Mercurial > repos > galaxyp > openms_openswathworkflow

comparison OpenSwathWorkflow.xml @ 1:34479f097d1b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:46:58 -0400
parents 99766e796721
children 372279190f47
comparison
equal deleted inserted replaced
0:99766e796721 1:34479f097d1b
65 #end if 65 #end if
66 #if $param_Scoring_TransitionGroupPicker_min_peak_width: 66 #if $param_Scoring_TransitionGroupPicker_min_peak_width:
67 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width 67 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
68 #end if 68 #end if
69 #if $param_Scoring_TransitionGroupPicker_background_subtraction: 69 #if $param_Scoring_TransitionGroupPicker_background_subtraction:
70 -Scoring:TransitionGroupPicker:background_subtraction $param_Scoring_TransitionGroupPicker_background_subtraction 70 -Scoring:TransitionGroupPicker:background_subtraction
71 #if " " in str($param_Scoring_TransitionGroupPicker_background_subtraction):
72 "$param_Scoring_TransitionGroupPicker_background_subtraction"
73 #else
74 $param_Scoring_TransitionGroupPicker_background_subtraction
75 #end if
71 #end if 76 #end if
72 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks: 77 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
73 -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks" 78 -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
74 #end if 79 #end if
75 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z: 80 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
101 #end if 106 #end if
102 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: 107 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
103 -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages 108 -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
104 #end if 109 #end if
105 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: 110 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
106 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks 111 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
112 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks):
113 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks"
114 #else
115 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
116 #end if
107 #end if 117 #end if
108 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method: 118 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
109 -Scoring:TransitionGroupPicker:PeakPickerMRM:method $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method 119 -Scoring:TransitionGroupPicker:PeakPickerMRM:method
120 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method):
121 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method"
122 #else
123 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
124 #end if
110 #end if 125 #end if
111 #if $param_Scoring_DIAScoring_dia_extraction_window: 126 #if $param_Scoring_DIAScoring_dia_extraction_window:
112 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window 127 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
113 #end if 128 #end if
114 #if $param_Scoring_DIAScoring_dia_centroided: 129 #if $param_Scoring_DIAScoring_dia_centroided:
131 #end if 146 #end if
132 #if $param_Scoring_EMGScoring_max_iteration: 147 #if $param_Scoring_EMGScoring_max_iteration:
133 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration 148 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
134 #end if 149 #end if
135 #if $param_outlierDetection_outlierMethod: 150 #if $param_outlierDetection_outlierMethod:
136 -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod 151 -outlierDetection:outlierMethod
152 #if " " in str($param_outlierDetection_outlierMethod):
153 "$param_outlierDetection_outlierMethod"
154 #else
155 $param_outlierDetection_outlierMethod
156 #end if
137 #end if 157 #end if
138 #if $param_outlierDetection_useIterativeChauvenet: 158 #if $param_outlierDetection_useIterativeChauvenet:
139 -outlierDetection:useIterativeChauvenet 159 -outlierDetection:useIterativeChauvenet
140 #end if 160 #end if
141 #if $param_outlierDetection_RANSACMaxIterations: 161 #if $param_outlierDetection_RANSACMaxIterations:
198 #end if 218 #end if
199 #if $adv_opts.param_use_elution_model_score: 219 #if $adv_opts.param_use_elution_model_score:
200 -use_elution_model_score 220 -use_elution_model_score
201 #end if 221 #end if
202 #if $adv_opts.param_readOptions: 222 #if $adv_opts.param_readOptions:
203 -readOptions $adv_opts.param_readOptions 223 -readOptions
224 #if " " in str($adv_opts.param_readOptions):
225 "$adv_opts.param_readOptions"
226 #else
227 $adv_opts.param_readOptions
228 #end if
204 #end if 229 #end if
205 #if $adv_opts.param_mz_correction_function: 230 #if $adv_opts.param_mz_correction_function:
206 -mz_correction_function $adv_opts.param_mz_correction_function 231 -mz_correction_function
232 #if " " in str($adv_opts.param_mz_correction_function):
233 "$adv_opts.param_mz_correction_function"
234 #else
235 $adv_opts.param_mz_correction_function
236 #end if
207 #end if 237 #end if
208 #if $adv_opts.param_tempDirectory: 238 #if $adv_opts.param_tempDirectory:
209 -tempDirectory "$adv_opts.param_tempDirectory" 239 -tempDirectory "$adv_opts.param_tempDirectory"
210 #end if 240 #end if
211 #if $adv_opts.param_extraction_function: 241 #if $adv_opts.param_extraction_function:
212 -extraction_function $adv_opts.param_extraction_function 242 -extraction_function
243 #if " " in str($adv_opts.param_extraction_function):
244 "$adv_opts.param_extraction_function"
245 #else
246 $adv_opts.param_extraction_function
247 #end if
213 #end if 248 #end if
214 #if $adv_opts.param_batchSize: 249 #if $adv_opts.param_batchSize:
215 -batchSize $adv_opts.param_batchSize 250 -batchSize $adv_opts.param_batchSize
216 #end if 251 #end if
217 #if $adv_opts.param_force: 252 #if $adv_opts.param_force:
222 #end if 257 #end if
223 #if $adv_opts.param_Scoring_write_convex_hull: 258 #if $adv_opts.param_Scoring_write_convex_hull:
224 -Scoring:write_convex_hull 259 -Scoring:write_convex_hull
225 #end if 260 #end if
226 #if $adv_opts.param_Scoring_Scores_use_shape_score: 261 #if $adv_opts.param_Scoring_Scores_use_shape_score:
227 -Scoring:Scores:use_shape_score $adv_opts.param_Scoring_Scores_use_shape_score 262 -Scoring:Scores:use_shape_score
263 #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score):
264 "$adv_opts.param_Scoring_Scores_use_shape_score"
265 #else
266 $adv_opts.param_Scoring_Scores_use_shape_score
267 #end if
228 #end if 268 #end if
229 #if $adv_opts.param_Scoring_Scores_use_coelution_score: 269 #if $adv_opts.param_Scoring_Scores_use_coelution_score:
230 -Scoring:Scores:use_coelution_score $adv_opts.param_Scoring_Scores_use_coelution_score 270 -Scoring:Scores:use_coelution_score
271 #if " " in str($adv_opts.param_Scoring_Scores_use_coelution_score):
272 "$adv_opts.param_Scoring_Scores_use_coelution_score"
273 #else
274 $adv_opts.param_Scoring_Scores_use_coelution_score
275 #end if
231 #end if 276 #end if
232 #if $adv_opts.param_Scoring_Scores_use_rt_score: 277 #if $adv_opts.param_Scoring_Scores_use_rt_score:
233 -Scoring:Scores:use_rt_score $adv_opts.param_Scoring_Scores_use_rt_score 278 -Scoring:Scores:use_rt_score
279 #if " " in str($adv_opts.param_Scoring_Scores_use_rt_score):
280 "$adv_opts.param_Scoring_Scores_use_rt_score"
281 #else
282 $adv_opts.param_Scoring_Scores_use_rt_score
283 #end if
234 #end if 284 #end if
235 #if $adv_opts.param_Scoring_Scores_use_library_score: 285 #if $adv_opts.param_Scoring_Scores_use_library_score:
236 -Scoring:Scores:use_library_score $adv_opts.param_Scoring_Scores_use_library_score 286 -Scoring:Scores:use_library_score
287 #if " " in str($adv_opts.param_Scoring_Scores_use_library_score):
288 "$adv_opts.param_Scoring_Scores_use_library_score"
289 #else
290 $adv_opts.param_Scoring_Scores_use_library_score
291 #end if
237 #end if 292 #end if
238 #if $adv_opts.param_Scoring_Scores_use_intensity_score: 293 #if $adv_opts.param_Scoring_Scores_use_intensity_score:
239 -Scoring:Scores:use_intensity_score $adv_opts.param_Scoring_Scores_use_intensity_score 294 -Scoring:Scores:use_intensity_score
295 #if " " in str($adv_opts.param_Scoring_Scores_use_intensity_score):
296 "$adv_opts.param_Scoring_Scores_use_intensity_score"
297 #else
298 $adv_opts.param_Scoring_Scores_use_intensity_score
299 #end if
240 #end if 300 #end if
241 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score: 301 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
242 -Scoring:Scores:use_nr_peaks_score $adv_opts.param_Scoring_Scores_use_nr_peaks_score 302 -Scoring:Scores:use_nr_peaks_score
303 #if " " in str($adv_opts.param_Scoring_Scores_use_nr_peaks_score):
304 "$adv_opts.param_Scoring_Scores_use_nr_peaks_score"
305 #else
306 $adv_opts.param_Scoring_Scores_use_nr_peaks_score
307 #end if
243 #end if 308 #end if
244 #if $adv_opts.param_Scoring_Scores_use_total_xic_score: 309 #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
245 -Scoring:Scores:use_total_xic_score $adv_opts.param_Scoring_Scores_use_total_xic_score 310 -Scoring:Scores:use_total_xic_score
311 #if " " in str($adv_opts.param_Scoring_Scores_use_total_xic_score):
312 "$adv_opts.param_Scoring_Scores_use_total_xic_score"
313 #else
314 $adv_opts.param_Scoring_Scores_use_total_xic_score
315 #end if
246 #end if 316 #end if
247 #if $adv_opts.param_Scoring_Scores_use_sn_score: 317 #if $adv_opts.param_Scoring_Scores_use_sn_score:
248 -Scoring:Scores:use_sn_score $adv_opts.param_Scoring_Scores_use_sn_score 318 -Scoring:Scores:use_sn_score
319 #if " " in str($adv_opts.param_Scoring_Scores_use_sn_score):
320 "$adv_opts.param_Scoring_Scores_use_sn_score"
321 #else
322 $adv_opts.param_Scoring_Scores_use_sn_score
323 #end if
249 #end if 324 #end if
250 #if $adv_opts.param_Scoring_Scores_use_dia_scores: 325 #if $adv_opts.param_Scoring_Scores_use_dia_scores:
251 -Scoring:Scores:use_dia_scores $adv_opts.param_Scoring_Scores_use_dia_scores 326 -Scoring:Scores:use_dia_scores
327 #if " " in str($adv_opts.param_Scoring_Scores_use_dia_scores):
328 "$adv_opts.param_Scoring_Scores_use_dia_scores"
329 #else
330 $adv_opts.param_Scoring_Scores_use_dia_scores
331 #end if
252 #end if 332 #end if
253 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation: 333 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
254 -Scoring:Scores:use_ms1_correlation 334 -Scoring:Scores:use_ms1_correlation
255 #end if 335 #end if
256 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan: 336 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan: