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comparison MSSimulator.xml @ 1:a4c3db6825f4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:59:36 -0400
parents 7c2b85eb3ccf
children 66f0ddeb23f3
comparison
equal deleted inserted replaced
0:7c2b85eb3ccf 1:a4c3db6825f4
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="MSSimulator" name="MSSimulator" version="2.1.0"> 4 <tool id="MSSimulator" name="MSSimulator" version="2.2.0">
5 <description>A highly configurable simulator for mass spectrometry experiments.</description> 5 <description>A highly configurable simulator for mass spectrometry experiments.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MSSimulator</token> 7 <token name="@EXECUTABLE@">MSSimulator</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
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:
310 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses 350 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses
311 #end if 351 #end if
312 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks: 352 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
313 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks 353 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
314 #end if 354 #end if
355 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges:
356 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges
357 #end if
315 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions: 358 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
316 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions 359 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
317 #end if 360 #end if
318 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion: 361 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion:
319 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion 362 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
320 #end if 363 #end if
321 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions: 364 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions:
322 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions 365 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions
366 #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions):
367 "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions"
368 #else
369 $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions
370 #end if
323 #end if 371 #end if
324 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions: 372 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions:
325 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions 373 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions
374 #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions):
375 "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions"
376 #else
377 $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions
378 #end if
326 #end if 379 #end if
327 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions: 380 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
328 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions 381 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
329 #end if 382 #end if
330 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions: 383 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions:
425 #end if 478 #end if
426 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity: 479 #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 480 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity
428 #end if 481 #end if
429 #if $param_algorithm_MSSim_Global_ionization_type: 482 #if $param_algorithm_MSSim_Global_ionization_type:
430 -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type 483 -algorithm:MSSim:Global:ionization_type
484 #if " " in str($param_algorithm_MSSim_Global_ionization_type):
485 "$param_algorithm_MSSim_Global_ionization_type"
486 #else
487 $param_algorithm_MSSim_Global_ionization_type
488 #end if
431 #end if 489 #end if
432 #if $param_algorithm_MSSim_Labeling_type: 490 #if $param_algorithm_MSSim_Labeling_type:
433 -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type 491 -algorithm:MSSim:Labeling:type
492 #if " " in str($param_algorithm_MSSim_Labeling_type):
493 "$param_algorithm_MSSim_Labeling_type"
494 #else
495 $param_algorithm_MSSim_Labeling_type
496 #end if
434 #end if 497 #end if
435 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift: 498 #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 499 -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift
437 #end if 500 #end if
438 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins: 501 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
439 -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins 502 -algorithm:MSSim:Labeling:ICPL:label_proteins
503 #if " " in str($param_algorithm_MSSim_Labeling_ICPL_label_proteins):
504 "$param_algorithm_MSSim_Labeling_ICPL_label_proteins"
505 #else
506 $param_algorithm_MSSim_Labeling_ICPL_label_proteins
507 #end if
440 #end if 508 #end if
441 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift: 509 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
442 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift 510 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
443 #end if 511 #end if
444 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine: 512 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine:
452 #end if 520 #end if
453 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine: 521 #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" 522 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine"
455 #end if 523 #end if
456 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ: 524 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
457 -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ 525 -algorithm:MSSim:Labeling:itraq:iTRAQ
526 #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ):
527 "$param_algorithm_MSSim_Labeling_itraq_iTRAQ"
528 #else
529 $param_algorithm_MSSim_Labeling_itraq_iTRAQ
530 #end if
458 #end if 531 #end if
459 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift: 532 #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 533 -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift
461 #end if 534 #end if
462 535
486 #end if 559 #end if
487 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency: 560 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency:
488 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency 561 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
489 #end if 562 #end if
490 #if $param_algorithm_RandomNumberGenerators_biological: 563 #if $param_algorithm_RandomNumberGenerators_biological:
491 -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological 564 -algorithm:RandomNumberGenerators:biological
565 #if " " in str($param_algorithm_RandomNumberGenerators_biological):
566 "$param_algorithm_RandomNumberGenerators_biological"
567 #else
568 $param_algorithm_RandomNumberGenerators_biological
569 #end if
492 #end if 570 #end if
493 #if $param_algorithm_RandomNumberGenerators_technical: 571 #if $param_algorithm_RandomNumberGenerators_technical:
494 -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical 572 -algorithm:RandomNumberGenerators:technical
573 #if " " in str($param_algorithm_RandomNumberGenerators_technical):
574 "$param_algorithm_RandomNumberGenerators_technical"
575 #else
576 $param_algorithm_RandomNumberGenerators_technical
577 #end if
495 #end if 578 #end if
496 #if $adv_opts.adv_opts_selector=='advanced': 579 #if $adv_opts.adv_opts_selector=='advanced':
497 #if $adv_opts.param_force: 580 #if $adv_opts.param_force:
498 -force 581 -force
499 #end if 582 #end if
541 <remove value="&quot;"/> 624 <remove value="&quot;"/>
542 </valid> 625 </valid>
543 </sanitizer> 626 </sanitizer>
544 </param> 627 </param>
545 <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) "> 628 <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) ">
546 <option value="leukocyte elastase">leukocyte elastase</option> 629 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
630 <option value="Trypsin/P">Trypsin/P</option>
631 <option value="Formic_acid">Formic_acid</option>
632 <option value="TrypChymo">TrypChymo</option>
633 <option value="V8-DE">V8-DE</option>
634 <option value="CNBr">CNBr</option>
635 <option value="Chymotrypsin">Chymotrypsin</option>
636 <option value="Asp-N">Asp-N</option>
547 <option value="Lys-C">Lys-C</option> 637 <option value="Lys-C">Lys-C</option>
638 <option value="PepsinA">PepsinA</option>
639 <option value="Lys-C/P">Lys-C/P</option>
640 <option value="Asp-N_ambic">Asp-N_ambic</option>
641 <option value="Arg-C">Arg-C</option>
642 <option value="proline endopeptidase">proline endopeptidase</option>
643 <option value="Trypsin" selected="true">Trypsin</option>
644 <option value="2-iodobenzoate">2-iodobenzoate</option>
548 <option value="no cleavage">no cleavage</option> 645 <option value="no cleavage">no cleavage</option>
549 <option value="unspecific cleavage">unspecific cleavage</option> 646 <option value="unspecific cleavage">unspecific cleavage</option>
550 <option value="Trypsin" selected="true">Trypsin</option>
551 <option value="Trypsin/P">Trypsin/P</option>
552 <option value="CNBr">CNBr</option>
553 <option value="Formic_acid">Formic_acid</option>
554 <option value="Lys-C/P">Lys-C/P</option>
555 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
556 <option value="2-iodobenzoate">2-iodobenzoate</option>
557 <option value="proline endopeptidase">proline endopeptidase</option>
558 <option value="Chymotrypsin">Chymotrypsin</option>
559 <option value="V8-E">V8-E</option> 647 <option value="V8-E">V8-E</option>
560 <option value="V8-DE">V8-DE</option> 648 <option value="leukocyte elastase">leukocyte elastase</option>
561 <option value="Asp-N_ambic">Asp-N_ambic</option>
562 <option value="TrypChymo">TrypChymo</option>
563 <option value="Arg-C">Arg-C</option>
564 <option value="Asp-N">Asp-N</option>
565 <option value="PepsinA">PepsinA</option>
566 </param> 649 </param>
567 <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)"> 650 <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
568 <option value="trained">trained</option> 651 <option value="trained">trained</option>
569 <option value="naive" selected="true">naive</option> 652 <option value="naive" selected="true">naive</option>
570 </param> 653 </param>
745 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes" falsevalue="" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes) "/> 828 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes" falsevalue="" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes) "/>
746 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope) "/> 829 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope) "/>
747 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/> 830 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/>
748 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/> 831 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/>
749 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/> 832 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/>
833 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" falsevalue="" checked="false" optional="True" label="Adds precursor peaks with all charges in the given range" help="(-add_all_precursor_charges) "/>
750 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/> 834 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/>
751 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/> 835 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/>
752 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) "> 836 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) ">
753 <option value="true" selected="true">true</option> 837 <option value="true" selected="true">true</option>
754 <option value="false">false</option> 838 <option value="false">false</option>