Mercurial > repos > galaxyp > openms_mssimulator
comparison MSSimulator.xml @ 1:0d788b696572 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author | galaxyp |
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date | Tue, 18 Apr 2017 15:41:04 -0400 |
parents | ae8e96c8f9a4 |
children | fcbdc271f48c |
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0:ae8e96c8f9a4 | 1:0d788b696572 |
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36 #end if | 36 #end if |
37 #if $param_out_id: | 37 #if $param_out_id: |
38 -out_id $param_out_id | 38 -out_id $param_out_id |
39 #end if | 39 #end if |
40 #if $param_algorithm_MSSim_Digestion_enzyme: | 40 #if $param_algorithm_MSSim_Digestion_enzyme: |
41 -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme | 41 -algorithm:MSSim:Digestion:enzyme |
42 #if " " in str($param_algorithm_MSSim_Digestion_enzyme): | |
43 "$param_algorithm_MSSim_Digestion_enzyme" | |
44 #else | |
45 $param_algorithm_MSSim_Digestion_enzyme | |
46 #end if | |
42 #end if | 47 #end if |
43 #if $param_algorithm_MSSim_Digestion_model: | 48 #if $param_algorithm_MSSim_Digestion_model: |
44 -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model | 49 -algorithm:MSSim:Digestion:model |
50 #if " " in str($param_algorithm_MSSim_Digestion_model): | |
51 "$param_algorithm_MSSim_Digestion_model" | |
52 #else | |
53 $param_algorithm_MSSim_Digestion_model | |
54 #end if | |
45 #end if | 55 #end if |
46 #if $param_algorithm_MSSim_Digestion_min_peptide_length: | 56 #if $param_algorithm_MSSim_Digestion_min_peptide_length: |
47 -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length | 57 -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length |
48 #end if | 58 #end if |
49 #if $param_algorithm_MSSim_Digestion_model_trained_threshold: | 59 #if $param_algorithm_MSSim_Digestion_model_trained_threshold: |
51 #end if | 61 #end if |
52 #if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages: | 62 #if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages: |
53 -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages | 63 -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages |
54 #end if | 64 #end if |
55 #if $param_algorithm_MSSim_RT_rt_column: | 65 #if $param_algorithm_MSSim_RT_rt_column: |
56 -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column | 66 -algorithm:MSSim:RT:rt_column |
67 #if " " in str($param_algorithm_MSSim_RT_rt_column): | |
68 "$param_algorithm_MSSim_RT_rt_column" | |
69 #else | |
70 $param_algorithm_MSSim_RT_rt_column | |
71 #end if | |
57 #end if | 72 #end if |
58 #if $param_algorithm_MSSim_RT_auto_scale: | 73 #if $param_algorithm_MSSim_RT_auto_scale: |
59 -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale | 74 -algorithm:MSSim:RT:auto_scale |
75 #if " " in str($param_algorithm_MSSim_RT_auto_scale): | |
76 "$param_algorithm_MSSim_RT_auto_scale" | |
77 #else | |
78 $param_algorithm_MSSim_RT_auto_scale | |
79 #end if | |
60 #end if | 80 #end if |
61 #if $param_algorithm_MSSim_RT_total_gradient_time: | 81 #if $param_algorithm_MSSim_RT_total_gradient_time: |
62 -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time | 82 -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time |
63 #end if | 83 #end if |
64 #if $param_algorithm_MSSim_RT_sampling_rate: | 84 #if $param_algorithm_MSSim_RT_sampling_rate: |
165 #end if | 185 #end if |
166 #if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit: | 186 #if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit: |
167 -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit | 187 -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit |
168 #end if | 188 #end if |
169 #if $param_algorithm_MSSim_RawSignal_enabled: | 189 #if $param_algorithm_MSSim_RawSignal_enabled: |
170 -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled | 190 -algorithm:MSSim:RawSignal:enabled |
191 #if " " in str($param_algorithm_MSSim_RawSignal_enabled): | |
192 "$param_algorithm_MSSim_RawSignal_enabled" | |
193 #else | |
194 $param_algorithm_MSSim_RawSignal_enabled | |
195 #end if | |
171 #end if | 196 #end if |
172 #if $param_algorithm_MSSim_RawSignal_peak_shape: | 197 #if $param_algorithm_MSSim_RawSignal_peak_shape: |
173 -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape | 198 -algorithm:MSSim:RawSignal:peak_shape |
199 #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape): | |
200 "$param_algorithm_MSSim_RawSignal_peak_shape" | |
201 #else | |
202 $param_algorithm_MSSim_RawSignal_peak_shape | |
203 #end if | |
174 #end if | 204 #end if |
175 #if $param_algorithm_MSSim_RawSignal_resolution_value: | 205 #if $param_algorithm_MSSim_RawSignal_resolution_value: |
176 -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value | 206 -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value |
177 #end if | 207 #end if |
178 #if $param_algorithm_MSSim_RawSignal_resolution_type: | 208 #if $param_algorithm_MSSim_RawSignal_resolution_type: |
179 -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type | 209 -algorithm:MSSim:RawSignal:resolution:type |
210 #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type): | |
211 "$param_algorithm_MSSim_RawSignal_resolution_type" | |
212 #else | |
213 $param_algorithm_MSSim_RawSignal_resolution_type | |
214 #end if | |
180 #end if | 215 #end if |
181 #if $param_algorithm_MSSim_RawSignal_baseline_scaling: | 216 #if $param_algorithm_MSSim_RawSignal_baseline_scaling: |
182 -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling | 217 -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling |
183 #end if | 218 #end if |
184 #if $param_algorithm_MSSim_RawSignal_baseline_shape: | 219 #if $param_algorithm_MSSim_RawSignal_baseline_shape: |
219 #end if | 254 #end if |
220 #if $param_algorithm_MSSim_RawSignal_noise_detector_stddev: | 255 #if $param_algorithm_MSSim_RawSignal_noise_detector_stddev: |
221 -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev | 256 -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev |
222 #end if | 257 #end if |
223 #if $param_algorithm_MSSim_RawTandemSignal_status: | 258 #if $param_algorithm_MSSim_RawTandemSignal_status: |
224 -algorithm:MSSim:RawTandemSignal:status $param_algorithm_MSSim_RawTandemSignal_status | 259 -algorithm:MSSim:RawTandemSignal:status |
260 #if " " in str($param_algorithm_MSSim_RawTandemSignal_status): | |
261 "$param_algorithm_MSSim_RawTandemSignal_status" | |
262 #else | |
263 $param_algorithm_MSSim_RawTandemSignal_status | |
264 #end if | |
225 #end if | 265 #end if |
226 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode: | 266 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode: |
227 -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode | 267 -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode |
228 #end if | 268 #end if |
229 #if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file: | 269 #if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file: |
317 #end if | 357 #end if |
318 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion: | 358 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion: |
319 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion | 359 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion |
320 #end if | 360 #end if |
321 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions: | 361 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions: |
322 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions | 362 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions |
363 #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions): | |
364 "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" | |
365 #else | |
366 $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions | |
367 #end if | |
323 #end if | 368 #end if |
324 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions: | 369 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions: |
325 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions | 370 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions |
371 #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions): | |
372 "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions" | |
373 #else | |
374 $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions | |
375 #end if | |
326 #end if | 376 #end if |
327 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions: | 377 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions: |
328 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions | 378 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions |
329 #end if | 379 #end if |
330 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions: | 380 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions: |
425 #end if | 475 #end if |
426 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity: | 476 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity: |
427 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity | 477 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity |
428 #end if | 478 #end if |
429 #if $param_algorithm_MSSim_Global_ionization_type: | 479 #if $param_algorithm_MSSim_Global_ionization_type: |
430 -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type | 480 -algorithm:MSSim:Global:ionization_type |
481 #if " " in str($param_algorithm_MSSim_Global_ionization_type): | |
482 "$param_algorithm_MSSim_Global_ionization_type" | |
483 #else | |
484 $param_algorithm_MSSim_Global_ionization_type | |
485 #end if | |
431 #end if | 486 #end if |
432 #if $param_algorithm_MSSim_Labeling_type: | 487 #if $param_algorithm_MSSim_Labeling_type: |
433 -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type | 488 -algorithm:MSSim:Labeling:type |
489 #if " " in str($param_algorithm_MSSim_Labeling_type): | |
490 "$param_algorithm_MSSim_Labeling_type" | |
491 #else | |
492 $param_algorithm_MSSim_Labeling_type | |
493 #end if | |
434 #end if | 494 #end if |
435 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift: | 495 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift: |
436 -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift | 496 -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift |
437 #end if | 497 #end if |
438 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins: | 498 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins: |
439 -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins | 499 -algorithm:MSSim:Labeling:ICPL:label_proteins |
500 #if " " in str($param_algorithm_MSSim_Labeling_ICPL_label_proteins): | |
501 "$param_algorithm_MSSim_Labeling_ICPL_label_proteins" | |
502 #else | |
503 $param_algorithm_MSSim_Labeling_ICPL_label_proteins | |
504 #end if | |
440 #end if | 505 #end if |
441 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift: | 506 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift: |
442 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift | 507 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift |
443 #end if | 508 #end if |
444 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine: | 509 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine: |
452 #end if | 517 #end if |
453 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine: | 518 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine: |
454 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" | 519 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" |
455 #end if | 520 #end if |
456 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ: | 521 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ: |
457 -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ | 522 -algorithm:MSSim:Labeling:itraq:iTRAQ |
523 #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ): | |
524 "$param_algorithm_MSSim_Labeling_itraq_iTRAQ" | |
525 #else | |
526 $param_algorithm_MSSim_Labeling_itraq_iTRAQ | |
527 #end if | |
458 #end if | 528 #end if |
459 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift: | 529 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift: |
460 -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift | 530 -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift |
461 #end if | 531 #end if |
462 | 532 |
486 #end if | 556 #end if |
487 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency: | 557 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency: |
488 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency | 558 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency |
489 #end if | 559 #end if |
490 #if $param_algorithm_RandomNumberGenerators_biological: | 560 #if $param_algorithm_RandomNumberGenerators_biological: |
491 -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological | 561 -algorithm:RandomNumberGenerators:biological |
562 #if " " in str($param_algorithm_RandomNumberGenerators_biological): | |
563 "$param_algorithm_RandomNumberGenerators_biological" | |
564 #else | |
565 $param_algorithm_RandomNumberGenerators_biological | |
566 #end if | |
492 #end if | 567 #end if |
493 #if $param_algorithm_RandomNumberGenerators_technical: | 568 #if $param_algorithm_RandomNumberGenerators_technical: |
494 -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical | 569 -algorithm:RandomNumberGenerators:technical |
570 #if " " in str($param_algorithm_RandomNumberGenerators_technical): | |
571 "$param_algorithm_RandomNumberGenerators_technical" | |
572 #else | |
573 $param_algorithm_RandomNumberGenerators_technical | |
574 #end if | |
495 #end if | 575 #end if |
496 #if $adv_opts.adv_opts_selector=='advanced': | 576 #if $adv_opts.adv_opts_selector=='advanced': |
497 #if $adv_opts.param_force: | 577 #if $adv_opts.param_force: |
498 -force | 578 -force |
499 #end if | 579 #end if |