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comparison maxquant.xml @ 6:f2f79f0be7d1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
author galaxyp
date Mon, 01 Jun 2020 15:50:52 +0000
parents 1cdde5989a2d
children 710a80ad14f5
comparison
equal deleted inserted replaced
5:1cdde5989a2d 6:f2f79f0be7d1
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy2">
2 <macros> 2 <macros>
3 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> 4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output_opts['output']</filter> 5 <filter>'@NAME@' in output_opts['output']</filter>
6 </data> 6 </data>
89 lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios} 89 lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}
90 lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms} 90 lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}
91 advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities} 91 advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}
92 matchBetweenRuns: ${search_opts.match_between_runs} 92 matchBetweenRuns: ${search_opts.match_between_runs}
93 includeContaminants: ${search_opts.incl_contaminants} 93 includeContaminants: ${search_opts.incl_contaminants}
94 minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length}
95 maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length}
96 decoyMode: ${search_opts.decoy_mode}
97 peptideFdr: ${search_opts.psm_fdr}
98 proteinFdr: ${search_opts.protein_fdr}
94 quantMode: ${protein_quant.peptides_for_quantification} 99 quantMode: ${protein_quant.peptides_for_quantification}
95 restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot} 100 restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot}
96 #if $protein_quant.only_unmod_prot.unmod_prot == 'True': 101 #if $protein_quant.only_unmod_prot.unmod_prot == 'True':
97 #if $protein_quant.only_unmod_prot.mods_used_prot_quant: 102 #if $protein_quant.only_unmod_prot.mods_used_prot_quant:
98 restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}] 103 restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}]
149 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount} 154 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
150 #end if 155 #end if
151 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2': 156 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
152 lcmsRunType: 'Reporter ion MS2' 157 lcmsRunType: 'Reporter ion MS2'
153 reporterMassTolerance: 0.003 158 reporterMassTolerance: 0.003
154 reporterPif: ${pg.quant_method.reporter_pif} 159 #if $pg.quant_method.filter_by_pif.filter_pif == 'True':
160 reporterPif: ${pg.quant_method.filter_by_pif.reporter_pif}
161 #else:
162 reporterPif: 0
163 #end if
155 reporterFraction: 0 164 reporterFraction: 0
156 reporterBasePeakRatio: 0 165 reporterBasePeakRatio: 0
157 filterPif: ${pg.quant_method.filter_pif} 166 filterPif: ${pg.quant_method.filter_by_pif.filter_pif}
158 isobaricLabels: 167 isobaricLabels:
159 #if $pg.quant_method.iso_labels.labeling == 'custom': 168 #if $pg.quant_method.iso_labels.labeling == 'custom':
160 #for $l in $pg.quant_method.iso_labels.iso_label: 169 #for $l in $pg.quant_method.iso_labels.iso_label:
161 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] 170 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
162 #end for 171 #end for
273 help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/> 282 help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/>
274 <param name="incl_contaminants" type="boolean" checked="true" 283 <param name="incl_contaminants" type="boolean" checked="true"
275 label="Include contaminants" 284 label="Include contaminants"
276 truevalue="True" falsevalue="False" 285 truevalue="True" falsevalue="False"
277 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)"/> 286 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)"/>
278 287 <param name="decoy_mode" type="select"
288 label="Decoy mode"
289 help="The decoy sequences can be generated by reversing or randomizing the original protein sequences. Reversing is recommended.">
290 <option value="revert" selected="true">Revert</option>
291 <option value="randomize">Randomize</option>
292 </param>
293 <param name="psm_fdr" type="float" label="PSM FDR" min="0" value="0.01"
294 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."/>
295 <param name="protein_fdr" type="float" label="Protein FDR" min="0" value="0.01"
296 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."/>
297 <param name="min_pep_length" type="integer" label="Minimum peptide length for unspecific searches" min="1" value="8"
298 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"/>
299 <param name="max_pep_length" type="integer" label="Maximum peptide length for unspecific searches" min="1" value="25"
300 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"/>
279 </section> 301 </section>
280 302
281 <section name="protein_quant" title="Protein quantification" expanded="true"> 303 <section name="protein_quant" title="Protein quantification" expanded="true">
282 304
283 <param name="peptides_for_quantification" type="select" label="Peptides for quantification" 305 <param name="peptides_for_quantification" type="select" label="Peptides for quantification"
296 </param> 318 </param>
297 <when value="True"> 319 <when value="True">
298 <param name="mods_used_prot_quant" type="select" multiple="true" 320 <param name="mods_used_prot_quant" type="select" multiple="true"
299 label="Modifications used in protein quantification" 321 label="Modifications used in protein quantification"
300 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"> 322 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">
323 <expand macro="default_mod_option" value="Oxidation (M)"/>
324 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
301 <expand macro="modification"/> 325 <expand macro="modification"/>
302 </param> 326 </param>
303 <!-- note: the following default is different to the mquant default --> 327 <!-- note: the following default is different to the mquant default -->
304 <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true" 328 <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
305 truevalue="True" falsevalue="False" 329 truevalue="True" falsevalue="False"
458 label="TMT-like" 482 label="TMT-like"
459 truevalue="True" falsevalue="False"/> 483 truevalue="True" falsevalue="False"/>
460 </repeat> 484 </repeat>
461 </when> 485 </when>
462 </conditional> 486 </conditional>
463 <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF" 487 <conditional name="filter_by_pif">
464 truevalue="True" falsevalue="False" 488 <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"
465 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."/> 489 truevalue="True" falsevalue="False"
466 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" max="1" 490 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."/>
467 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> 491 <when value="True">
492 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
493 max="1"
494 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
495 </when>
496 <when value="False"></when>
497 </conditional>
468 </when> 498 </when>
469 </conditional> 499 </conditional>
470 </repeat> 500 </repeat>
471 501
472 <expand macro="ptxqc-opts"/> 502 <expand macro="ptxqc-opts"/>
538 <param name="ftype" value=".mzxml" /> 568 <param name="ftype" value=".mzxml" />
539 <param name="fasta_files" value="bsa.fasta" /> 569 <param name="fasta_files" value="bsa.fasta" />
540 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 570 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
541 <param name="description_parse_rule" value="&gt;(.*)" /> 571 <param name="description_parse_rule" value="&gt;(.*)" />
542 <param name="incl_contaminants" value="False" /> <!-- non-default value --> 572 <param name="incl_contaminants" value="False" /> <!-- non-default value -->
573 <param name="min_pep_length" value="7" /> <!-- non-default value -->
574 <param name="max_pep_length" value="24" /> <!-- non-default value -->
575 <param name="decoy_mode" value="randomize" /> <!-- non-default value -->
576 <param name="psm_fdr" value="0.5" /> <!-- non-default value -->
577 <param name="protein_fdr" value="0.4" /> <!-- non-default value -->
543 <section name="protein_quant"> 578 <section name="protein_quant">
544 <param name="peptides_for_quantification" value="0"/><!-- non-default value --> 579 <param name="peptides_for_quantification" value="0"/><!-- non-default value -->
545 <conditional name="only_unmod_prot"> 580 <conditional name="only_unmod_prot">
546 <param name="unmod_prot" value="True"/> 581 <param name="unmod_prot" value="True"/>
547 <param name="mods_used_prot_quant" value="Pro5,Pro6"/> 582 <param name="mods_used_prot_quant" value="Pro5,Pro6"/>
566 <param name="internallabel" value="TMT2plex-Lys127" /> 601 <param name="internallabel" value="TMT2plex-Lys127" />
567 <param name="terminallabel" value="TMT2plex-Nter127" /> 602 <param name="terminallabel" value="TMT2plex-Nter127" />
568 <param name="tmtlike" value="True" /> 603 <param name="tmtlike" value="True" />
569 </repeat> 604 </repeat>
570 </conditional> 605 </conditional>
571 <param name="filter_pif" value="False" /> 606 <conditional name="filter_by_pif">
572 <param name="reporter_pif" value="0.6" /> 607 <param name="filter_pif" value="False"/>
608 <param name="reporter_pif"
609 value="0.6"/> <!-- as filter_pif is False this value will be ignored and 0 used instead -->
610 </conditional>
573 </conditional> 611 </conditional>
574 </repeat> 612 </repeat>
575 <repeat name="paramGroups"> 613 <repeat name="paramGroups">
576 <param name="files" value="BSA_min_22"/> 614 <param name="files" value="BSA_min_22"/>
577 <param name="variableModifications" value="" /> 615 <param name="variableModifications" value="" />
578 <param name="fixedModifications" value="" /> 616 <param name="fixedModifications" value="" />
579 <param name="enzymes" value="" /> 617 <param name="enzymes" value="" />
580 <conditional name="quant_method"> 618 <conditional name="quant_method">
581 <param name="select_quant_method" value="reporter_ion_ms2" /> 619 <param name="select_quant_method" value="reporter_ion_ms2"/>
582 <conditional name="iso_labels"> 620 <conditional name="iso_labels">
583 <param name="labeling" value="itraq4plex" /> 621 <param name="labeling" value="itraq4plex"/>
584 </conditional> 622 </conditional>
585 <param name="filter_pif" value="True" /> 623 <conditional name="filter_by_pif">
586 <param name="reporter_pif" value="0.8" /> 624 <param name="filter_pif" value="True"/>
625 <param name="reporter_pif" value="0.8"/> <!-- as filter_pif is True this value is used -->
626 </conditional>
587 </conditional> 627 </conditional>
588 </repeat> 628 </repeat>
589 <param name="dry_run" value="True" /> 629 <param name="dry_run" value="True" />
590 <param name="output" value="config,mqpar,mzTab" /> 630 <param name="output" value="config,mqpar,mzTab" />
591 <output name="config" file="02/config.yml" lines_diff="2" /> 631 <output name="config" file="02/config.yml" lines_diff="2" />