a/test-data/04/mqpar.xml Wed Apr 15 11:17:42 2020 -0400 +++ b/test-data/04/mqpar.xml Wed May 06 13:35:51 2020 -0400 |
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| @@ -77,16 +77,13 @@ <minPeptides>1</minPeptides> <minRazorPeptides>1</minRazorPeptides> <minUniquePeptides>0</minUniquePeptides> - <useCounterparts>False</useCounterparts> + <useCounterparts>True</useCounterparts> <advancedSiteIntensities>True</advancedSiteIntensities> <customProteinQuantification>False</customProteinQuantification> <customProteinQuantificationFile/> <minRatioCount>2</minRatioCount> <restrictProteinQuantification>True</restrictProteinQuantification> - <restrictMods> - <string>Oxidation (M)</string> - <string>Acetyl (Protein N-term)</string> - </restrictMods> + <restrictMods/> <matchingTimeWindow>0</matchingTimeWindow> <matchingIonMobilityWindow>0</matchingIonMobilityWindow> <alignmentTimeWindow>0</alignmentTimeWindow> |