Mercurial > repos > galaxyp > fragpipe
comparison macros.xml @ 6:59fec1e2a6c3 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
| author | galaxyp |
|---|---|
| date | Sun, 30 Mar 2025 23:00:45 +0000 |
| parents | e06c94fe89cc |
| children |
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| 5:e06c94fe89cc | 6:59fec1e2a6c3 |
|---|---|
| 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@">5</token> | 4 <token name="@VERSION_SUFFIX@">6</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> |
| 82 '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas && | 82 '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas && |
| 83 | 83 |
| 84 #if str($database_options) != 'none' | 84 #if str($database_options) != 'none' |
| 85 philosopher workspace --init && | 85 philosopher workspace --init && |
| 86 philosopher database --custom genericized_db.fas --prefix rev_ | 86 philosopher database --custom genericized_db.fas --prefix rev_ |
| 87 #if str($database_options) != 'decoy_and_contam' | 87 #if str($database_options) == 'decoy_and_contam' |
| 88 --contam | 88 --contam |
| 89 #end if | 89 #end if |
| 90 --contamprefix && | 90 --contamprefix && |
| 91 ln -s *-decoys-*.fas final_db.fas && | 91 ln -s *-decoys-*.fas final_db.fas && |
| 92 #else | 92 #else |
| 164 <section name="msfragger" expanded="false" title="MSFragger Options"> | 164 <section name="msfragger" expanded="false" title="MSFragger Options"> |
| 165 <expand macro="msfragger_default"/> | 165 <expand macro="msfragger_default"/> |
| 166 </section> | 166 </section> |
| 167 <expand macro="validation" | 167 <expand macro="validation" |
| 168 pep="false" | 168 pep="false" |
| 169 perc="true" | 169 perc="false" |
| 170 boost="false" | 170 boost="true" |
| 171 no="false" | 171 no="false" |
| 172 masswidth="5" | 172 masswidth="5" |
| 173 clevel="0" | 173 clevel="0" |
| 174 accmass="true" | 174 accmass="true" |
| 175 decoyprobs="true" | 175 decoyprobs="true" |
| 210 <section name="msfragger" expanded="false" title="MSFragger Options"> | 210 <section name="msfragger" expanded="false" title="MSFragger Options"> |
| 211 <expand macro="msfragger_nonspecific_HLA"/> | 211 <expand macro="msfragger_nonspecific_HLA"/> |
| 212 </section> | 212 </section> |
| 213 <expand macro="validation" | 213 <expand macro="validation" |
| 214 pep="false" | 214 pep="false" |
| 215 perc="true" | 215 perc="false" |
| 216 boost="false" | 216 boost="true" |
| 217 no="true" | 217 no="true" |
| 218 masswidth="5" | 218 masswidth="5" |
| 219 clevel="0" | 219 clevel="0" |
| 220 accmass="true" | 220 accmass="true" |
| 221 decoyprobs="true" | 221 decoyprobs="true" |
| 230 | 230 |
| 231 <when value="LFQ-MBR"> | 231 <when value="LFQ-MBR"> |
| 232 <section name="msfragger" expanded="false" title="MSFragger Options"> | 232 <section name="msfragger" expanded="false" title="MSFragger Options"> |
| 233 <expand macro="msfragger_LFQ_MBR"/> | 233 <expand macro="msfragger_LFQ_MBR"/> |
| 234 </section> | 234 </section> |
| 235 <!-- MSBooster should be enabled once included in FragPipe Galaxy tool --> | |
| 236 <expand macro="validation" | 235 <expand macro="validation" |
| 237 pep="false" | 236 pep="false" |
| 238 perc="true" | 237 perc="false" |
| 239 boost="false" | 238 boost="true" |
| 240 no="true" | 239 no="true" |
| 241 masswidth="5" | 240 masswidth="5" |
| 242 clevel="0" | 241 clevel="0" |
| 243 accmass="true" | 242 accmass="true" |
| 244 decoyprobs="true" | 243 decoyprobs="true" |
| 268 <section name="msfragger" expanded="false" title="MSFragger Options"> | 267 <section name="msfragger" expanded="false" title="MSFragger Options"> |
| 269 <expand macro="msfragger_TMT"/> | 268 <expand macro="msfragger_TMT"/> |
| 270 </section> | 269 </section> |
| 271 <expand macro="validation" | 270 <expand macro="validation" |
| 272 pep="false" | 271 pep="false" |
| 273 perc="true" | 272 perc="false" |
| 274 boost="false" | 273 boost="true" |
| 275 no="false" | 274 no="false" |
| 276 masswidth="5" | 275 masswidth="5" |
| 277 clevel="0" | 276 clevel="0" |
| 278 accmass="true" | 277 accmass="true" |
| 279 decoyprobs="true" | 278 decoyprobs="true" |
| 522 #set $wfdict['percolator.run-percolator'] = 'false' | 521 #set $wfdict['percolator.run-percolator'] = 'false' |
| 523 @PEPTIDEPROPHET@ | 522 @PEPTIDEPROPHET@ |
| 524 #elif $prfx.run_psm_validation == 'percolator' | 523 #elif $prfx.run_psm_validation == 'percolator' |
| 525 #set $wfdict['run-psm-validation'] = 'true' | 524 #set $wfdict['run-psm-validation'] = 'true' |
| 526 #set $wfdict['msbooster.run-msbooster'] = 'false' | 525 #set $wfdict['msbooster.run-msbooster'] = 'false' |
| 527 #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false' | 526 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' |
| 528 @PERCOLATOR@ | 527 @PERCOLATOR@ |
| 529 #elif $prfx.run_psm_validation == 'msbooster_percolator' | 528 #elif $prfx.run_psm_validation == 'msbooster_percolator' |
| 530 #set $wfdict['run-psm-validation'] = 'true' | 529 #set $wfdict['run-psm-validation'] = 'true' |
| 531 #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false' | 530 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' |
| 532 @MSBOOSTER@ | 531 @MSBOOSTER@ |
| 533 @PERCOLATOR@ | 532 @PERCOLATOR@ |
| 534 #end if | 533 #end if |
| 535 @PROTEINPROPHET@ | 534 @PROTEINPROPHET@ |
| 536 @PHIREPORT@ | 535 @PHIREPORT@ |