| Previous changeset 6:2133b0be850a (2020-05-06) Next changeset 8:ea0a1d50c83f (2020-06-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" |
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modified:
maxquant.xml mqparam.py 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 2133b0be850a -r d253b379322b maxquant.xml --- a/maxquant.xml Wed May 06 13:35:51 2020 -0400 +++ b/maxquant.xml Mon Jun 01 11:51:25 2020 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1">\n+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy2">\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@@ -91,6 +91,11 @@\n advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}\n matchBetweenRuns: ${search_opts.match_between_runs}\n includeContaminants: ${search_opts.incl_contaminants}\n+ minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length}\n+ maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length}\n+ decoyMode: ${search_opts.decoy_mode}\n+ peptideFdr: ${search_opts.psm_fdr}\n+ proteinFdr: ${search_opts.protein_fdr}\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@@ -151,10 +156,14 @@\n #if $pg.quant_method.select_quant_method == \'reporter_ion_ms2\':\n lcmsRunType: \'Reporter ion MS2\'\n reporterMassTolerance: 0.003\n- reporterPif: ${pg.quant_method.reporter_pif}\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_pif}\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@@ -275,7 +284,20 @@\n label="Include contaminants"\n truevalue="True" falsevalue="False"\n help="\xe2\x80\x98Yes\xe2\x80\x99 means that proteins from a contaminant list are automatically added to the list of proteins for in silico digestion (in the fasta file)"/>\n-\n+ <param name="decoy_mode" type="select"\n+ label="Decoy mode"\n+ help="The decoy sequences can be generated by reversing or randomizing the original protein sequences. Reversing is recommended.">\n+ <option value="revert" selected="true">Revert</option>\n+ <option value="randomize">Randomize</option>\n+ </param>\n+ <param name="psm_fdr" type="float" label="PSM FDR" min="0" value="0.01"\n+ help="Specify the desired false discovery rate (FDR) at the peptide spectrum match (PSM) level. It is determined by the target-decoy approach. A value of 0.01 stands for 1% FDR."/>\n+ <param name="protein_fdr" type="float" label="Protein FDR" min="0" value="0.01"\n+ help="Specify the desired false discovery rate (FDR) at the protein level. It is determined by the target-decoy approach. A value of 0.01 stands for 1% FDR."/>\n+ <param name="min_pep_length" type="integer" label="Minimum peptide length for unspecific searches" min="1" value="8"\n+ help="During unspecific searches peptides that have fewer amino acids than this value will be discarded. This applies also to semi-specific (e.g. semi tryptic) searches"/>\n+ <param name="max_pep_length" type="integer" label="Maximum peptide length for unspecific searches" min="1" value="25"\n+ help="During unspecific searches peptides that have more amino acids than this value will be discarded. This applies also to semi-specific (e.g. semi tryptic) searches"/>\n </section>\n \n <section name="protein_quant" title="Protein quantificati'..b'on to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>\n- <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" max="1"\n- help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>\n+ <conditional name="filter_by_pif">\n+ <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"\n+ truevalue="True" falsevalue="False"\n+ help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>\n+ <when value="True">\n+ <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"\n+ max="1"\n+ help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>\n+ </when>\n+ <when value="False"></when>\n+ </conditional>\n </when>\n </conditional>\n </repeat>\n@@ -540,6 +570,11 @@\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+ <param name="min_pep_length" value="7" /> <!-- non-default value -->\n+ <param name="max_pep_length" value="24" /> <!-- non-default value -->\n+ <param name="decoy_mode" value="randomize" /> <!-- non-default value -->\n+ <param name="psm_fdr" value="0.5" /> <!-- non-default value -->\n+ <param name="protein_fdr" value="0.4" /> <!-- 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@@ -568,8 +603,11 @@\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 name="filter_by_pif">\n+ <param name="filter_pif" value="False"/>\n+ <param name="reporter_pif"\n+ value="0.6"/> <!-- as filter_pif is False this value will be ignored and 0 used instead -->\n+ </conditional>\n </conditional>\n </repeat>\n <repeat name="paramGroups">\n@@ -578,12 +616,14 @@\n <param name="fixedModifications" value="" />\n <param name="enzymes" value="" />\n <conditional name="quant_method">\n- <param name="select_quant_method" value="reporter_ion_ms2" />\n+ <param name="select_quant_method" value="reporter_ion_ms2"/>\n <conditional name="iso_labels">\n- <param name="labeling" value="itraq4plex" />\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 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' |
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| diff -r 2133b0be850a -r d253b379322b mqparam.py --- a/mqparam.py Wed May 06 13:35:51 2020 -0400 +++ b/mqparam.py Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -343,8 +343,8 @@ self[i].set_silac(*silac) isobaricLabels = pg.pop('isobaricLabels', False) if isobaricLabels: - for l in isobaricLabels: - self[i].set_isobaric_label(*l) + for ibl in isobaricLabels: + self[i].set_isobaric_label(*ibl) for el in ['fixedModifications', 'variableModifications', 'enzymes']: lst = pg.pop(el, None) if lst is not None: |
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| diff -r 2133b0be850a -r d253b379322b test-data/01/config.yml --- a/test-data/01/config.yml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/01/config.yml Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -14,9 +14,14 @@ advancedSiteIntensities: True matchBetweenRuns: False includeContaminants: True + minPeptideLengthForUnspecificSearch: 8 + maxPeptideLengthForUnspecificSearch: 25 + decoyMode: revert + peptideFdr: 0.01 + proteinFdr: 0.01 quantMode: 1 restrictProteinQuantification: True - restrictMods: [] + restrictMods: [Oxidation (M),Acetyl (Protein N-term)] useCounterparts: True paramGroups: - files: ['BSA_min_23.mzXML'] |
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| diff -r 2133b0be850a -r d253b379322b test-data/01/mqpar.xml --- a/test-data/01/mqpar.xml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/01/mqpar.xml Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -83,7 +83,10 @@ <customProteinQuantificationFile/> <minRatioCount>2</minRatioCount> <restrictProteinQuantification>True</restrictProteinQuantification> - <restrictMods/> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> <matchingTimeWindow>0</matchingTimeWindow> <matchingIonMobilityWindow>0</matchingIonMobilityWindow> <alignmentTimeWindow>0</alignmentTimeWindow> |
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| diff -r 2133b0be850a -r d253b379322b test-data/02/config.yml --- a/test-data/02/config.yml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/02/config.yml Mon Jun 01 11:51:25 2020 -0400 |
| [ |
| @@ -14,6 +14,11 @@ 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] @@ -27,7 +32,7 @@ enzymeMode: 0 lcmsRunType: 'Reporter ion MS2' reporterMassTolerance: 0.003 - reporterPif: 0.6 + reporterPif: 0 reporterFraction: 0 reporterBasePeakRatio: 0 filterPif: False |
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| diff -r 2133b0be850a -r d253b379322b test-data/02/mqpar.xml --- a/test-data/02/mqpar.xml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/02/mqpar.xml Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -25,7 +25,7 @@ <separateLfq>False</separateLfq> <lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios> <lfqRequireMsms>True</lfqRequireMsms> - <decoyMode>revert</decoyMode> + <decoyMode>randomize</decoyMode> <boxCarMode>all</boxCarMode> <includeContaminants>False</includeContaminants> <maxPeptideMass>4600</maxPeptideMass> @@ -68,11 +68,11 @@ </intensityPredictionsFile> <minPepLen>7</minPepLen> <psmFdrCrosslink>0.01</psmFdrCrosslink> - <peptideFdr>0.01</peptideFdr> - <proteinFdr>0.01</proteinFdr> + <peptideFdr>0.5</peptideFdr> + <proteinFdr>0.4</proteinFdr> <siteFdr>0.01</siteFdr> - <minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch> - <maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch> + <minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch> + <maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch> <useNormRatiosForOccupancy>True</useNormRatiosForOccupancy> <minPeptides>1</minPeptides> <minRazorPeptides>1</minRazorPeptides> @@ -267,7 +267,7 @@ <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin> <matchLabelTimeTolMin>0</matchLabelTimeTolMin> <reporterMassTolerance>0.003</reporterMassTolerance> - <reporterPif>0.6</reporterPif> + <reporterPif>0</reporterPif> <filterPif>False</filterPif> <reporterFraction>0</reporterFraction> <reporterBasePeakRatio>0</reporterBasePeakRatio> |
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| diff -r 2133b0be850a -r d253b379322b test-data/03/config.yml --- a/test-data/03/config.yml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/03/config.yml Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -16,9 +16,14 @@ advancedSiteIntensities: True matchBetweenRuns: False includeContaminants: True + minPeptideLengthForUnspecificSearch: 8 + maxPeptideLengthForUnspecificSearch: 25 + decoyMode: revert + peptideFdr: 0.01 + proteinFdr: 0.01 quantMode: 1 restrictProteinQuantification: True - restrictMods: [] + restrictMods: [Oxidation (M),Acetyl (Protein N-term)] useCounterparts: True paramGroups: - files: ['BSA_min_22.mzxml'] |
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| diff -r 2133b0be850a -r d253b379322b test-data/03/mqpar.xml --- a/test-data/03/mqpar.xml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/03/mqpar.xml Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -83,7 +83,10 @@ <customProteinQuantificationFile/> <minRatioCount>2</minRatioCount> <restrictProteinQuantification>True</restrictProteinQuantification> - <restrictMods/> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> <matchingTimeWindow>0</matchingTimeWindow> <matchingIonMobilityWindow>0</matchingIonMobilityWindow> <alignmentTimeWindow>0</alignmentTimeWindow> |
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| diff -r 2133b0be850a -r d253b379322b test-data/04/config.yml --- a/test-data/04/config.yml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/04/config.yml Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -14,9 +14,14 @@ advancedSiteIntensities: True matchBetweenRuns: False includeContaminants: True + minPeptideLengthForUnspecificSearch: 8 + maxPeptideLengthForUnspecificSearch: 25 + decoyMode: revert + peptideFdr: 0.01 + proteinFdr: 0.01 quantMode: 1 restrictProteinQuantification: True - restrictMods: [] + restrictMods: [Oxidation (M),Acetyl (Protein N-term)] useCounterparts: True paramGroups: - files: ['BSA_min_23.mzXML', 'BSA_min_22.mzxml'] |
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| diff -r 2133b0be850a -r d253b379322b test-data/04/mqpar.xml --- a/test-data/04/mqpar.xml Wed May 06 13:35:51 2020 -0400 +++ b/test-data/04/mqpar.xml Mon Jun 01 11:51:25 2020 -0400 |
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| @@ -83,7 +83,10 @@ <customProteinQuantificationFile/> <minRatioCount>2</minRatioCount> <restrictProteinQuantification>True</restrictProteinQuantification> - <restrictMods/> + <restrictMods> + <string>Oxidation (M)</string> + <string>Acetyl (Protein N-term)</string> + </restrictMods> <matchingTimeWindow>0</matchingTimeWindow> <matchingIonMobilityWindow>0</matchingIonMobilityWindow> <alignmentTimeWindow>0</alignmentTimeWindow> |