Mercurial > repos > galaxyp > fragpipe

comparison macros.xml @ 4:e969a182e3cb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
author galaxyp
date Fri, 13 Dec 2024 15:17:28 +0000
parents da9ebef968bd
children
comparison
equal deleted inserted replaced
3:da9ebef968bd 4:e969a182e3cb
1 <macros> 1 <macros>
2 <import>msfragger_macros.xml</import> 2 <import>msfragger_macros.xml</import>
3 <token name="@TOOL_VERSION@">20.0</token> 3 <token name="@TOOL_VERSION@">20.0</token>
4 <token name="@VERSION_SUFFIX@">3</token> 4 <token name="@VERSION_SUFFIX@">4</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
348 </xml> 348 </xml>
349 349
350 <!-- Set Percolator workflow options --> 350 <!-- Set Percolator workflow options -->
351 <token name="@PERCOLATOR@"><![CDATA[ 351 <token name="@PERCOLATOR@"><![CDATA[
352 #set $prc = $wf.validation.validation_tab.psm_validation.percolator 352 #set $prc = $wf.validation.validation_tab.psm_validation.percolator
353 #set $wfdict['run-validation-tab'] = $wf.validation.validation_tab.run_validation
354 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
355 #set $wfdict['percolator.run-percolator'] = 'true' 353 #set $wfdict['percolator.run-percolator'] = 'true'
356 #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files) 354 #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files)
357 #set $wfdict['percolator.min-prob'] = str($prc.min_prob) 355 #set $wfdict['percolator.min-prob'] = str($prc.min_prob)
358 ]]></token> 356 ]]></token>
357
358 <xml name="msbooster">
359 <section name="msbooster" expanded="true" title="MSBooster">
360 <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
361 <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
362 <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/>
363 </section>
364 </xml>
365 <token name="@MSBOOSTER@"><![CDATA[
366 #set $prfx = $wf.validation.validation_tab.psm_validation.msbooster
367 #set $wfdict['msbooster.run-msbooster'] = 'true'
368 #set $wfdict['msbooster.predict-rt'] = str($prfx.predict_rt)
369 #set $wfdict['msbooster.predict-spectra'] = str($prfx.predict_spectra)
370 #set $wfdict['msbooster.use-correlated-features'] = str($prfx.use_correlated_features)
371 ]]></token>
372
359 373
360 <!-- Philosopher Report (phi-report) options --> 374 <!-- Philosopher Report (phi-report) options -->
361 <xml name="phi_report"> 375 <xml name="phi_report">
362 <conditional name="phi_report"> 376 <conditional name="phi_report">
363 <param name="run_phi_report" type="select" label="Generate Philosopher Reports"> 377 <param name="run_phi_report" type="select" label="Generate Philosopher Reports">
422 <!-- CrystalC options --> 436 <!-- CrystalC options -->
423 <xml name="crystalc"> 437 <xml name="crystalc">
424 <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/> 438 <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/>
425 </xml> 439 </xml>
426 440
427 <!-- MSBooster options. Disabled until DIA-NN integrated.
428 <xml name="msbooster">
429 <section name="msbooster" expanded="false" title="MSBooster">
430 <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
431 <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
432 <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/>
433 </section>
434 </xml>
435 -->
436
437 <!-- Protein Prophet options --> 441 <!-- Protein Prophet options -->
438 <xml name="protein_prophet" token_minprob="0.05"> 442 <xml name="protein_prophet" token_minprob="0.05">
439 <conditional name="protein_prophet"> 443 <conditional name="protein_prophet">
440 <param name="run_protein_prophet" type="select" label="Run Protein Prophet"> 444 <param name="run_protein_prophet" type="select" label="Run Protein Prophet">
441 <option value="true" selected="true">Yes</option> 445 <option value="true" selected="true">Yes</option>
482 <yield/> <!-- crystalc --> 486 <yield/> <!-- crystalc -->
483 <conditional name="psm_validation"> 487 <conditional name="psm_validation">
484 <param name="run_psm_validation" type="select" label="PSM Validation"> 488 <param name="run_psm_validation" type="select" label="PSM Validation">
485 <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option> 489 <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option>
486 <option value="percolator" selected="@PERC@">Run Percolator</option> 490 <option value="percolator" selected="@PERC@">Run Percolator</option>
487 <!-- MSBooster disabled until DIA-NN integrated
488 <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option> 491 <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option>
489 -->
490 <option value="no" selected="@NO@">Use workflow values</option> 492 <option value="no" selected="@NO@">Use workflow values</option>
491 </param> 493 </param>
492 <when value="peptide_prophet"> 494 <when value="peptide_prophet">
493 <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/> 495 <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/>
494 </when> 496 </when>
495 <when value="percolator"> 497 <when value="percolator">
496 <expand macro="percolator"/> 498 <expand macro="percolator"/>
497 </when> 499 </when>
498 <!-- MSBooster disabled until DIA-NN integrated
499 <when value="msbooster_percolator"> 500 <when value="msbooster_percolator">
500 <expand macro="msbooster"/> 501 <expand macro="msbooster"/>
501 <expand macro="percolator"/> 502 <expand macro="percolator"/>
502 </when> 503 </when>
503 -->
504 <when value="no"> 504 <when value="no">
505 </when> 505 </when>
506 </conditional> 506 </conditional>
507 <expand macro="protein_prophet" minprob="@PROTP_MINPROB@"/> 507 <expand macro="protein_prophet" minprob="@PROTP_MINPROB@"/>
508 <expand macro="phi_report"/> 508 <expand macro="phi_report"/>
522 #set $wfdict['percolator.run-percolator'] = 'false' 522 #set $wfdict['percolator.run-percolator'] = 'false'
523 @PEPTIDEPROPHET@ 523 @PEPTIDEPROPHET@
524 #elif $prfx.run_psm_validation == 'percolator' 524 #elif $prfx.run_psm_validation == 'percolator'
525 #set $wfdict['run-psm-validation'] = 'true' 525 #set $wfdict['run-psm-validation'] = 'true'
526 #set $wfdict['msbooster.run-msbooster'] = 'false' 526 #set $wfdict['msbooster.run-msbooster'] = 'false'
527 #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false'
527 @PERCOLATOR@ 528 @PERCOLATOR@
528 ##elif $prfx.run_psm_validation == 'msbooster_percolator' 529 #elif $prfx.run_psm_validation == 'msbooster_percolator'
529 # MSBooster disabled until DIA-NN integrated. 530 #set $wfdict['run-psm-validation'] = 'true'
531 #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false'
532 @MSBOOSTER@
533 @PERCOLATOR@
530 #end if 534 #end if
531 @PROTEINPROPHET@ 535 @PROTEINPROPHET@
532 @PHIREPORT@ 536 @PHIREPORT@
533 ]]></token> 537 ]]></token>
534 538