maxquant: maxquant.xml comparison

comparison maxquant.xml @ 9:fe479bf15bd3 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"

author	galaxyp
date	Fri, 12 Mar 2021 08:39:34 +0000
parents	710a80ad14f5
children	68d8dcdbddb1

comparison

equal deleted inserted replaced

-:55f8e3f91e0b
+:fe479bf15bd3
-<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@">
 <filter>'@NAME@' in output_opts['output']</filter>
 </data>
 #end if
 separateLfq: ${protein_quant.lfq_opts.separateLfq}
 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}
 decoyMode: ${search_opts.decoy_mode}
 peptideFdr: ${search_opts.psm_fdr}
 - [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
+#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"/>
 </configfiles>
 help="The minimum number of unique peptides a protein group should have to be considered as identified and reported in the final table."/>
 <param name="calc_peak_properties" type="boolean" checked="false"
 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"
+<conditional name="mbr">
-label="Match between runs"
+<param name="match_between_runs" type="select"
-truevalue="True" falsevalue="False"
+label="Match between runs"
-help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS 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"
 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"
 help="Select a method if needed.">
 <option value="">None</option>
 <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">
 <param name="light_labels" type="select" label="light labels"
 multiple="true" help="Select zero or more light modifications.">
 label="Skip normalization"
 truevalue="True" falsevalue="False"
 help="If checked the high-speed version of MaxLFQ is used. This is recommended for large numbers of samples (Experiments). For less than 10 samples the original MaxLFQ normalization algorithm is used."/>
 </when>
 <when value="reporter_ion_ms2">
+<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>
+<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>
 <param name="output" value="config,mqpar,mzTab" />
 <output name="config" file="02/config.yml" lines_diff="2" />
 <!-- 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="&gt;([^\s]*)" />
+<param name="description_parse_rule" value="&gt;(.*)" />
+<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" />
 <param name="fasta_files" value="bsa.fasta" />
 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
 </repeat>
 <param name="dry_run" value="True" />
 <param name="output" value="config,mqpar" />
 <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="^&gt;.*\|(.*)\|.*$" />
+<param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
+<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" />
 <param name="fasta_files" value="bsa.fasta" />
 - label free (LFQ): Protein intensity will be reported as 'LFQ intensity' columns in the proteinGroups table
 - label based: quantifies MS1 labelled samples ('SILAC', 'Dimethyl', 'ICAT', 'ICPL', 'mTRAQ', '18 O')
 - 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
 **Output files**

Mercurial > repos > galaxyp > maxquant

comparison maxquant.xml @ 9:fe479bf15bd3 draft