Mercurial > repos > galaxyp > openms_mssimulator

comparison MSSimulator.xml @ 0:7c2b85eb3ccf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:59:29 -0500
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children a4c3db6825f4
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-1:000000000000 0:7c2b85eb3ccf
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.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MSSimulator" name="MSSimulator" version="2.1.0">
5 <description>A highly configurable simulator for mass spectrometry experiments.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MSSimulator</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MSSimulator
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_out:
20 -out $param_out
21 #end if
22 #if $param_out_pm:
23 -out_pm $param_out_pm
24 #end if
25 #if $param_out_fm:
26 -out_fm $param_out_fm
27 #end if
28 #if $param_out_cm:
29 -out_cm $param_out_cm
30 #end if
31 #if $param_out_lcm:
32 -out_lcm $param_out_lcm
33 #end if
34 #if $param_out_cntm:
35 -out_cntm $param_out_cntm
36 #end if
37 #if $param_out_id:
38 -out_id $param_out_id
39 #end if
40 #if $param_algorithm_MSSim_Digestion_enzyme:
41 -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme
42 #end if
43 #if $param_algorithm_MSSim_Digestion_model:
44 -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model
45 #end if
46 #if $param_algorithm_MSSim_Digestion_min_peptide_length:
47 -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
48 #end if
49 #if $param_algorithm_MSSim_Digestion_model_trained_threshold:
50 -algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold
51 #end if
52 #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
54 #end if
55 #if $param_algorithm_MSSim_RT_rt_column:
56 -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column
57 #end if
58 #if $param_algorithm_MSSim_RT_auto_scale:
59 -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale
60 #end if
61 #if $param_algorithm_MSSim_RT_total_gradient_time:
62 -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
63 #end if
64 #if $param_algorithm_MSSim_RT_sampling_rate:
65 -algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate
66 #end if
67 #if $param_algorithm_MSSim_RT_scan_window_min:
68 -algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min
69 #end if
70 #if $param_algorithm_MSSim_RT_scan_window_max:
71 -algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max
72 #end if
73 #if $param_algorithm_MSSim_RT_variation_feature_stddev:
74 -algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev
75 #end if
76 #if $param_algorithm_MSSim_RT_variation_affine_offset:
77 -algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset
78 #end if
79 #if $param_algorithm_MSSim_RT_variation_affine_scale:
80 -algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale
81 #end if
82 #if $param_algorithm_MSSim_RT_column_condition_distortion:
83 -algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion
84 #end if
85 #if $param_algorithm_MSSim_RT_profile_shape_width_value:
86 -algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value
87 #end if
88 #if $param_algorithm_MSSim_RT_profile_shape_width_variance:
89 -algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance
90 #end if
91 #if $param_algorithm_MSSim_RT_profile_shape_skewness_value:
92 -algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value
93 #end if
94 #if $param_algorithm_MSSim_RT_profile_shape_skewness_variance:
95 -algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance
96 #end if
97 #if $param_algorithm_MSSim_RT_HPLC_model_file:
98 -algorithm:MSSim:RT:HPLC:model_file "$param_algorithm_MSSim_RT_HPLC_model_file"
99 #end if
100 #if $param_algorithm_MSSim_RT_CE_pH:
101 -algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH
102 #end if
103 #if $param_algorithm_MSSim_RT_CE_alpha:
104 -algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha
105 #end if
106 #if $param_algorithm_MSSim_RT_CE_mu_eo:
107 -algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo
108 #end if
109 #if $param_algorithm_MSSim_RT_CE_lenght_d:
110 -algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d
111 #end if
112 #if $param_algorithm_MSSim_RT_CE_length_total:
113 -algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total
114 #end if
115 #if $param_algorithm_MSSim_RT_CE_voltage:
116 -algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage
117 #end if
118 #if $param_algorithm_MSSim_Detectability_dt_simulation_on:
119 -algorithm:MSSim:Detectability:dt_simulation_on
120 #end if
121 #if $param_algorithm_MSSim_Detectability_min_detect:
122 -algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect
123 #end if
124 #if $param_algorithm_MSSim_Detectability_dt_model_file:
125 -algorithm:MSSim:Detectability:dt_model_file "$param_algorithm_MSSim_Detectability_dt_model_file"
126 #end if
127
128 #if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
129 -algorithm:MSSim:Ionization:esi:ionized_residues
130 #for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
131 #if " " in str(token):
132 "$token.param_algorithm_MSSim_Ionization_esi_ionized_residues"
133 #else
134 $token.param_algorithm_MSSim_Ionization_esi_ionized_residues
135 #end if
136 #end for
137 #end if
138
139 #if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
140 -algorithm:MSSim:Ionization:esi:charge_impurity
141 #for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
142 #if " " in str(token):
143 "$token.param_algorithm_MSSim_Ionization_esi_charge_impurity"
144 #else
145 $token.param_algorithm_MSSim_Ionization_esi_charge_impurity
146 #end if
147 #end for
148 #end if
149 #if $param_algorithm_MSSim_Ionization_esi_ionization_probability:
150 -algorithm:MSSim:Ionization:esi:ionization_probability $param_algorithm_MSSim_Ionization_esi_ionization_probability
151 #end if
152
153 #if $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
154 -algorithm:MSSim:Ionization:maldi:ionization_probabilities
155 #for token in $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
156 #if " " in str(token):
157 "$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities"
158 #else
159 $token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities
160 #end if
161 #end for
162 #end if
163 #if $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit:
164 -algorithm:MSSim:Ionization:mz:lower_measurement_limit $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit
165 #end if
166 #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
168 #end if
169 #if $param_algorithm_MSSim_RawSignal_enabled:
170 -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled
171 #end if
172 #if $param_algorithm_MSSim_RawSignal_peak_shape:
173 -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape
174 #end if
175 #if $param_algorithm_MSSim_RawSignal_resolution_value:
176 -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value
177 #end if
178 #if $param_algorithm_MSSim_RawSignal_resolution_type:
179 -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type
180 #end if
181 #if $param_algorithm_MSSim_RawSignal_baseline_scaling:
182 -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling
183 #end if
184 #if $param_algorithm_MSSim_RawSignal_baseline_shape:
185 -algorithm:MSSim:RawSignal:baseline:shape $param_algorithm_MSSim_RawSignal_baseline_shape
186 #end if
187 #if $param_algorithm_MSSim_RawSignal_mz_sampling_points:
188 -algorithm:MSSim:RawSignal:mz:sampling_points $param_algorithm_MSSim_RawSignal_mz_sampling_points
189 #end if
190 #if $param_algorithm_MSSim_RawSignal_contaminants_file:
191 -algorithm:MSSim:RawSignal:contaminants:file "$param_algorithm_MSSim_RawSignal_contaminants_file"
192 #end if
193 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev:
194 -algorithm:MSSim:RawSignal:variation:mz:error_stddev $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev
195 #end if
196 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_mean:
197 -algorithm:MSSim:RawSignal:variation:mz:error_mean $param_algorithm_MSSim_RawSignal_variation_mz_error_mean
198 #end if
199 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale:
200 -algorithm:MSSim:RawSignal:variation:intensity:scale $param_algorithm_MSSim_RawSignal_variation_intensity_scale
201 #end if
202 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev:
203 -algorithm:MSSim:RawSignal:variation:intensity:scale_stddev $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev
204 #end if
205 #if $param_algorithm_MSSim_RawSignal_noise_shot_rate:
206 -algorithm:MSSim:RawSignal:noise:shot:rate $param_algorithm_MSSim_RawSignal_noise_shot_rate
207 #end if
208 #if $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean:
209 -algorithm:MSSim:RawSignal:noise:shot:intensity-mean $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean
210 #end if
211 #if $param_algorithm_MSSim_RawSignal_noise_white_mean:
212 -algorithm:MSSim:RawSignal:noise:white:mean $param_algorithm_MSSim_RawSignal_noise_white_mean
213 #end if
214 #if $param_algorithm_MSSim_RawSignal_noise_white_stddev:
215 -algorithm:MSSim:RawSignal:noise:white:stddev $param_algorithm_MSSim_RawSignal_noise_white_stddev
216 #end if
217 #if $param_algorithm_MSSim_RawSignal_noise_detector_mean:
218 -algorithm:MSSim:RawSignal:noise:detector:mean $param_algorithm_MSSim_RawSignal_noise_detector_mean
219 #end if
220 #if $param_algorithm_MSSim_RawSignal_noise_detector_stddev:
221 -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev
222 #end if
223 #if $param_algorithm_MSSim_RawTandemSignal_status:
224 -algorithm:MSSim:RawTandemSignal:status $param_algorithm_MSSim_RawTandemSignal_status
225 #end if
226 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode:
227 -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode
228 #end if
229 #if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file:
230 -algorithm:MSSim:RawTandemSignal:svm_model_set_file "$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file"
231 #end if
232 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin:
233 -algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin
234 #end if
235 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance:
236 -algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance
237 #end if
238 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window:
239 -algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window
240 #end if
241 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks:
242 -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks
243 #end if
244
245 #if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
246 -algorithm:MSSim:RawTandemSignal:Precursor:charge_filter
247 #for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
248 #if " " in str(token):
249 "$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter"
250 #else
251 $token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter
252 #end if
253 #end for
254 #end if
255 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion:
256 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion
257 #end if
258 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time:
259 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time
260 #end if
261 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size:
262 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size
263 #end if
264 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt:
265 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt
266 #end if
267 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt:
268 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt
269 #end if
270 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size:
271 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size
272 #end if
273 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size:
274 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size
275 #end if
276 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability:
277 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability
278 #end if
279 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight:
280 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight
281 #end if
282 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz:
283 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz
284 #end if
285 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz:
286 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz
287 #end if
288 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule:
289 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule
290 #end if
291 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids:
292 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids
293 #end if
294 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability:
295 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability
296 #end if
297 #if $param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra:
298 -algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra
299 #end if
300 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes:
301 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes
302 #end if
303 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope:
304 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope
305 #end if
306 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo:
307 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo
308 #end if
309 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses:
310 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses
311 #end if
312 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
313 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
314 #end if
315 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
316 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
317 #end if
318 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion:
319 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
320 #end if
321 #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
323 #end if
324 #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
326 #end if
327 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
328 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
329 #end if
330 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions:
331 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions
332 #end if
333 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions:
334 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions
335 #end if
336 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions:
337 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions
338 #end if
339 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity:
340 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity
341 #end if
342 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity:
343 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity
344 #end if
345 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity:
346 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity
347 #end if
348 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity:
349 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity
350 #end if
351 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity:
352 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity
353 #end if
354 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity:
355 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity
356 #end if
357 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity:
358 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity
359 #end if
360 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity:
361 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity
362 #end if
363 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity:
364 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity
365 #end if
366 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity:
367 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity
368 #end if
369 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes:
370 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes
371 #end if
372 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope:
373 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope
374 #end if
375 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo:
376 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo
377 #end if
378 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion:
379 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion
380 #end if
381 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions:
382 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions
383 #end if
384 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions:
385 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions
386 #end if
387 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions:
388 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions
389 #end if
390 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions:
391 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions
392 #end if
393 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions:
394 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions
395 #end if
396 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions:
397 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions
398 #end if
399 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions:
400 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions
401 #end if
402 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions:
403 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions
404 #end if
405 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses:
406 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses
407 #end if
408 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity:
409 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity
410 #end if
411 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity:
412 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity
413 #end if
414 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity:
415 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity
416 #end if
417 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity:
418 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity
419 #end if
420 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity:
421 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity
422 #end if
423 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity:
424 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity
425 #end if
426 #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
428 #end if
429 #if $param_algorithm_MSSim_Global_ionization_type:
430 -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type
431 #end if
432 #if $param_algorithm_MSSim_Labeling_type:
433 -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type
434 #end if
435 #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
437 #end if
438 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
439 -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins
440 #end if
441 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
442 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
443 #end if
444 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine:
445 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine"
446 #end if
447 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine:
448 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine"
449 #end if
450 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine:
451 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine"
452 #end if
453 #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"
455 #end if
456 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
457 -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ
458 #end if
459 #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
461 #end if
462
463 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
464 -algorithm:MSSim:Labeling:itraq:channel_active_4plex
465 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
466 #if " " in str(token):
467 "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex"
468 #else
469 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex
470 #end if
471 #end for
472 #end if
473
474 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
475 -algorithm:MSSim:Labeling:itraq:channel_active_8plex
476 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
477 #if " " in str(token):
478 "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex"
479 #else
480 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex
481 #end if
482 #end for
483 #end if
484 #if $param_algorithm_MSSim_Labeling_itraq_Y_contamination:
485 -algorithm:MSSim:Labeling:itraq:Y_contamination $param_algorithm_MSSim_Labeling_itraq_Y_contamination
486 #end if
487 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency:
488 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
489 #end if
490 #if $param_algorithm_RandomNumberGenerators_biological:
491 -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological
492 #end if
493 #if $param_algorithm_RandomNumberGenerators_technical:
494 -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical
495 #end if
496 #if $adv_opts.adv_opts_selector=='advanced':
497 #if $adv_opts.param_force:
498 -force
499 #end if
500 #if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size:
501 -algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size
502 #end if
503 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label:
504 -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label"
505 #end if
506 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label:
507 -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label"
508 #end if
509 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label:
510 -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label"
511 #end if
512
513 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
514 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex
515 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
516 #if " " in str(token):
517 "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex"
518 #else
519 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex
520 #end if
521 #end for
522 #end if
523
524 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
525 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex
526 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
527 #if " " in str(token):
528 "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex"
529 #else
530 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex
531 #end if
532 #end for
533 #end if
534 #end if
535 </command>
536 <inputs>
537 <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input protein sequences" help="(-in) ">
538 <sanitizer>
539 <valid initial="string.printable">
540 <remove value="'"/>
541 <remove value="&quot;"/>
542 </valid>
543 </sanitizer>
544 </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) ">
546 <option value="leukocyte elastase">leukocyte elastase</option>
547 <option value="Lys-C">Lys-C</option>
548 <option value="no cleavage">no cleavage</option>
549 <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>
560 <option value="V8-DE">V8-DE</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>
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)">
568 <option value="trained">trained</option>
569 <option value="naive" selected="true">naive</option>
570 </param>
571 <param name="param_algorithm_MSSim_Digestion_min_peptide_length" type="integer" min="1" optional="True" value="3" label="Minimum peptide length after digestion (shorter ones will be discarded)" help="(-min_peptide_length) "/>
572 <param name="param_algorithm_MSSim_Digestion_model_trained_threshold" type="float" min="-2.0" max="4.0" optional="True" value="0.5" label="Model threshold for calling a cleavage" help="(-threshold) Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage"/>
573 <param name="param_algorithm_MSSim_Digestion_model_naive_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Maximum number of missed cleavages considered" help="(-missed_cleavages) All possible resulting peptides will be created"/>
574 <param name="param_algorithm_MSSim_RT_rt_column" display="radio" type="select" optional="False" value="HPLC" label="Modelling of an RT or CE column" help="(-rt_column) ">
575 <option value="none">none</option>
576 <option value="HPLC" selected="true">HPLC</option>
577 <option value="CE">CE</option>
578 </param>
579 <param name="param_algorithm_MSSim_RT_auto_scale" display="radio" type="select" optional="False" value="true" label="Scale predicted RT's/MT's to given 'total_gradient_time'?" help="(-auto_scale) If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence">
580 <option value="true" selected="true">true</option>
581 <option value="false">false</option>
582 </param>
583 <param name="param_algorithm_MSSim_RT_total_gradient_time" type="float" min="1e-05" optional="True" value="2500.0" label="The duration [s] of the gradient" help="(-total_gradient_time) "/>
584 <param name="param_algorithm_MSSim_RT_sampling_rate" type="float" min="0.01" max="60.0" optional="True" value="2.0" label="Time interval [s] between consecutive scans" help="(-sampling_rate) "/>
585 <param name="param_algorithm_MSSim_RT_scan_window_min" type="float" min="0.0" optional="True" value="500.0" label="Start of RT Scan Window [s]" help="(-min) "/>
586 <param name="param_algorithm_MSSim_RT_scan_window_max" type="float" min="1.0" optional="True" value="1500.0" label="End of RT Scan Window [s]" help="(-max) "/>
587 <param name="param_algorithm_MSSim_RT_variation_feature_stddev" type="integer" value="3" label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" help="(-feature_stddev) "/>
588 <param name="param_algorithm_MSSim_RT_variation_affine_offset" type="integer" value="0" label="Global offset in retention time [s] from predicted model" help="(-affine_offset) "/>
589 <param name="param_algorithm_MSSim_RT_variation_affine_scale" type="integer" value="1" label="Global scaling in retention time from predicted model" help="(-affine_scale) "/>
590 <param name="param_algorithm_MSSim_RT_column_condition_distortion" type="integer" min="0" max="10" optional="True" value="0" label="Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (" help="(-distortion) e.g. Orbitrap) distortion should be &gt;4"/>
591 <param name="param_algorithm_MSSim_RT_profile_shape_width_value" type="float" min="0.0" optional="True" value="9.0" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile" help="(-value) This does not correspond directly to the width in [s]"/>
592 <param name="param_algorithm_MSSim_RT_profile_shape_width_variance" type="float" min="0.0" optional="True" value="1.6" label="Random component of the width (set to 0 to disable randomness), i.e" help="(-variance) scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be &gt;= 0)"/>
593 <param name="param_algorithm_MSSim_RT_profile_shape_skewness_value" type="float" value="0.1" label="Asymmetric component of the EGH" help="(-value) Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile"/>
594 <param name="param_algorithm_MSSim_RT_profile_shape_skewness_variance" type="float" min="0.0" optional="True" value="0.3" label="Random component of skewness (set to 0 to disable randomness), i.e" help="(-variance) scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be &gt; 0)"/>
595 <param name="param_algorithm_MSSim_RT_HPLC_model_file" type="text" size="30" value="examples/simulation/RTPredict.model" label="SVM model for retention time prediction" help="(-model_file) ">
596 <sanitizer>
597 <valid initial="string.printable">
598 <remove value="'"/>
599 <remove value="&quot;"/>
600 </valid>
601 </sanitizer>
602 </param>
603 <param name="param_algorithm_MSSim_RT_CE_pH" type="float" min="0.0" max="14.0" optional="True" value="3.0" label="pH of buffe" help="(-pH) "/>
604 <param name="param_algorithm_MSSim_RT_CE_alpha" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Exponent Alpha used to calculate mobility" help="(-alpha) "/>
605 <param name="param_algorithm_MSSim_RT_CE_mu_eo" type="float" min="0.0" max="5.0" optional="True" value="0.0" label="Electroosmotic flow" help="(-mu_eo) "/>
606 <param name="param_algorithm_MSSim_RT_CE_lenght_d" type="float" min="0.0" max="1000.0" optional="True" value="70.0" label="Length of capillary [cm] from injection site to MS" help="(-lenght_d) "/>
607 <param name="param_algorithm_MSSim_RT_CE_length_total" type="float" min="0.0" max="1000.0" optional="True" value="75.0" label="Total length of capillary [cm]" help="(-length_total) "/>
608 <param name="param_algorithm_MSSim_RT_CE_voltage" type="float" min="0.0" optional="True" value="1000.0" label="Voltage applied to capillary" help="(-voltage) "/>
609 <param name="param_algorithm_MSSim_Detectability_dt_simulation_on" display="radio" type="boolean" truevalue="-algorithm:MSSim:Detectability:dt_simulation_on" falsevalue="" checked="false" optional="True" label="Modelling detectibility enabled?" help="(-dt_simulation_on) This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count"/>
610 <param name="param_algorithm_MSSim_Detectability_min_detect" type="float" value="0.5" label="Minimum peptide detectability accepted" help="(-min_detect) Peptides with a lower score will be removed"/>
611 <param name="param_algorithm_MSSim_Detectability_dt_model_file" type="text" size="30" value="examples/simulation/DTPredict.model" label="SVM model for peptide detectability prediction" help="(-dt_model_file) ">
612 <sanitizer>
613 <valid initial="string.printable">
614 <remove value="'"/>
615 <remove value="&quot;"/>
616 </valid>
617 </sanitizer>
618 </param>
619 <repeat name="rep_param_algorithm_MSSim_Ionization_esi_ionized_residues" min="0" max="1" title="param_algorithm_MSSim_Ionization_esi_ionized_residues">
620 <param name="param_algorithm_MSSim_Ionization_esi_ionized_residues" type="select" optional="True" value="Arg Lys His" label="List of residues (as three letter code) that will be considered during ES ionization" help="(-ionized_residues) The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization">
621 <option value="Ala">Ala</option>
622 <option value="Cys">Cys</option>
623 <option value="Asp">Asp</option>
624 <option value="Glu">Glu</option>
625 <option value="Phe">Phe</option>
626 <option value="Gly">Gly</option>
627 <option value="His">His</option>
628 <option value="Ile">Ile</option>
629 <option value="Lys">Lys</option>
630 <option value="Leu">Leu</option>
631 <option value="Met">Met</option>
632 <option value="Asn">Asn</option>
633 <option value="Pro">Pro</option>
634 <option value="Gln">Gln</option>
635 <option value="Arg">Arg</option>
636 <option value="Sec">Sec</option>
637 <option value="Ser">Ser</option>
638 <option value="Thr">Thr</option>
639 <option value="Val">Val</option>
640 <option value="Trp">Trp</option>
641 <option value="Tyr">Tyr</option>
642 </param>
643 </repeat>
644 <repeat name="rep_param_algorithm_MSSim_Ionization_esi_charge_impurity" min="0" max="1" title="param_algorithm_MSSim_Ionization_esi_charge_impurity">
645 <param name="param_algorithm_MSSim_Ionization_esi_charge_impurity" type="text" size="30" value="H+:1" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally)," help="(-charge_impurity) e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])">
646 <sanitizer>
647 <valid initial="string.printable">
648 <remove value="'"/>
649 <remove value="&quot;"/>
650 </valid>
651 </sanitizer>
652 </param>
653 </repeat>
654 <param name="param_algorithm_MSSim_Ionization_esi_ionization_probability" type="float" value="0.8" label="Probability for the binomial distribution of the ESI charge states" help="(-ionization_probability) "/>
655 <repeat name="rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" min="0" max="1" title="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities">
656 <param name="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" type="text" size="30" value="0.9 0.1" label="List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)" help="(-ionization_probabilities) ">
657 <sanitizer>
658 <valid initial="string.printable">
659 <remove value="'"/>
660 <remove value="&quot;"/>
661 </valid>
662 </sanitizer>
663 </param>
664 </repeat>
665 <param name="param_algorithm_MSSim_Ionization_mz_lower_measurement_limit" type="float" min="0.0" optional="True" value="200.0" label="Lower m/z detector limit" help="(-lower_measurement_limit) "/>
666 <param name="param_algorithm_MSSim_Ionization_mz_upper_measurement_limit" type="float" min="0.0" optional="True" value="2500.0" label="Upper m/z detector limit" help="(-upper_measurement_limit) "/>
667 <param name="param_algorithm_MSSim_RawSignal_enabled" display="radio" type="select" optional="False" value="true" label="Enable RAW signal simulation?" help="(-enabled) (select 'false' if you only need feature-maps)">
668 <option value="true" selected="true">true</option>
669 <option value="false">false</option>
670 </param>
671 <param name="param_algorithm_MSSim_RawSignal_peak_shape" display="radio" type="select" optional="False" value="Gaussian" label="Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian" help="(-peak_shape) ">
672 <option value="Gaussian" selected="true">Gaussian</option>
673 <option value="Lorentzian">Lorentzian</option>
674 </param>
675 <param name="param_algorithm_MSSim_RawSignal_resolution_value" type="integer" value="50000" label="Instrument resolution at 400 Th" help="(-value) "/>
676 <param name="param_algorithm_MSSim_RawSignal_resolution_type" display="radio" type="select" optional="False" value="linear" label="How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass" help="(-type) ">
677 <option value="constant">constant</option>
678 <option value="linear" selected="true">linear</option>
679 <option value="sqrt">sqrt</option>
680 </param>
681 <param name="param_algorithm_MSSim_RawSignal_baseline_scaling" type="float" min="0.0" optional="True" value="0.0" label="Scale of baseline" help="(-scaling) Set to 0 to disable simulation of baseline"/>
682 <param name="param_algorithm_MSSim_RawSignal_baseline_shape" type="float" min="0.0" optional="True" value="0.5" label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)" help="(-shape) "/>
683 <param name="param_algorithm_MSSim_RawSignal_mz_sampling_points" type="integer" min="2" optional="True" value="3" label="Number of raw data points per FWHM of the peak" help="(-sampling_points) "/>
684 <param name="param_algorithm_MSSim_RawSignal_contaminants_file" type="text" size="30" value="examples/simulation/contaminants.csv" label="Contaminants file with sum formula and absolute RT interval" help="(-file) See 'OpenMS/examples/simulation/contaminants.txt' for details">
685 <sanitizer>
686 <valid initial="string.printable">
687 <remove value="'"/>
688 <remove value="&quot;"/>
689 </valid>
690 </sanitizer>
691 </param>
692 <param name="param_algorithm_MSSim_RawSignal_variation_mz_error_stddev" type="float" value="0.0" label="Standard deviation for m/z errors" help="(-error_stddev) Set to 0 to disable simulation of m/z errors"/>
693 <param name="param_algorithm_MSSim_RawSignal_variation_mz_error_mean" type="float" value="0.0" label="Average systematic m/z error (Da)" help="(-error_mean) "/>
694 <param name="param_algorithm_MSSim_RawSignal_variation_intensity_scale" type="float" min="0.0" optional="True" value="100.0" label="Constant scale factor of the feature intensity" help="(-scale) Set to 1.0 to get the real intensity values provided in the FASTA file"/>
695 <param name="param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev" type="float" min="0.0" optional="True" value="0.0" label="Standard deviation of peak intensity (relative to the scaled peak height)" help="(-scale_stddev) Set to 0 to get simple rescaled intensities"/>
696 <param name="param_algorithm_MSSim_RawSignal_noise_shot_rate" type="float" min="0.0" optional="True" value="0.0" label="Poisson rate of shot noise per unit m/z" help="(-rate) Set this to 0 to disable simulation of shot noise"/>
697 <param name="param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean" type="float" value="1.0" label="Shot noise intensity mean (exponentially distributed with given mean)" help="(-intensity-mean) "/>
698 <param name="param_algorithm_MSSim_RawSignal_noise_white_mean" type="float" value="0.0" label="Mean value of white noise being added to each measured signal" help="(-mean) "/>
699 <param name="param_algorithm_MSSim_RawSignal_noise_white_stddev" type="float" value="0.0" label="Standard deviation of white noise being added to each measured signal" help="(-stddev) "/>
700 <param name="param_algorithm_MSSim_RawSignal_noise_detector_mean" type="float" value="0.0" label="Mean value of the detector noise being added to the complete measurement" help="(-mean) "/>
701 <param name="param_algorithm_MSSim_RawSignal_noise_detector_stddev" type="float" value="0.0" label="Standard deviation of the detector noise being added to the complete measurement" help="(-stddev) "/>
702 <param name="param_algorithm_MSSim_RawTandemSignal_status" display="radio" type="select" optional="False" value="disabled" label="Create Tandem-MS scans?" help="(-status) ">
703 <option value="disabled" selected="true">disabled</option>
704 <option value="precursor">precursor</option>
705 <option value="MS^E">MS^E</option>
706 </param>
707 <param name="param_algorithm_MSSim_RawTandemSignal_tandem_mode" type="integer" min="0" max="2" optional="True" value="0" label="Algorithm to generate the tandem-MS spectra" help="(-tandem_mode) 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity &lt;br&gt;"/>
708 <param name="param_algorithm_MSSim_RawTandemSignal_svm_model_set_file" type="text" size="30" value="examples/simulation/SvmModelSet.model" label="File containing the filenames of SVM Models for different charge variants" help="(-svm_model_set_file) ">
709 <sanitizer>
710 <valid initial="string.printable">
711 <remove value="'"/>
712 <remove value="&quot;"/>
713 </valid>
714 </sanitizer>
715 </param>
716 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help="(-ms2_spectra_per_rt_bin) "/>
717 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance" type="float" min="0.0001" optional="True" value="2.0" label="The minimal distance (in Th) between two peaks for concurrent selection for fragmentation" help="(-min_mz_peak_distance) Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor"/>
718 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window" type="float" min="0.0" optional="True" value="2.0" label="All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation" help="(-mz_isolation_window) "/>
719 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks" falsevalue="" checked="false" optional="True" label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" help="(-exclude_overlapping_peaks) "/>
720 <repeat name="rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" min="0" max="1" title="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter">
721 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" type="text" min="1" max="5" optional="True" size="30" value="2 3" label="Charges considered for MS2 fragmentation" help="(-charge_filter) ">
722 <sanitizer>
723 <valid initial="string.printable">
724 <remove value="'"/>
725 <remove value="&quot;"/>
726 </valid>
727 </sanitizer>
728 </param>
729 </repeat>
730 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion" falsevalue="" checked="false" optional="True" label="If true dynamic exclusion is applied" help="(-use_dynamic_exclusion) "/>
731 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded" help="(-exclusion_time) "/>
732 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list" help="(-max_list_size) "/>
733 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds" help="(-min_rt) "/>
734 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds" help="(-max_rt) "/>
735 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds" help="(-rt_step_size) "/>
736 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds" help="(-rt_window_size) "/>
737 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified" help="(-min_protein_id_probability) "/>
738 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/>
739 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help="(-min_mz) "/>
740 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help="(-max_mz) "/>
741 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/>
742 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids) "/>
743 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability) "/>
744 <param name="param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra" falsevalue="" checked="false" optional="True" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot)" help="(-add_single_spectra) They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead"/>
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) "/>
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) "/>
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) "/>
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) "/>
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) "/>
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) "/>
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) "/>
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) ">
753 <option value="true" selected="true">true</option>
754 <option value="false">false</option>
755 </param>
756 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of b-ions to the spectrum" help="(-add_b_ions) ">
757 <option value="true" selected="true">true</option>
758 <option value="false">false</option>
759 </param>
760 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions" falsevalue="" checked="false" optional="True" label="Add peaks of a-ions to the spectrum" help="(-add_a_ions) "/>
761 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions" falsevalue="" checked="false" optional="True" label="Add peaks of c-ions to the spectrum" help="(-add_c_ions) "/>
762 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions" falsevalue="" checked="false" optional="True" label="Add peaks of x-ions to the spectrum" help="(-add_x_ions) "/>
763 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions" falsevalue="" checked="false" optional="True" label="Add peaks of z-ions to the spectrum" help="(-add_z_ions) "/>
764 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity) "/>
765 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity) "/>
766 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity) "/>
767 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity) "/>
768 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity) "/>
769 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity) "/>
770 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity" type="float" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help="(-relative_loss_intensity) "/>
771 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity" type="float" value="1.0" label="Intensity of the precursor peak" help="(-precursor_intensity) "/>
772 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity" type="float" value="1.0" label="Intensity of the H2O loss peak of the precurso" help="(-precursor_H2O_intensity) "/>
773 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity" type="float" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help="(-precursor_NH3_intensity) "/>
774 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes" falsevalue="" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes) "/>
775 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_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) "/>
776 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM: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) "/>
777 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM: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) "/>
778 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions" falsevalue="" checked="false" optional="True" label="Add peaks of y-ions to the spectrum" help="(-hide_y_ions) "/>
779 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions" falsevalue="" checked="false" optional="True" label="Add peaks of y-ions to the spectrum" help="(-hide_y2_ions) "/>
780 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions" falsevalue="" checked="false" optional="True" label="Add peaks of b-ions to the spectrum" help="(-hide_b_ions) "/>
781 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions" falsevalue="" checked="false" optional="True" label="Add peaks of b-ions to the spectrum" help="(-hide_b2_ions) "/>
782 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions" falsevalue="" checked="false" optional="True" label="Add peaks of a-ions to the spectrum" help="(-hide_a_ions) "/>
783 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions" falsevalue="" checked="false" optional="True" label="Add peaks of c-ions to the spectrum" help="(-hide_c_ions) "/>
784 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions" falsevalue="" checked="false" optional="True" label="Add peaks of x-ions to the spectrum" help="(-hide_x_ions) "/>
785 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions" falsevalue="" checked="false" optional="True" label="Add peaks of z-ions to the spectrum" help="(-hide_z_ions) "/>
786 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_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="(-hide_losses) "/>
787 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity) "/>
788 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity) "/>
789 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity) "/>
790 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity) "/>
791 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity) "/>
792 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity) "/>
793 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity" type="float" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help="(-relative_loss_intensity) "/>
794 <param name="param_algorithm_MSSim_Global_ionization_type" display="radio" type="select" optional="False" value="ESI" label="Type of Ionization (MALDI or ESI)" help="(-ionization_type) ">
795 <option value="MALDI">MALDI</option>
796 <option value="ESI" selected="true">ESI</option>
797 </param>
798 <param name="param_algorithm_MSSim_Labeling_type" type="select" optional="False" value="labelfree" label="Select the labeling type you want for your experiment" help="(-type) ">
799 <option value="ICPL">ICPL</option>
800 <option value="SILAC">SILAC</option>
801 <option value="itraq">itraq</option>
802 <option value="labelfree" selected="true">labelfree</option>
803 <option value="o18">o18</option>
804 </param>
805 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift" type="float" value="0.0" label="Fixed retention time shift between labeled pairs" help="(-ICPL_fixed_rtshift) If set to 0.0 only the retention times, computed by the RT model step are used"/>
806 <param name="param_algorithm_MSSim_Labeling_ICPL_label_proteins" display="radio" type="select" optional="False" value="true" label="Enables protein-labeling" help="(-label_proteins) (select 'false' if you only need peptide-labeling)">
807 <option value="true" selected="true">true</option>
808 <option value="false">false</option>
809 </param>
810 <param name="param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift" type="float" min="0.0" optional="True" value="0.0001" label="Fixed retention time shift between labeled peptides" help="(-fixed_rtshift) If set to 0.0 only the retention times computed by the RT model step are used"/>
811 <param name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine" type="text" size="30" value="UniMod:481" label="Modification of Lysine in the medium SILAC channel" help="(-modification_lysine) ">
812 <sanitizer>
813 <valid initial="string.printable">
814 <remove value="'"/>
815 <remove value="&quot;"/>
816 </valid>
817 </sanitizer>
818 </param>
819 <param name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine" type="text" size="30" value="UniMod:188" label="Modification of Arginine in the medium SILAC channel" help="(-modification_arginine) ">
820 <sanitizer>
821 <valid initial="string.printable">
822 <remove value="'"/>
823 <remove value="&quot;"/>
824 </valid>
825 </sanitizer>
826 </param>
827 <param name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine" type="text" size="30" value="UniMod:259" label="Modification of Lysine in the heavy SILAC channel" help="(-modification_lysine) If left empty, two channelSILAC is assumed">
828 <sanitizer>
829 <valid initial="string.printable">
830 <remove value="'"/>
831 <remove value="&quot;"/>
832 </valid>
833 </sanitizer>
834 </param>
835 <param name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" type="text" size="30" value="UniMod:267" label="Modification of Arginine in the heavy SILAC channel" help="(-modification_arginine) If left empty, two-channel SILAC is assumed">
836 <sanitizer>
837 <valid initial="string.printable">
838 <remove value="'"/>
839 <remove value="&quot;"/>
840 </valid>
841 </sanitizer>
842 </param>
843 <param name="param_algorithm_MSSim_Labeling_itraq_iTRAQ" display="radio" type="select" optional="False" value="4plex" label="4plex or 8plex iTRAQ?" help="(-iTRAQ) ">
844 <option value="4plex" selected="true">4plex</option>
845 <option value="8plex">8plex</option>
846 </param>
847 <param name="param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift" type="float" min="0.0" max="0.5" optional="True" value="0.1" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of" help="(-reporter_mass_shift) e.g. 114.1, 115.1)"/>
848 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex">
849 <param name="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" type="text" size="30" value="114:myReference" label="Four-plex only: Each channel that was used in the experiment and its description (114-117) in format &lt;channel&gt;:&lt;name&gt;," help="(-channel_active_4plex) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;">
850 <sanitizer>
851 <valid initial="string.printable">
852 <remove value="'"/>
853 <remove value="&quot;"/>
854 </valid>
855 </sanitizer>
856 </param>
857 </repeat>
858 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex">
859 <param name="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" type="text" size="30" value="113:myReference" label="Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format &lt;channel&gt;:&lt;name&gt;," help="(-channel_active_8plex) e.g. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot;">
860 <sanitizer>
861 <valid initial="string.printable">
862 <remove value="'"/>
863 <remove value="&quot;"/>
864 </valid>
865 </sanitizer>
866 </param>
867 </repeat>
868 <param name="param_algorithm_MSSim_Labeling_itraq_Y_contamination" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="Efficiency of labeling tyrosine ('Y') residues" help="(-Y_contamination) 0=off, 1=full labeling"/>
869 <param name="param_algorithm_MSSim_Labeling_o18_labeling_efficiency" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" help="(-labeling_efficiency) "/>
870 <param name="param_algorithm_RandomNumberGenerators_biological" display="radio" type="select" optional="False" value="random" label="Controls the 'biological' randomness of the generated data (" help="(-biological) e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
871 <option value="reproducible">reproducible</option>
872 <option value="random" selected="true">random</option>
873 </param>
874 <param name="param_algorithm_RandomNumberGenerators_technical" display="radio" type="select" optional="False" value="random" label="Controls the 'technical' randomness of the generated data (" help="(-technical) e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
875 <option value="reproducible">reproducible</option>
876 <option value="random" selected="true">random</option>
877 </param>
878 <expand macro="advanced_options">
879 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
880 <param name="param_algorithm_MSSim_Ionization_esi_max_impurity_set_size" type="integer" value="3" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state" help="(-max_impurity_set_size) E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'"/>
881 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label" type="text" size="30" value="UniMod:365" label="UniMod Id of the light channel ICPL label" help="(-ICPL_light_channel_label) ">
882 <sanitizer>
883 <valid initial="string.printable">
884 <remove value="'"/>
885 <remove value="&quot;"/>
886 </valid>
887 </sanitizer>
888 </param>
889 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label" type="text" size="30" value="UniMod:687" label="UniMod Id of the medium channel ICPL label" help="(-ICPL_medium_channel_label) ">
890 <sanitizer>
891 <valid initial="string.printable">
892 <remove value="'"/>
893 <remove value="&quot;"/>
894 </valid>
895 </sanitizer>
896 </param>
897 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label" type="text" size="30" value="UniMod:364" label="UniMod Id of the heavy channel ICPL label" help="(-ICPL_heavy_channel_label) ">
898 <sanitizer>
899 <valid initial="string.printable">
900 <remove value="'"/>
901 <remove value="&quot;"/>
902 </valid>
903 </sanitizer>
904 </param>
905 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex">
906 <param name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" type="text" size="30" value="114:0/1/5.9/0.2 115:0/2/5.6/0.1 116:0/3/4.5/0.1 117:0.1/4/3.5/0.1" label="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="(-isotope_correction_values_4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' ">
907 <sanitizer>
908 <valid initial="string.printable">
909 <remove value="'"/>
910 <remove value="&quot;"/>
911 </valid>
912 </sanitizer>
913 </param>
914 </repeat>
915 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex">
916 <param name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" type="text" size="30" value="113:0/0/6.89/0.22 114:0/0.94/5.9/0.16 115:0/1.88/4.9/0.1 116:0/2.82/3.9/0.07 117:0.06/3.77/2.99/0 118:0.09/4.71/1.88/0 119:0.14/5.66/0.87/0 121:0.27/7.44/0.18/0" label="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="(-isotope_correction_values_8plex) e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' ">
917 <sanitizer>
918 <valid initial="string.printable">
919 <remove value="'"/>
920 <remove value="&quot;"/>
921 </valid>
922 </sanitizer>
923 </param>
924 </repeat>
925 </expand>
926 </inputs>
927 <outputs>
928 <data name="param_out" format="mzml"/>
929 <data name="param_out_pm" format="mzml"/>
930 <data name="param_out_fm" format="featurexml"/>
931 <data name="param_out_cm" format="consensusxml"/>
932 <data name="param_out_lcm" format="consensusxml"/>
933 <data name="param_out_cntm" format="featurexml"/>
934 <data name="param_out_id" format="idxml"/>
935 </outputs>
936 <help>A highly configurable simulator for mass spectrometry experiments.
937
938
939 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html</help>
940 </tool>