Mercurial > repos > galaxyp > maxquant
diff maxquant.xml @ 10:f522c08e900c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
| author | galaxyp |
|---|---|
| date | Fri, 12 Mar 2021 08:41:06 +0000 |
| parents | ea0a1d50c83f |
| children | d72c96ad9a16 |
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--- a/maxquant.xml Fri Feb 19 21:24:41 2021 +0000 +++ b/maxquant.xml Fri Mar 12 08:41:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy3"> +<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy4"> <macros> <xml name="output" token_format="tabular" token_label="default description" token_name="default"> <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> @@ -89,7 +89,14 @@ lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios} lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms} advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities} - matchBetweenRuns: ${search_opts.match_between_runs} + matchBetweenRuns: ${search_opts.mbr.match_between_runs} + #if $search_opts.mbr.match_between_runs == 'True': + matchingTimeWindow: ${search_opts.mbr.matching_time_window} + matchingIonMobilityWindow: ${search_opts.mbr.matching_ion_mobility_window} + alignmentTimeWindow: ${search_opts.mbr.alignment_time_window} + alignmentIonMobilityWindow: ${search_opts.mbr.alignment_ion_mobility_window} + matchUnidentifiedFeatures: ${search_opts.mbr.match_unidentified_features} + #end if includeContaminants: ${search_opts.incl_contaminants} minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length} maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length} @@ -223,7 +230,78 @@ - [iodoTMT6plex-Cys130,'',0,0,0,0,True] - [iodoTMT6plex-Cys131,'',0,0,0,0,True] #end if - #end if + #end if + #if $pg.quant_method.select_quant_method == 'reporter_ion_ms3': + lcmsRunType: 'Reporter ion MS3' + reporterMassTolerance: 0.003 + #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_by_pif.filter_pif} + isobaricLabels: + #if $pg.quant_method.iso_labels.labeling == 'custom': + #for $l in $pg.quant_method.iso_labels.iso_label: + - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] + #end for + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': + - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] + - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt6plex': + - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] + - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True] + - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True] + - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True] + - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True] + - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt8plex': + - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] + - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True] + - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True] + - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True] + - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True] + - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True] + - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True] + - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': + @TMT10PLEX@ + #end if + #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': + @TMT10PLEX@ + - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] + #end if + #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': + - [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] + #end if + #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': + - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] + - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False] + - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False] + - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False] + - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False] + - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False] + - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False] + - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False] + #end if + #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex': + - [iodoTMT6plex-Cys126,'',0,0,0,0,True] + - [iodoTMT6plex-Cys127,'',0,0,0,0,True] + - [iodoTMT6plex-Cys128,'',0,0,0,0,True] + - [iodoTMT6plex-Cys129,'',0,0,0,0,True] + - [iodoTMT6plex-Cys130,'',0,0,0,0,True] + - [iodoTMT6plex-Cys131,'',0,0,0,0,True] + #end if + #end if #end for </configfile> <expand macro="ptxqc"/> @@ -276,10 +354,29 @@ label="Calculate peak properties" truevalue="True" falsevalue="False" help="If checked, several quantities characterizing peaks and isotopes patterns are calculated. This may lead to a substantial increase in computation time."/> - <param name="match_between_runs" type="boolean" checked="false" - label="Match between runs" - truevalue="True" falsevalue="False" - help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/> + <conditional name="mbr"> + <param name="match_between_runs" type="select" + label="Match between runs" + help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."> + <option value="False" selected="true">No</option> + <option value="True">Yes</option> + </param> + <when value="False"/> + <when value="True"> + <param name="matching_time_window" type="float" label="Match Time Window [min]" min="0" value="0.7" + help="The time window that is used in 'Match between runs' for the transfer of identifications."/> + <param name="matching_ion_mobility_window" type="float" label="Match Ion Mobility Window" min="0" value="0.05" + help="The ion mobility window that is used in 'Match between runs' for the transfer of identifications."/> + <param name="alignment_time_window" type="integer" label="Alignment Time Window [min]" min="0" value="20" + help="The time window that is used in retention time alignment to search for the best alignment function."/> + <param name="alignment_ion_mobility_window" type="integer" label="Alignment Ion Mobility" min="0" value="1" + help="The ion mobility window that is used in ion mobility alignment to search for the best alignment function."/> + <param name="match_unidentified_features" type="boolean" checked="false" + label="Match unidentified Features" + truevalue="True" falsevalue="False" + help="Also unidentified peptide features will be matched between runs. Their expression profiles over multiple samples are written into the table called 'matchedFeatures.txt'."/> + </when> + </conditional> <param name="incl_contaminants" type="boolean" checked="true" label="Include contaminants" truevalue="True" falsevalue="False" @@ -410,6 +507,7 @@ <option value="lfq">label free quantification</option> <option value="silac">label based quantification</option> <option value="reporter_ion_ms2">reporter ion MS2</option> + <option value="reporter_ion_ms3">reporter ion MS3</option> </param> <when value=""/> <when value="silac"> @@ -496,6 +594,60 @@ <when value="False"></when> </conditional> </when> + <when value="reporter_ion_ms3"> + <conditional name="iso_labels"> + <param name="labeling" type="select" label="isobaric labeling" + help="Select one of the standard labelings (correction factors are zero) or create a custom labeling."> + <option value="custom">custom</option> + <option value="tmt2plex">TMT2plex</option> + <option value="tmt6plex">TMT6plex</option> + <option value="tmt8plex">TMT8plex</option> + <option value="tmt10plex">TMT10plex</option> + <option value="tmt11plex">TMT11plex</option> + <option value="itraq4plex">iTRAQ4plex</option> + <option value="itraq8plex">iTRAQ8plex</option> + <option value="iodotmt6plex">iodoTMT6plex</option> + </param> + + <when value="tmt2plex"></when> + <when value="tmt6plex"></when> + <when value="tmt8plex"></when> + <when value="tmt10plex"></when> + <when value="tmt11plex"></when> + <when value="itraq4plex"></when> + <when value="itraq8plex"></when> + <when value="iodotmt6plex"></when> + <when value="custom"> + <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> + <param name="internallabel" type="select" label="internal label" help="contains Lys"> + <expand macro="iso_labels"/> + </param> + <param name="terminallabel" type="select" label="terminal label" help="contains Nter"> + <option value="">None</option> + <expand macro="iso_labels"/> + </param> + <param name="cm2" type="float" label="correction factor -2%" value="0.0"/> + <param name="cm1" type="float" label="correction factor -1%" value="0.0"/> + <param name="cp1" type="float" label="correction factor +1%" value="0.0"/> + <param name="cp2" type="float" label="correction factor +2%" value="0.0"/> + <param type="boolean" name="tmtlike" checked="false" + label="TMT-like" + truevalue="True" falsevalue="False"/> + </repeat> + </when> + </conditional> + <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> @@ -632,6 +784,82 @@ <!-- high difference due to unconsistant xml formatting in MQ --> <output name="mqpar" file="02/mqpar.xml" lines_diff="24" /> </test> + <!-- reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only --> + <test expect_num_outputs="3"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="bsa.fasta" /> + <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"> + <param name="unmod_prot" value="True"/> + <param name="mods_used_prot_quant" value="Pro5,Pro6"/> + </conditional> + </section> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_23.mzXML"/> + <param name="variableModifications" value="Oxidation (M)" /> + <param name="fixedModifications" value="" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="reporter_ion_ms3" /> + <conditional name="iso_labels"> + <param name="labeling" value="custom" /> + <repeat name="iso_label"> + <param name="internallabel" value="TMT2plex-Lys126" /> + <param name="terminallabel" value="TMT2plex-Nter126" /> + <param name="tmtlike" value="True" /> + <param name="cp1" value="6.7" /> + <param name="cp2" value="3" /> + </repeat> + <repeat name="iso_label"> + <param name="internallabel" value="TMT2plex-Lys127" /> + <param name="terminallabel" value="TMT2plex-Nter127" /> + <param name="tmtlike" value="True" /> + </repeat> + </conditional> + <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"> + <param name="files" value="BSA_min_22"/> + <param name="variableModifications" value="" /> + <param name="fixedModifications" value="" /> + <param name="enzymes" value="" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="reporter_ion_ms3"/> + <conditional name="iso_labels"> + <param name="labeling" value="itraq4plex"/> + </conditional> + <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" /> + <param name="output" value="config,mqpar,mzTab" /> + <output name="config" file="06/config.yml" lines_diff="2"> + <assert_contents> + <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" /> + </assert_contents> + </output> + <output name="mqpar" file="06/mqpar.xml" lines_diff="6"> + <assert_contents> + <has_text_matching expression=".lcmsRunType.Reporter ion MS3.\/lcmsRunType." /> + </assert_contents> + </output> + </test> <!-- lfq, testing yaml conf file and mqpar.xml only --> <test expect_num_outputs="2"> <param name="ftype" value=".mzxml" /> @@ -654,6 +882,37 @@ <output name="config" file="03/config.yml" lines_diff="2" /> <output name="mqpar" file="03/mqpar.xml" lines_diff="10" /> </test> + <!-- Test for MBR --> + <test expect_num_outputs="2"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value="^>.*\|(.*)\|.*$" /> + <param name="description_parse_rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" /> + <param name="min_unique_pep" value="1" /> + <param name="ibaq" value="True" /> + <param name="match_between_runs" value="True" /> + <param name="ibaqLogFit" value="False" /> + <repeat name="paramGroups"> + <param name="files" value="BSA_min_22"/> + <param name="maxMissedCleavages" value="1"/> + <param name="variableModifications" value="Oxidation (M)" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="lfq" /> + </conditional> + </repeat> + <param name="dry_run" value="True" /> + <param name="output" value="config,mqpar" /> + <output name="config" file="05/config.yml" lines_diff="2"> + <assert_contents> + <has_text_matching expression="matchBetweenRuns\: True" /> + </assert_contents> + </output> + <output name="mqpar" file="05/mqpar.xml" lines_diff="4"> + <assert_contents> + <has_text_matching expression=".matchBetweenRuns.True.\/matchBetweenRuns." /> + </assert_contents> + </output> + </test> <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only --> <test expect_num_outputs="2"> <param name="ftype" value=".mzxml" /> @@ -744,7 +1003,7 @@ - for two channels: choose options from light and heavy sections - for three channels: choose options from light, medium and heavy sections - - 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 + - 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 - PTXQC quality control: quality control software creates an automatic quality control pdf report