Mercurial > repos > galaxyp > maxquant
diff maxquant.xml @ 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 |
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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" />