comparison maxquant.xml @ 7:d253b379322b draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"

6:2133b0be850a

<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1">
    <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>

            lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}
            lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}
            advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}
            matchBetweenRuns: ${search_opts.match_between_runs}
            includeContaminants: ${search_opts.incl_contaminants}
            quantMode: ${protein_quant.peptides_for_quantification}
            restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot}
            #if $protein_quant.only_unmod_prot.unmod_prot == 'True':
            #if $protein_quant.only_unmod_prot.mods_used_prot_quant:
            restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}]

                lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
                #end if
                #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
                lcmsRunType: 'Reporter ion MS2'
                reporterMassTolerance: 0.003
                reporterPif: ${pg.quant_method.reporter_pif}
                reporterFraction: 0
                reporterBasePeakRatio: 0
                filterPif: ${pg.quant_method.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

                   help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/>
            <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)"/>

        </section>

        <section name="protein_quant" title="Protein quantification" expanded="true">

            <param name="peptides_for_quantification" type="select" label="Peptides for quantification"

                </param>
                <when value="True">
                    <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="modification"/>
                    </param>
                    <!-- note: the following default is different to the mquant default -->
                    <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
                           truevalue="True" falsevalue="False"

                                       label="TMT-like"
                                       truevalue="True" falsevalue="False"/>
                            </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."/>
                </when>
            </conditional>
        </repeat>

        <expand macro="ptxqc-opts"/>

            <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 -->
            <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"/>

                            <param name="internallabel" value="TMT2plex-Lys127" />
                            <param name="terminallabel" value="TMT2plex-Nter127" />
                            <param name="tmtlike" value="True" />
                        </repeat>
                    </conditional>
                    <param name="filter_pif" value="False" />
                    <param name="reporter_pif" value="0.6" />
                </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_ms2" />
                    <conditional name="iso_labels">
                        <param name="labeling" value="itraq4plex" />
                    </conditional>
                    <param name="filter_pif" value="True" />
                    <param name="reporter_pif" value="0.8" />
                </conditional>
            </repeat>
            <param name="dry_run" value="True" />
            <param name="output" value="config,mqpar,mzTab" />
            <output name="config" file="02/config.yml" lines_diff="2" />

7:d253b379322b

<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@">
                <filter>'@NAME@' in output_opts['output']</filter>
            </data>

            lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}
            lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}
            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':
            #if $protein_quant.only_unmod_prot.mods_used_prot_quant:
            restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}]

                lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
                #end if
                #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
                lcmsRunType: 'Reporter ion MS2'
                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

                   help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/>
            <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"
                   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">

            <param name="peptides_for_quantification" type="select" label="Peptides for quantification"

                </param>
                <when value="True">
                    <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 -->
                    <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
                           truevalue="True" falsevalue="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>

        <expand macro="ptxqc-opts"/>

            <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"/>

                            <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_ms2"/>
                    <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="02/config.yml" lines_diff="2" />