Mercurial > repos > galaxyp > maxquant
changeset 7:d253b379322b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
| author | galaxyp |
|---|---|
| date | Mon, 01 Jun 2020 11:51:25 -0400 |
| parents | 2133b0be850a |
| children | ea0a1d50c83f |
| files | 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 |
| diffstat | 10 files changed, 99 insertions(+), 30 deletions(-) [+] |
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--- a/maxquant.xml Wed May 06 13:35:51 2020 -0400 +++ b/maxquant.xml Mon Jun 01 11:51:25 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1"> +<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy2"> <macros> <xml name="output" token_format="tabular" token_label="default description" token_name="default"> <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> @@ -91,6 +91,11 @@ advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities} matchBetweenRuns: ${search_opts.match_between_runs} includeContaminants: ${search_opts.incl_contaminants} + minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length} + maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length} + decoyMode: ${search_opts.decoy_mode} + peptideFdr: ${search_opts.psm_fdr} + proteinFdr: ${search_opts.protein_fdr} quantMode: ${protein_quant.peptides_for_quantification} restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot} #if $protein_quant.only_unmod_prot.unmod_prot == 'True': @@ -151,10 +156,14 @@ #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2': lcmsRunType: 'Reporter ion MS2' reporterMassTolerance: 0.003 - reporterPif: ${pg.quant_method.reporter_pif} + #if $pg.quant_method.filter_by_pif.filter_pif == 'True': + reporterPif: ${pg.quant_method.filter_by_pif.reporter_pif} + #else: + reporterPif: 0 + #end if reporterFraction: 0 reporterBasePeakRatio: 0 - filterPif: ${pg.quant_method.filter_pif} + filterPif: ${pg.quant_method.filter_by_pif.filter_pif} isobaricLabels: #if $pg.quant_method.iso_labels.labeling == 'custom': #for $l in $pg.quant_method.iso_labels.iso_label: @@ -275,7 +284,20 @@ label="Include contaminants" truevalue="True" falsevalue="False" help="‘Yes’ means that proteins from a contaminant list are automatically added to the list of proteins for in silico digestion (in the fasta file)"/> - + <param name="decoy_mode" type="select" + label="Decoy mode" + help="The decoy sequences can be generated by reversing or randomizing the original protein sequences. Reversing is recommended."> + <option value="revert" selected="true">Revert</option> + <option value="randomize">Randomize</option> + </param> + <param name="psm_fdr" type="float" label="PSM FDR" min="0" value="0.01" + 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."/> + <param name="protein_fdr" type="float" label="Protein FDR" min="0" value="0.01" + 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."/> + <param name="min_pep_length" type="integer" label="Minimum peptide length for unspecific searches" min="1" value="8" + 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"/> + <param name="max_pep_length" type="integer" label="Maximum peptide length for unspecific searches" min="1" value="25" + 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"/> </section> <section name="protein_quant" title="Protein quantification" expanded="true"> @@ -298,6 +320,8 @@ <param name="mods_used_prot_quant" type="select" multiple="true" label="Modifications used in protein quantification" help="Peptides containing only these modifications will be used for the quantification of proteins in addition to unmodified peptides. This includes ratio and intensity calculations including iBAQ"> + <expand macro="default_mod_option" value="Oxidation (M)"/> + <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> <expand macro="modification"/> </param> <!-- note: the following default is different to the mquant default --> @@ -460,11 +484,17 @@ </repeat> </when> </conditional> - <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF" - truevalue="True" falsevalue="False" - 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."/> - <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" max="1" - help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> + <conditional name="filter_by_pif"> + <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF" + truevalue="True" falsevalue="False" + 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."/> + <when value="True"> + <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" + max="1" + help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> + </when> + <when value="False"></when> + </conditional> </when> </conditional> </repeat> @@ -540,6 +570,11 @@ <param name="identifier_parse_rule" value=">([^\s]*)" /> <param name="description_parse_rule" value=">(.*)" /> <param name="incl_contaminants" value="False" /> <!-- non-default value --> + <param name="min_pep_length" value="7" /> <!-- non-default value --> + <param name="max_pep_length" value="24" /> <!-- non-default value --> + <param name="decoy_mode" value="randomize" /> <!-- non-default value --> + <param name="psm_fdr" value="0.5" /> <!-- non-default value --> + <param name="protein_fdr" value="0.4" /> <!-- non-default value --> <section name="protein_quant"> <param name="peptides_for_quantification" value="0"/><!-- non-default value --> <conditional name="only_unmod_prot"> @@ -568,8 +603,11 @@ <param name="tmtlike" value="True" /> </repeat> </conditional> - <param name="filter_pif" value="False" /> - <param name="reporter_pif" value="0.6" /> + <conditional name="filter_by_pif"> + <param name="filter_pif" value="False"/> + <param name="reporter_pif" + value="0.6"/> <!-- as filter_pif is False this value will be ignored and 0 used instead --> + </conditional> </conditional> </repeat> <repeat name="paramGroups"> @@ -578,12 +616,14 @@ <param name="fixedModifications" value="" /> <param name="enzymes" value="" /> <conditional name="quant_method"> - <param name="select_quant_method" value="reporter_ion_ms2" /> + <param name="select_quant_method" value="reporter_ion_ms2"/> <conditional name="iso_labels"> - <param name="labeling" value="itraq4plex" /> + <param name="labeling" value="itraq4plex"/> </conditional> - <param name="filter_pif" value="True" /> - <param name="reporter_pif" value="0.8" /> + <conditional name="filter_by_pif"> + <param name="filter_pif" value="True"/> + <param name="reporter_pif" value="0.8"/> <!-- as filter_pif is True this value is used --> + </conditional> </conditional> </repeat> <param name="dry_run" value="True" />
--- a/mqparam.py Wed May 06 13:35:51 2020 -0400 +++ b/mqparam.py Mon Jun 01 11:51:25 2020 -0400 @@ -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:
--- 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 @@ -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']
--- 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 @@ -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>
--- 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
--- 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 @@ -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>
--- 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 @@ -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']
--- 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 @@ -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>
--- 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 @@ -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']
--- 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 @@ -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>