comparison MSSimulator.xml @ 1:0d788b696572 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:41:04 -0400
parents ae8e96c8f9a4
children fcbdc271f48c
comparison
equal deleted inserted replaced
0:ae8e96c8f9a4 1:0d788b696572
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