Mercurial > repos > galaxyp > openms_openswathworkflow

comparison OpenSwathWorkflow.xml @ 1:190554cf2195 draft

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/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:52:16 -0400
parents 380ced982ec7
children 56988709dec6
comparison
equal deleted inserted replaced
0:380ced982ec7 1:190554cf2195
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.1.0"> 4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.2.0.1">
5 <description>Complete workflow to run OpenSWATH</description> 5 <description>Complete workflow to run OpenSWATH</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathWorkflow</token> 7 <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
32 #end if 32 #end if
33 #if $param_out_features: 33 #if $param_out_features:
34 -out_features $param_out_features 34 -out_features $param_out_features
35 #end if 35 #end if
36 #if $param_out_tsv: 36 #if $param_out_tsv:
37 -out_tsv "$param_out_tsv" 37 -out_tsv $param_out_tsv
38 #end if
39 #if $param_out_osw:
40 -out_osw $param_out_osw
38 #end if 41 #end if
39 #if $param_out_chrom: 42 #if $param_out_chrom:
40 -out_chrom $param_out_chrom 43 -out_chrom $param_out_chrom
41 #end if 44 #end if
42 #if $param_rt_extraction_window: 45 #if $param_rt_extraction_window:
46 -mz_extraction_window $param_mz_extraction_window 49 -mz_extraction_window $param_mz_extraction_window
47 #end if 50 #end if
48 #if $param_ppm: 51 #if $param_ppm:
49 -ppm 52 -ppm
50 #end if 53 #end if
54 #if $param_sonar:
55 -sonar
56 #end if
51 #if $param_Scoring_stop_report_after_feature: 57 #if $param_Scoring_stop_report_after_feature:
52 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature 58 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
53 #end if 59 #end if
54 #if $param_Scoring_rt_normalization_factor: 60 #if $param_Scoring_rt_normalization_factor:
55 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor 61 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
65 #end if 71 #end if
66 #if $param_Scoring_TransitionGroupPicker_min_peak_width: 72 #if $param_Scoring_TransitionGroupPicker_min_peak_width:
67 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width 73 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
68 #end if 74 #end if
69 #if $param_Scoring_TransitionGroupPicker_background_subtraction: 75 #if $param_Scoring_TransitionGroupPicker_background_subtraction:
70 -Scoring:TransitionGroupPicker:background_subtraction $param_Scoring_TransitionGroupPicker_background_subtraction 76 -Scoring:TransitionGroupPicker:background_subtraction
77 #if " " in str($param_Scoring_TransitionGroupPicker_background_subtraction):
78 "$param_Scoring_TransitionGroupPicker_background_subtraction"
79 #else
80 $param_Scoring_TransitionGroupPicker_background_subtraction
81 #end if
71 #end if 82 #end if
72 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks: 83 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
73 -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks" 84 -Scoring:TransitionGroupPicker:recalculate_peaks
85 #if " " in str($param_Scoring_TransitionGroupPicker_recalculate_peaks):
86 "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
87 #else
88 $param_Scoring_TransitionGroupPicker_recalculate_peaks
89 #end if
74 #end if 90 #end if
75 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z: 91 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
76 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z 92 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
77 #end if 93 #end if
78 #if $param_Scoring_TransitionGroupPicker_minimal_quality: 94 #if $param_Scoring_TransitionGroupPicker_minimal_quality:
79 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality 95 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
80 #end if 96 #end if
81 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality: 97 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
82 -Scoring:TransitionGroupPicker:compute_peak_quality "$param_Scoring_TransitionGroupPicker_compute_peak_quality" 98 -Scoring:TransitionGroupPicker:compute_peak_quality
99 #if " " in str($param_Scoring_TransitionGroupPicker_compute_peak_quality):
100 "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
101 #else
102 $param_Scoring_TransitionGroupPicker_compute_peak_quality
103 #end if
83 #end if 104 #end if
84 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: 105 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
85 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length 106 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
86 #end if 107 #end if
87 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: 108 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
101 #end if 122 #end if
102 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: 123 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
103 -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages 124 -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
104 #end if 125 #end if
105 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: 126 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
106 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks 127 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
128 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks):
129 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks"
130 #else
131 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
132 #end if
107 #end if 133 #end if
108 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method: 134 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
109 -Scoring:TransitionGroupPicker:PeakPickerMRM:method $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method 135 -Scoring:TransitionGroupPicker:PeakPickerMRM:method
136 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method):
137 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method"
138 #else
139 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
140 #end if
110 #end if 141 #end if
111 #if $param_Scoring_DIAScoring_dia_extraction_window: 142 #if $param_Scoring_DIAScoring_dia_extraction_window:
112 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window 143 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
113 #end if 144 #end if
114 #if $param_Scoring_DIAScoring_dia_centroided: 145 #if $param_Scoring_DIAScoring_dia_centroided:
131 #end if 162 #end if
132 #if $param_Scoring_EMGScoring_max_iteration: 163 #if $param_Scoring_EMGScoring_max_iteration:
133 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration 164 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
134 #end if 165 #end if
135 #if $param_outlierDetection_outlierMethod: 166 #if $param_outlierDetection_outlierMethod:
136 -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod 167 -outlierDetection:outlierMethod
168 #if " " in str($param_outlierDetection_outlierMethod):
169 "$param_outlierDetection_outlierMethod"
170 #else
171 $param_outlierDetection_outlierMethod
172 #end if
137 #end if 173 #end if
138 #if $param_outlierDetection_useIterativeChauvenet: 174 #if $param_outlierDetection_useIterativeChauvenet:
139 -outlierDetection:useIterativeChauvenet 175 -outlierDetection:useIterativeChauvenet
140 #end if 176 #end if
141 #if $param_outlierDetection_RANSACMaxIterations: 177 #if $param_outlierDetection_RANSACMaxIterations:
198 #end if 234 #end if
199 #if $adv_opts.param_use_elution_model_score: 235 #if $adv_opts.param_use_elution_model_score:
200 -use_elution_model_score 236 -use_elution_model_score
201 #end if 237 #end if
202 #if $adv_opts.param_readOptions: 238 #if $adv_opts.param_readOptions:
203 -readOptions $adv_opts.param_readOptions 239 -readOptions
240 #if " " in str($adv_opts.param_readOptions):
241 "$adv_opts.param_readOptions"
242 #else
243 $adv_opts.param_readOptions
244 #end if
204 #end if 245 #end if
205 #if $adv_opts.param_mz_correction_function: 246 #if $adv_opts.param_mz_correction_function:
206 -mz_correction_function $adv_opts.param_mz_correction_function 247 -mz_correction_function
248 #if " " in str($adv_opts.param_mz_correction_function):
249 "$adv_opts.param_mz_correction_function"
250 #else
251 $adv_opts.param_mz_correction_function
252 #end if
253 #end if
254 #if $adv_opts.param_irt_mz_extraction_window:
255 -irt_mz_extraction_window $adv_opts.param_irt_mz_extraction_window
256 #end if
257 #if $adv_opts.param_ppm_irtwindow:
258 -ppm_irtwindow
207 #end if 259 #end if
208 #if $adv_opts.param_tempDirectory: 260 #if $adv_opts.param_tempDirectory:
209 -tempDirectory "$adv_opts.param_tempDirectory" 261 -tempDirectory "$adv_opts.param_tempDirectory"
210 #end if 262 #end if
211 #if $adv_opts.param_extraction_function: 263 #if $adv_opts.param_extraction_function:
212 -extraction_function $adv_opts.param_extraction_function 264 -extraction_function
265 #if " " in str($adv_opts.param_extraction_function):
266 "$adv_opts.param_extraction_function"
267 #else
268 $adv_opts.param_extraction_function
269 #end if
213 #end if 270 #end if
214 #if $adv_opts.param_batchSize: 271 #if $adv_opts.param_batchSize:
215 -batchSize $adv_opts.param_batchSize 272 -batchSize $adv_opts.param_batchSize
216 #end if 273 #end if
217 #if $adv_opts.param_force: 274 #if $adv_opts.param_force:
218 -force 275 -force
219 #end if 276 #end if
277 #if $adv_opts.param_Library_retentionTimeInterpretation:
278 -Library:retentionTimeInterpretation
279 #if " " in str($adv_opts.param_Library_retentionTimeInterpretation):
280 "$adv_opts.param_Library_retentionTimeInterpretation"
281 #else
282 $adv_opts.param_Library_retentionTimeInterpretation
283 #end if
284 #end if
285 #if $adv_opts.param_Library_override_group_label_check:
286 -Library:override_group_label_check
287 #end if
288 #if $adv_opts.param_Library_force_invalid_mods:
289 -Library:force_invalid_mods
290 #end if
220 #if $adv_opts.param_Scoring_quantification_cutoff: 291 #if $adv_opts.param_Scoring_quantification_cutoff:
221 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff 292 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
222 #end if 293 #end if
223 #if $adv_opts.param_Scoring_write_convex_hull: 294 #if $adv_opts.param_Scoring_write_convex_hull:
224 -Scoring:write_convex_hull 295 -Scoring:write_convex_hull
225 #end if 296 #end if
297 #if $adv_opts.param_Scoring_TransitionGroupPicker_use_precursors:
298 -Scoring:TransitionGroupPicker:use_precursors
299 #end if
226 #if $adv_opts.param_Scoring_Scores_use_shape_score: 300 #if $adv_opts.param_Scoring_Scores_use_shape_score:
227 -Scoring:Scores:use_shape_score $adv_opts.param_Scoring_Scores_use_shape_score 301 -Scoring:Scores:use_shape_score
302 #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score):
303 "$adv_opts.param_Scoring_Scores_use_shape_score"
304 #else
305 $adv_opts.param_Scoring_Scores_use_shape_score
306 #end if
228 #end if 307 #end if
229 #if $adv_opts.param_Scoring_Scores_use_coelution_score: 308 #if $adv_opts.param_Scoring_Scores_use_coelution_score:
230 -Scoring:Scores:use_coelution_score $adv_opts.param_Scoring_Scores_use_coelution_score 309 -Scoring:Scores:use_coelution_score
310 #if " " in str($adv_opts.param_Scoring_Scores_use_coelution_score):
311 "$adv_opts.param_Scoring_Scores_use_coelution_score"
312 #else
313 $adv_opts.param_Scoring_Scores_use_coelution_score
314 #end if
231 #end if 315 #end if
232 #if $adv_opts.param_Scoring_Scores_use_rt_score: 316 #if $adv_opts.param_Scoring_Scores_use_rt_score:
233 -Scoring:Scores:use_rt_score $adv_opts.param_Scoring_Scores_use_rt_score 317 -Scoring:Scores:use_rt_score
318 #if " " in str($adv_opts.param_Scoring_Scores_use_rt_score):
319 "$adv_opts.param_Scoring_Scores_use_rt_score"
320 #else
321 $adv_opts.param_Scoring_Scores_use_rt_score
322 #end if
234 #end if 323 #end if
235 #if $adv_opts.param_Scoring_Scores_use_library_score: 324 #if $adv_opts.param_Scoring_Scores_use_library_score:
236 -Scoring:Scores:use_library_score $adv_opts.param_Scoring_Scores_use_library_score 325 -Scoring:Scores:use_library_score
326 #if " " in str($adv_opts.param_Scoring_Scores_use_library_score):
327 "$adv_opts.param_Scoring_Scores_use_library_score"
328 #else
329 $adv_opts.param_Scoring_Scores_use_library_score
330 #end if
237 #end if 331 #end if
238 #if $adv_opts.param_Scoring_Scores_use_intensity_score: 332 #if $adv_opts.param_Scoring_Scores_use_intensity_score:
239 -Scoring:Scores:use_intensity_score $adv_opts.param_Scoring_Scores_use_intensity_score 333 -Scoring:Scores:use_intensity_score
334 #if " " in str($adv_opts.param_Scoring_Scores_use_intensity_score):
335 "$adv_opts.param_Scoring_Scores_use_intensity_score"
336 #else
337 $adv_opts.param_Scoring_Scores_use_intensity_score
338 #end if
240 #end if 339 #end if
241 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score: 340 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
242 -Scoring:Scores:use_nr_peaks_score $adv_opts.param_Scoring_Scores_use_nr_peaks_score 341 -Scoring:Scores:use_nr_peaks_score
342 #if " " in str($adv_opts.param_Scoring_Scores_use_nr_peaks_score):
343 "$adv_opts.param_Scoring_Scores_use_nr_peaks_score"
344 #else
345 $adv_opts.param_Scoring_Scores_use_nr_peaks_score
346 #end if
243 #end if 347 #end if
244 #if $adv_opts.param_Scoring_Scores_use_total_xic_score: 348 #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
245 -Scoring:Scores:use_total_xic_score $adv_opts.param_Scoring_Scores_use_total_xic_score 349 -Scoring:Scores:use_total_xic_score
350 #if " " in str($adv_opts.param_Scoring_Scores_use_total_xic_score):
351 "$adv_opts.param_Scoring_Scores_use_total_xic_score"
352 #else
353 $adv_opts.param_Scoring_Scores_use_total_xic_score
354 #end if
246 #end if 355 #end if
247 #if $adv_opts.param_Scoring_Scores_use_sn_score: 356 #if $adv_opts.param_Scoring_Scores_use_sn_score:
248 -Scoring:Scores:use_sn_score $adv_opts.param_Scoring_Scores_use_sn_score 357 -Scoring:Scores:use_sn_score
358 #if " " in str($adv_opts.param_Scoring_Scores_use_sn_score):
359 "$adv_opts.param_Scoring_Scores_use_sn_score"
360 #else
361 $adv_opts.param_Scoring_Scores_use_sn_score
362 #end if
249 #end if 363 #end if
250 #if $adv_opts.param_Scoring_Scores_use_dia_scores: 364 #if $adv_opts.param_Scoring_Scores_use_dia_scores:
251 -Scoring:Scores:use_dia_scores $adv_opts.param_Scoring_Scores_use_dia_scores 365 -Scoring:Scores:use_dia_scores
366 #if " " in str($adv_opts.param_Scoring_Scores_use_dia_scores):
367 "$adv_opts.param_Scoring_Scores_use_dia_scores"
368 #else
369 $adv_opts.param_Scoring_Scores_use_dia_scores
370 #end if
252 #end if 371 #end if
253 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation: 372 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
254 -Scoring:Scores:use_ms1_correlation 373 -Scoring:Scores:use_ms1_correlation
255 #end if 374 #end if
375 #if $adv_opts.param_Scoring_Scores_use_sonar_scores:
376 -Scoring:Scores:use_sonar_scores
377 #end if
256 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan: 378 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
257 -Scoring:Scores:use_ms1_fullscan 379 -Scoring:Scores:use_ms1_fullscan
258 #end if 380 #end if
259 #if $adv_opts.param_Scoring_Scores_use_uis_scores: 381 #if $adv_opts.param_Scoring_Scores_use_uis_scores:
260 -Scoring:Scores:use_uis_scores 382 -Scoring:Scores:use_uis_scores
261 #end if 383 #end if
262 #end if 384 #end if
263 </command> 385 </command>
264 <inputs> 386 <inputs>
265 <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> 387 <param name="param_in" type="data" format="mzml,mzxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
266 <sanitizer> 388 <sanitizer>
267 <valid initial="string.printable"> 389 <valid initial="string.printable">
268 <remove value="'"/> 390 <remove value="'"/>
269 <remove value="&quot;"/> 391 <remove value="&quot;"/>
270 </valid> 392 </valid>
271 </sanitizer> 393 </sanitizer>
272 </param> 394 </param>
273 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/> 395 <param name="param_tr" type="data" format="traml,tabular,pqp" optional="False" label="transition file ('TraML','tsv','pqp')" help="(-tr) "/>
274 <param name="param_tr_type" display="radio" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) "> 396 <param name="param_tr_type" display="radio" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) ">
275 <option value="traML">traML</option> 397 <option value="traML">traML</option>
276 <option value="tsv">tsv</option> 398 <option value="tsv">tsv</option>
277 <option value="csv">csv</option> 399 <option value="pqp">pqp</option>
278 </param> 400 </param>
279 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/> 401 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
280 <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) ">
281 <sanitizer>
282 <valid initial="string.printable">
283 <remove value="'"/>
284 <remove value="&quot;"/>
285 </valid>
286 </sanitizer>
287 </param>
288 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/> 402 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/>
289 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/> 403 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/>
290 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/> 404 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
405 <param name="param_sonar" display="radio" type="boolean" truevalue="-sonar" falsevalue="" checked="false" optional="True" label="data is scanning SWATH data" help="(-sonar) "/>
291 <param name="param_Scoring_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/> 406 <param name="param_Scoring_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/>
292 <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)"/> 407 <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)"/>
293 <param name="param_Scoring_uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_sn) "/> 408 <param name="param_Scoring_uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_sn) "/>
294 <param name="param_Scoring_uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_peak_area) "/> 409 <param name="param_Scoring_uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_peak_area) "/>
295 <param name="param_Scoring_TransitionGroupPicker_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/> 410 <param name="param_Scoring_TransitionGroupPicker_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
297 <param name="param_Scoring_TransitionGroupPicker_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that"> 412 <param name="param_Scoring_TransitionGroupPicker_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
298 <option value="none" selected="true">none</option> 413 <option value="none" selected="true">none</option>
299 <option value="smoothed">smoothed</option> 414 <option value="smoothed">smoothed</option>
300 <option value="original">original</option> 415 <option value="original">original</option>
301 </param> 416 </param>
302 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"> 417 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" display="radio" type="select" optional="False" value="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large">
303 <sanitizer> 418 <option value="true" selected="true">true</option>
304 <valid initial="string.printable"> 419 <option value="false">false</option>
305 <remove value="'"/>
306 <remove value="&quot;"/>
307 </valid>
308 </sanitizer>
309 </param> 420 </param>
310 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> 421 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
311 <param name="param_Scoring_TransitionGroupPicker_minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> 422 <param name="param_Scoring_TransitionGroupPicker_minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
312 <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="true" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"> 423 <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" display="radio" type="select" optional="False" value="true" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">
313 <sanitizer> 424 <option value="true" selected="true">true</option>
314 <valid initial="string.printable"> 425 <option value="false">false</option>
315 <remove value="'"/>
316 <remove value="&quot;"/>
317 </valid>
318 </sanitizer>
319 </param> 426 </param>
320 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/> 427 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
321 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/> 428 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
322 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> 429 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
323 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" falsevalue="" checked="false" optional="True" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "/> 430 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" falsevalue="" checked="false" optional="True" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "/>
357 <param name="param_outlierDetection_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="(-NrRTBins) This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/> 464 <param name="param_outlierDetection_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="(-NrRTBins) This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
358 <param name="param_outlierDetection_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/> 465 <param name="param_outlierDetection_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/>
359 <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/> 466 <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
360 <expand macro="advanced_options"> 467 <expand macro="advanced_options">
361 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) If set, tr_irt may be omitted"/> 468 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) If set, tr_irt may be omitted"/>
362 <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/> 469 <param name="param_swath_windows_file" type="data" format="txt" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
363 <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/> 470 <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/>
364 <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/> 471 <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/>
365 <param name="param_enable_uis_scoring" display="radio" type="boolean" truevalue="-enable_uis_scoring" falsevalue="" checked="false" optional="True" label="Enable additional scoring of identification assays" help="(-enable_uis_scoring) "/> 472 <param name="param_enable_uis_scoring" display="radio" type="boolean" truevalue="-enable_uis_scoring" falsevalue="" checked="false" optional="True" label="Enable additional scoring of identification assays" help="(-enable_uis_scoring) "/>
366 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/> 473 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
367 <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/> 474 <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/>
371 <param name="param_use_elution_model_score" display="radio" type="boolean" truevalue="-use_elution_model_score" falsevalue="" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score) "/> 478 <param name="param_use_elution_model_score" display="radio" type="boolean" truevalue="-use_elution_model_score" falsevalue="" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score) "/>
372 <param name="param_readOptions" display="radio" type="select" optional="False" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="(-readOptions) If you choose cache, make sure to also set tempDirectory"> 479 <param name="param_readOptions" display="radio" type="select" optional="False" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="(-readOptions) If you choose cache, make sure to also set tempDirectory">
373 <option value="normal" selected="true">normal</option> 480 <option value="normal" selected="true">normal</option>
374 <option value="cache">cache</option> 481 <option value="cache">cache</option>
375 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option> 482 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
483 <option value="workingInMemory">workingInMemory</option>
376 </param> 484 </param>
377 <param name="param_mz_correction_function" type="select" optional="False" value="none" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="(-mz_correction_function) "> 485 <param name="param_mz_correction_function" type="select" optional="False" value="none" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="(-mz_correction_function) ">
378 <option value="none" selected="true">none</option> 486 <option value="none" selected="true">none</option>
379 <option value="unweighted_regression">unweighted_regression</option> 487 <option value="unweighted_regression">unweighted_regression</option>
380 <option value="weighted_regression">weighted_regression</option> 488 <option value="weighted_regression">weighted_regression</option>
381 <option value="quadratic_regression">quadratic_regression</option> 489 <option value="quadratic_regression">quadratic_regression</option>
382 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option> 490 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option>
383 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option> 491 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option>
384 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option> 492 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
385 </param> 493 </param>
494 <param name="param_irt_mz_extraction_window" type="float" value="0.05" label="Extraction window used for iRT and m/z correction (in Thomson, use ppm use -ppm flag)" help="(-irt_mz_extraction_window) "/>
495 <param name="param_ppm_irtwindow" display="radio" type="boolean" truevalue="-ppm_irtwindow" falsevalue="" checked="false" optional="True" label="iRT m/z extraction_window is in ppm" help="(-ppm_irtwindow) "/>
386 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) "> 496 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
387 <sanitizer> 497 <sanitizer>
388 <valid initial="string.printable"> 498 <valid initial="string.printable">
389 <remove value="'"/> 499 <remove value="'"/>
390 <remove value="&quot;"/> 500 <remove value="&quot;"/>
395 <option value="tophat" selected="true">tophat</option> 505 <option value="tophat" selected="true">tophat</option>
396 <option value="bartlett">bartlett</option> 506 <option value="bartlett">bartlett</option>
397 </param> 507 </param>
398 <param name="param_batchSize" type="integer" min="0" optional="True" value="0" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 500-1000)" help="(-batchSize) "/> 508 <param name="param_batchSize" type="integer" min="0" optional="True" value="0" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 500-1000)" help="(-batchSize) "/>
399 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 509 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
510 <param name="param_Library_retentionTimeInterpretation" display="radio" type="select" optional="False" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) ">
511 <option value="iRT" selected="true">iRT</option>
512 <option value="seconds">seconds</option>
513 <option value="minutes">minutes</option>
514 </param>
515 <param name="param_Library_override_group_label_check" display="radio" type="boolean" truevalue="-Library:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
516 <param name="param_Library_force_invalid_mods" display="radio" type="boolean" truevalue="-Library:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/>
400 <param name="param_Scoring_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff) "/> 517 <param name="param_Scoring_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff) "/>
401 <param name="param_Scoring_write_convex_hull" display="radio" type="boolean" truevalue="-Scoring:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/> 518 <param name="param_Scoring_write_convex_hull" display="radio" type="boolean" truevalue="-Scoring:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/>
519 <param name="param_Scoring_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
402 <param name="param_Scoring_Scores_use_shape_score" display="radio" type="select" optional="False" value="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) "> 520 <param name="param_Scoring_Scores_use_shape_score" display="radio" type="select" optional="False" value="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) ">
403 <option value="true" selected="true">true</option> 521 <option value="true" selected="true">true</option>
404 <option value="false">false</option> 522 <option value="false">false</option>
405 </param> 523 </param>
406 <param name="param_Scoring_Scores_use_coelution_score" display="radio" type="select" optional="False" value="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) "> 524 <param name="param_Scoring_Scores_use_coelution_score" display="radio" type="select" optional="False" value="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) ">
429 </param> 547 </param>
430 <param name="param_Scoring_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) "> 548 <param name="param_Scoring_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) ">
431 <option value="true" selected="true">true</option> 549 <option value="true" selected="true">true</option>
432 <option value="false">false</option> 550 <option value="false">false</option>
433 </param> 551 </param>
434 <param name="param_Scoring_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "> 552 <param name="param_Scoring_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) If turned off, will not use fragment ion spectra for scoring">
435 <option value="true" selected="true">true</option> 553 <option value="true" selected="true">true</option>
436 <option value="false">false</option> 554 <option value="false">false</option>
437 </param> 555 </param>
438 <param name="param_Scoring_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/> 556 <param name="param_Scoring_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
557 <param name="param_Scoring_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>
439 <param name="param_Scoring_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-Scoring:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/> 558 <param name="param_Scoring_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-Scoring:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/>
440 <param name="param_Scoring_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/> 559 <param name="param_Scoring_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
441 </expand> 560 </expand>
442 </inputs> 561 </inputs>
443 <outputs> 562 <outputs>
444 <data name="param_out_features" format="featurexml"/> 563 <data name="param_out_features" format="featurexml"/>
564 <data name="param_out_tsv" format="tabular"/>
565 <data name="param_out_osw" format="osw"/>
445 <data name="param_out_chrom" format="mzml"/> 566 <data name="param_out_chrom" format="mzml"/>
446 </outputs> 567 </outputs>
447 <help>Complete workflow to run OpenSWATH 568 <help>Complete workflow to run OpenSWATH
448 569
449 570