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comparison MSSimulator.xml @ 9:98bb49e7b5ba draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 19:46:59 +0000
parents d7cddde5703a
children 04228172e123
comparison
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8:b0f25a9d063c 9:98bb49e7b5ba
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 CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MSSimulator" name="MSSimulator" version="2.3.0"> 4 <tool id="MSSimulator" name="MSSimulator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MSSimulator 15 @EXT_FOO@
16 #import re
14 17
18 ## Preprocessing
19 mkdir in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out &&
23 #end if
24 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir out_pm &&
26 #end if
27 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir out_fm &&
29 #end if
30 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
31 mkdir out_cm &&
32 #end if
33 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 mkdir out_lcm &&
35 #end if
36 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 mkdir out_cntm &&
38 #end if
39 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
40 mkdir out_id &&
41 #end if
42
43 ## Main program call
44
45 set -o pipefail &&
46 @EXECUTABLE@ -write_ctd ./ &&
47 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
48 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
15 -in 49 -in
16 #for token in $param_in: 50 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
17 $token 51 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
18 #end for 52 -out
19 #if $param_out: 53 'out/output.${gxy2omsext("mzml")}'
20 -out $param_out 54 #end if
21 #end if 55 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 #if $param_out_pm: 56 -out_pm
23 -out_pm $param_out_pm 57 'out_pm/output.${gxy2omsext("mzml")}'
24 #end if 58 #end if
25 #if $param_out_fm: 59 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
26 -out_fm $param_out_fm 60 -out_fm
27 #end if 61 'out_fm/output.${gxy2omsext("featurexml")}'
28 #if $param_out_cm: 62 #end if
29 -out_cm $param_out_cm 63 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
30 #end if 64 -out_cm
31 #if $param_out_lcm: 65 'out_cm/output.${gxy2omsext("consensusxml")}'
32 -out_lcm $param_out_lcm 66 #end if
33 #end if 67 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 #if $param_out_cntm: 68 -out_lcm
35 -out_cntm $param_out_cntm 69 'out_lcm/output.${gxy2omsext("consensusxml")}'
36 #end if 70 #end if
37 #if $param_out_id: 71 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
38 -out_id $param_out_id 72 -out_cntm
39 #end if 73 'out_cntm/output.${gxy2omsext("featurexml")}'
40 #if $param_algorithm_MSSim_Digestion_enzyme: 74 #end if
41 -algorithm:MSSim:Digestion:enzyme 75 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
42 #if " " in str($param_algorithm_MSSim_Digestion_enzyme): 76 -out_id
43 "$param_algorithm_MSSim_Digestion_enzyme" 77 'out_id/output.${gxy2omsext("idxml")}'
44 #else 78 #end if
45 $param_algorithm_MSSim_Digestion_enzyme 79 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
46 #end if 80 | tee '$stdout'
47 #end if
48 #if $param_algorithm_MSSim_Digestion_model:
49 -algorithm:MSSim:Digestion:model
50 #if " " in str($param_algorithm_MSSim_Digestion_model):
51 "$param_algorithm_MSSim_Digestion_model"
52 #else
53 $param_algorithm_MSSim_Digestion_model
54 #end if
55 #end if
56 #if $param_algorithm_MSSim_Digestion_min_peptide_length:
57 -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
58 #end if
59 #if $param_algorithm_MSSim_Digestion_model_trained_threshold:
60 -algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold
61 #end if
62 #if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages:
63 -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages
64 #end if
65 #if $param_algorithm_MSSim_RT_rt_column:
66 -algorithm:MSSim:RT:rt_column
67 #if " " in str($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
72 #end if
73 #if $param_algorithm_MSSim_RT_auto_scale:
74 -algorithm:MSSim:RT:auto_scale
75 #if " " in str($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
80 #end if
81 #if $param_algorithm_MSSim_RT_total_gradient_time:
82 -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
83 #end if
84 #if $param_algorithm_MSSim_RT_sampling_rate:
85 -algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate
86 #end if
87 #if $param_algorithm_MSSim_RT_scan_window_min:
88 -algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min
89 #end if
90 #if $param_algorithm_MSSim_RT_scan_window_max:
91 -algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max
92 #end if
93 #if $param_algorithm_MSSim_RT_variation_feature_stddev:
94 -algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev
95 #end if
96 #if $param_algorithm_MSSim_RT_variation_affine_offset:
97 -algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset
98 #end if
99 #if $param_algorithm_MSSim_RT_variation_affine_scale:
100 -algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale
101 #end if
102 #if $param_algorithm_MSSim_RT_column_condition_distortion:
103 -algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion
104 #end if
105 #if $param_algorithm_MSSim_RT_profile_shape_width_value:
106 -algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value
107 #end if
108 #if $param_algorithm_MSSim_RT_profile_shape_width_variance:
109 -algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance
110 #end if
111 #if $param_algorithm_MSSim_RT_profile_shape_skewness_value:
112 -algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value
113 #end if
114 #if $param_algorithm_MSSim_RT_profile_shape_skewness_variance:
115 -algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance
116 #end if
117 #if $param_algorithm_MSSim_RT_HPLC_model_file:
118 -algorithm:MSSim:RT:HPLC:model_file "$param_algorithm_MSSim_RT_HPLC_model_file"
119 #end if
120 #if $param_algorithm_MSSim_RT_CE_pH:
121 -algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH
122 #end if
123 #if $param_algorithm_MSSim_RT_CE_alpha:
124 -algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha
125 #end if
126 #if $param_algorithm_MSSim_RT_CE_mu_eo:
127 -algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo
128 #end if
129 #if $param_algorithm_MSSim_RT_CE_lenght_d:
130 -algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d
131 #end if
132 #if $param_algorithm_MSSim_RT_CE_length_total:
133 -algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total
134 #end if
135 #if $param_algorithm_MSSim_RT_CE_voltage:
136 -algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage
137 #end if
138 #if $param_algorithm_MSSim_Detectability_dt_simulation_on:
139 -algorithm:MSSim:Detectability:dt_simulation_on
140 #end if
141 #if $param_algorithm_MSSim_Detectability_min_detect:
142 -algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect
143 #end if
144 #if $param_algorithm_MSSim_Detectability_dt_model_file:
145 -algorithm:MSSim:Detectability:dt_model_file "$param_algorithm_MSSim_Detectability_dt_model_file"
146 #end if 81 #end if
147 82
148 #if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues: 83 ## Postprocessing
149 -algorithm:MSSim:Ionization:esi:ionized_residues 84 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
150 #for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues: 85 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
151 #if " " in str(token): 86 #end if
152 "$token.param_algorithm_MSSim_Ionization_esi_ionized_residues" 87 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
153 #else 88 && mv 'out_pm/output.${gxy2omsext("mzml")}' '$out_pm'
154 $token.param_algorithm_MSSim_Ionization_esi_ionized_residues 89 #end if
155 #end if 90 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
156 #end for 91 && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
157 #end if 92 #end if
158 93 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
159 #if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity: 94 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
160 -algorithm:MSSim:Ionization:esi:charge_impurity 95 #end if
161 #for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity: 96 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
162 #if " " in str(token): 97 && mv 'out_lcm/output.${gxy2omsext("consensusxml")}' '$out_lcm'
163 "$token.param_algorithm_MSSim_Ionization_esi_charge_impurity" 98 #end if
164 #else 99 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
165 $token.param_algorithm_MSSim_Ionization_esi_charge_impurity 100 && mv 'out_cntm/output.${gxy2omsext("featurexml")}' '$out_cntm'
166 #end if 101 #end if
167 #end for 102 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
168 #end if 103 && mv 'out_id/output.${gxy2omsext("idxml")}' '$out_id'
169 #if $param_algorithm_MSSim_Ionization_esi_ionization_probability: 104 #end if
170 -algorithm:MSSim:Ionization:esi:ionization_probability $param_algorithm_MSSim_Ionization_esi_ionization_probability 105 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
171 #end if 106 && mv '@EXECUTABLE@.ctd' '$ctd_out'
172 107 #end if]]></command>
173 #if $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities: 108 <configfiles>
174 -algorithm:MSSim:Ionization:maldi:ionization_probabilities 109 <inputs name="args_json" data_style="paths"/>
175 #for token in $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities: 110 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
176 #if " " in str(token): 111 </configfiles>
177 "$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities"
178 #else
179 $token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities
180 #end if
181 #end for
182 #end if
183 #if $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit:
184 -algorithm:MSSim:Ionization:mz:lower_measurement_limit $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit
185 #end if
186 #if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit:
187 -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit
188 #end if
189 #if $param_algorithm_MSSim_RawSignal_enabled:
190 -algorithm:MSSim:RawSignal:enabled
191 #if " " in str($param_algorithm_MSSim_RawSignal_enabled):
192 "$param_algorithm_MSSim_RawSignal_enabled"
193 #else
194 $param_algorithm_MSSim_RawSignal_enabled
195 #end if
196 #end if
197 #if $param_algorithm_MSSim_RawSignal_peak_shape:
198 -algorithm:MSSim:RawSignal:peak_shape
199 #if " " in str($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
204 #end if
205 #if $param_algorithm_MSSim_RawSignal_resolution_value:
206 -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value
207 #end if
208 #if $param_algorithm_MSSim_RawSignal_resolution_type:
209 -algorithm:MSSim:RawSignal:resolution:type
210 #if " " in str($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
215 #end if
216 #if $param_algorithm_MSSim_RawSignal_baseline_scaling:
217 -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling
218 #end if
219 #if $param_algorithm_MSSim_RawSignal_baseline_shape:
220 -algorithm:MSSim:RawSignal:baseline:shape $param_algorithm_MSSim_RawSignal_baseline_shape
221 #end if
222 #if $param_algorithm_MSSim_RawSignal_mz_sampling_points:
223 -algorithm:MSSim:RawSignal:mz:sampling_points $param_algorithm_MSSim_RawSignal_mz_sampling_points
224 #end if
225 #if $param_algorithm_MSSim_RawSignal_contaminants_file:
226 -algorithm:MSSim:RawSignal:contaminants:file "$param_algorithm_MSSim_RawSignal_contaminants_file"
227 #end if
228 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev:
229 -algorithm:MSSim:RawSignal:variation:mz:error_stddev $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev
230 #end if
231 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_mean:
232 -algorithm:MSSim:RawSignal:variation:mz:error_mean $param_algorithm_MSSim_RawSignal_variation_mz_error_mean
233 #end if
234 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale:
235 -algorithm:MSSim:RawSignal:variation:intensity:scale $param_algorithm_MSSim_RawSignal_variation_intensity_scale
236 #end if
237 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev:
238 -algorithm:MSSim:RawSignal:variation:intensity:scale_stddev $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev
239 #end if
240 #if $param_algorithm_MSSim_RawSignal_noise_shot_rate:
241 -algorithm:MSSim:RawSignal:noise:shot:rate $param_algorithm_MSSim_RawSignal_noise_shot_rate
242 #end if
243 #if $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean:
244 -algorithm:MSSim:RawSignal:noise:shot:intensity-mean $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean
245 #end if
246 #if $param_algorithm_MSSim_RawSignal_noise_white_mean:
247 -algorithm:MSSim:RawSignal:noise:white:mean $param_algorithm_MSSim_RawSignal_noise_white_mean
248 #end if
249 #if $param_algorithm_MSSim_RawSignal_noise_white_stddev:
250 -algorithm:MSSim:RawSignal:noise:white:stddev $param_algorithm_MSSim_RawSignal_noise_white_stddev
251 #end if
252 #if $param_algorithm_MSSim_RawSignal_noise_detector_mean:
253 -algorithm:MSSim:RawSignal:noise:detector:mean $param_algorithm_MSSim_RawSignal_noise_detector_mean
254 #end if
255 #if $param_algorithm_MSSim_RawSignal_noise_detector_stddev:
256 -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev
257 #end if
258 #if $param_algorithm_MSSim_RawTandemSignal_status:
259 -algorithm:MSSim:RawTandemSignal:status
260 #if " " in str($param_algorithm_MSSim_RawTandemSignal_status):
261 "$param_algorithm_MSSim_RawTandemSignal_status"
262 #else
263 $param_algorithm_MSSim_RawTandemSignal_status
264 #end if
265 #end if
266 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode:
267 -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode
268 #end if
269 #if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file:
270 -algorithm:MSSim:RawTandemSignal:svm_model_set_file "$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file"
271 #end if
272 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin:
273 -algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin
274 #end if
275 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance:
276 -algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance
277 #end if
278 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window:
279 -algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window
280 #end if
281 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks:
282 -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks
283 #end if
284
285 #if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
286 -algorithm:MSSim:RawTandemSignal:Precursor:charge_filter
287 #for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
288 #if " " in str(token):
289 "$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter"
290 #else
291 $token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter
292 #end if
293 #end for
294 #end if
295 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion:
296 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion
297 #end if
298 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time:
299 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time
300 #end if
301 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size:
302 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size
303 #end if
304 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt:
305 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt
306 #end if
307 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt:
308 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt
309 #end if
310 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size:
311 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size
312 #end if
313 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size:
314 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size
315 #end if
316 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability:
317 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability
318 #end if
319 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight:
320 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight
321 #end if
322 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz:
323 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz
324 #end if
325 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz:
326 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz
327 #end if
328 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule:
329 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule
330 #end if
331 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids:
332 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids
333 #end if
334 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability:
335 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability
336 #end if
337 #if $param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra:
338 -algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra
339 #end if
340 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes:
341 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes
342 #end if
343 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope:
344 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope
345 #end if
346 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo:
347 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo
348 #end if
349 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses:
350 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses
351 #end if
352 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
353 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
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
358 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
359 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
360 #end if
361 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion:
362 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
363 #end if
364 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions:
365 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions
366 #if " " in str($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
371 #end if
372 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions:
373 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions
374 #if " " in str($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
379 #end if
380 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
381 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
382 #end if
383 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions:
384 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions
385 #end if
386 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions:
387 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions
388 #end if
389 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions:
390 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions
391 #end if
392 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity:
393 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity
394 #end if
395 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity:
396 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity
397 #end if
398 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity:
399 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity
400 #end if
401 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity:
402 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity
403 #end if
404 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity:
405 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity
406 #end if
407 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity:
408 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity
409 #end if
410 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity:
411 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity
412 #end if
413 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity:
414 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity
415 #end if
416 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity:
417 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity
418 #end if
419 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity:
420 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity
421 #end if
422 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes:
423 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes
424 #end if
425 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope:
426 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope
427 #end if
428 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo:
429 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo
430 #end if
431 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion:
432 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion
433 #end if
434 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions:
435 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions
436 #end if
437 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions:
438 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions
439 #end if
440 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions:
441 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions
442 #end if
443 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions:
444 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions
445 #end if
446 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions:
447 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions
448 #end if
449 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions:
450 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions
451 #end if
452 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions:
453 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions
454 #end if
455 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions:
456 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions
457 #end if
458 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses:
459 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses
460 #end if
461 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity:
462 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity
463 #end if
464 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity:
465 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity
466 #end if
467 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity:
468 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity
469 #end if
470 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity:
471 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity
472 #end if
473 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity:
474 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity
475 #end if
476 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity:
477 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity
478 #end if
479 #if $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
481 #end if
482 #if $param_algorithm_MSSim_Global_ionization_type:
483 -algorithm:MSSim:Global:ionization_type
484 #if " " in str($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
489 #end if
490 #if $param_algorithm_MSSim_Labeling_type:
491 -algorithm:MSSim:Labeling:type
492 #if " " in str($param_algorithm_MSSim_Labeling_type):
493 "$param_algorithm_MSSim_Labeling_type"
494 #else
495 $param_algorithm_MSSim_Labeling_type
496 #end if
497 #end if
498 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift:
499 -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift
500 #end if
501 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
502 -algorithm:MSSim:Labeling:ICPL:label_proteins
503 #if " " in str($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
508 #end if
509 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
510 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
511 #end if
512 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine:
513 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine"
514 #end if
515 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine:
516 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine"
517 #end if
518 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine:
519 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine"
520 #end if
521 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine:
522 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine"
523 #end if
524 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
525 -algorithm:MSSim:Labeling:itraq:iTRAQ
526 #if " " in str($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
531 #end if
532 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift:
533 -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift
534 #end if
535
536 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
537 -algorithm:MSSim:Labeling:itraq:channel_active_4plex
538 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
539 #if " " in str(token):
540 "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex"
541 #else
542 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex
543 #end if
544 #end for
545 #end if
546
547 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
548 -algorithm:MSSim:Labeling:itraq:channel_active_8plex
549 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
550 #if " " in str(token):
551 "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex"
552 #else
553 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex
554 #end if
555 #end for
556 #end if
557 #if $param_algorithm_MSSim_Labeling_itraq_Y_contamination:
558 -algorithm:MSSim:Labeling:itraq:Y_contamination $param_algorithm_MSSim_Labeling_itraq_Y_contamination
559 #end if
560 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency:
561 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
562 #end if
563 #if $param_algorithm_RandomNumberGenerators_biological:
564 -algorithm:RandomNumberGenerators:biological
565 #if " " in str($param_algorithm_RandomNumberGenerators_biological):
566 "$param_algorithm_RandomNumberGenerators_biological"
567 #else
568 $param_algorithm_RandomNumberGenerators_biological
569 #end if
570 #end if
571 #if $param_algorithm_RandomNumberGenerators_technical:
572 -algorithm:RandomNumberGenerators:technical
573 #if " " in str($param_algorithm_RandomNumberGenerators_technical):
574 "$param_algorithm_RandomNumberGenerators_technical"
575 #else
576 $param_algorithm_RandomNumberGenerators_technical
577 #end if
578 #end if
579 #if $adv_opts.adv_opts_selector=='advanced':
580 #if $adv_opts.param_force:
581 -force
582 #end if
583 #if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size:
584 -algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size
585 #end if
586 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label:
587 -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label"
588 #end if
589 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label:
590 -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label"
591 #end if
592 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label:
593 -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label"
594 #end if
595
596 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
597 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex
598 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
599 #if " " in str(token):
600 "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex"
601 #else
602 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex
603 #end if
604 #end for
605 #end if
606
607 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
608 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex
609 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
610 #if " " in str(token):
611 "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex"
612 #else
613 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex
614 #end if
615 #end for
616 #end if
617 #end if
618 ]]></command>
619 <inputs> 112 <inputs>
620 <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input protein sequences" help="(-in) "> 113 <param name="in" argument="-in" type="data" format="fasta" multiple="true" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/>
621 <sanitizer> 114 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
622 <valid initial="string.printable"> 115 <section name="MSSim" title="" help="" expanded="false">
623 <remove value="'"/> 116 <section name="Digestion" title="" help="" expanded="false">
624 <remove value="&quot;"/> 117 <param name="enzyme" argument="-algorithm:MSSim:Digestion:enzyme" type="select" optional="false" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="">
625 </valid> 118 <option value="PepsinA">PepsinA</option>
626 </sanitizer> 119 <option value="TrypChymo">TrypChymo</option>
120 <option value="Arg-C">Arg-C</option>
121 <option value="Arg-C/P">Arg-C/P</option>
122 <option value="Asp-N">Asp-N</option>
123 <option value="Asp-N/B">Asp-N/B</option>
124 <option value="Asp-N_ambic">Asp-N_ambic</option>
125 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
126 <option value="no cleavage">no cleavage</option>
127 <option value="unspecific cleavage">unspecific cleavage</option>
128 <option value="proline endopeptidase">proline endopeptidase</option>
129 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
130 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
131 <option value="2-iodobenzoate">2-iodobenzoate</option>
132 <option value="Chymotrypsin">Chymotrypsin</option>
133 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
134 <option value="CNBr">CNBr</option>
135 <option value="Formic_acid">Formic_acid</option>
136 <option value="Lys-C">Lys-C</option>
137 <option value="Lys-N">Lys-N</option>
138 <option value="Lys-C/P">Lys-C/P</option>
139 <option value="iodosobenzoate">iodosobenzoate</option>
140 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
141 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
142 <option value="Glu-C+P">Glu-C+P</option>
143 <option value="PepsinA + P">PepsinA + P</option>
144 <option value="cyanogen-bromide">cyanogen-bromide</option>
145 <option value="Clostripain/P">Clostripain/P</option>
146 <option value="Trypsin/P">Trypsin/P</option>
147 <option value="V8-DE">V8-DE</option>
148 <option value="V8-E">V8-E</option>
149 <option value="leukocyte elastase">leukocyte elastase</option>
150 <option value="Trypsin" selected="true">Trypsin</option>
151 <expand macro="list_string_san"/>
152 </param>
153 <param name="model" argument="-algorithm:MSSim:Digestion:model" display="radio" type="select" optional="false" label="The cleavage model to use for digestion" help="'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
154 <option value="trained">trained</option>
155 <option value="naive" selected="true">naive</option>
156 <expand macro="list_string_san"/>
157 </param>
158 <param name="min_peptide_length" argument="-algorithm:MSSim:Digestion:min_peptide_length" type="integer" optional="true" min="1" value="3" label="Minimum peptide length after digestion (shorter ones will be discarded)" help=""/>
159 <section name="model_trained" title="" help="" expanded="false">
160 <param name="threshold" argument="-algorithm:MSSim:Digestion:model_trained:threshold" type="float" optional="true" min="-2.0" max="4.0" value="0.5" label="Model threshold for calling a cleavage" help="Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage"/>
161 </section>
162 <section name="model_naive" title="" help="" expanded="false">
163 <param name="missed_cleavages" argument="-algorithm:MSSim:Digestion:model_naive:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Maximum number of missed cleavages considered" help="All possible resulting peptides will be created"/>
164 </section>
165 </section>
166 <section name="RT" title="" help="" expanded="false">
167 <param name="rt_column" argument="-algorithm:MSSim:RT:rt_column" display="radio" type="select" optional="false" label="Modelling of an RT or CE column" help="">
168 <option value="none">none</option>
169 <option value="HPLC" selected="true">HPLC</option>
170 <option value="CE">CE</option>
171 <expand macro="list_string_san"/>
172 </param>
173 <param name="auto_scale" argument="-algorithm:MSSim:RT:auto_scale" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Scale predicted RT's/MT's to given 'total_gradient_time'" help="If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence"/>
174 <param name="total_gradient_time" argument="-algorithm:MSSim:RT:total_gradient_time" type="float" optional="true" min="1e-05" value="2500.0" label="The duration [s] of the gradient" help=""/>
175 <param name="sampling_rate" argument="-algorithm:MSSim:RT:sampling_rate" type="float" optional="true" min="0.01" max="60.0" value="2.0" label="Time interval [s] between consecutive scans" help=""/>
176 <section name="scan_window" title="" help="" expanded="false">
177 <param name="min" argument="-algorithm:MSSim:RT:scan_window:min" type="float" optional="true" min="0.0" value="500.0" label="Start of RT Scan Window [s]" help=""/>
178 <param name="max" argument="-algorithm:MSSim:RT:scan_window:max" type="float" optional="true" min="1.0" value="1500.0" label="End of RT Scan Window [s]" help=""/>
179 </section>
180 <section name="variation" title="Random component that simulates technical/biological variation" help="" expanded="false">
181 <param name="feature_stddev" argument="-algorithm:MSSim:RT:variation:feature_stddev" type="integer" optional="true" value="3" label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" help=""/>
182 <param name="affine_offset" argument="-algorithm:MSSim:RT:variation:affine_offset" type="integer" optional="true" value="0" label="Global offset in retention time [s] from predicted model" help=""/>
183 <param name="affine_scale" argument="-algorithm:MSSim:RT:variation:affine_scale" type="integer" optional="true" value="1" label="Global scaling in retention time from predicted model" help=""/>
184 </section>
185 <section name="column_condition" title="" help="" expanded="false">
186 <param name="distortion" argument="-algorithm:MSSim:RT:column_condition:distortion" type="integer" optional="true" min="0" max="10" value="0" label="Distortion of the elution profiles" help="Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be &gt;4"/>
187 </section>
188 <section name="profile_shape" title="" help="" expanded="false">
189 <section name="width" title="Width of the EGH elution shape" help="i.e. the sigma^2 parameter, which is computed using 'value' + rnd_cauchy('variance')" expanded="false">
190 <param name="value" argument="-algorithm:MSSim:RT:profile_shape:width:value" type="float" optional="true" min="0.0" value="9.0" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile" help="This does not correspond directly to the width in [s]"/>
191 <param name="variance" argument="-algorithm:MSSim:RT:profile_shape:width:variance" type="float" optional="true" min="0.0" value="1.6" label="Random component of the width (set to 0 to disable randomness)" help="i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be &gt;= 0)"/>
192 </section>
193 <section name="skewness" title="Skewness of the EGH elution shape" help="i.e. the tau parameter, which is computed using 'value' + rnd_cauchy('variance')" expanded="false">
194 <param name="value" argument="-algorithm:MSSim:RT:profile_shape:skewness:value" type="float" optional="true" value="0.1" label="Asymmetric component of the EGH" help="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"/>
195 <param name="variance" argument="-algorithm:MSSim:RT:profile_shape:skewness:variance" type="float" optional="true" min="0.0" value="0.3" label="Random component of skewness (set to 0 to disable randomness)" help="i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be &gt; 0)"/>
196 </section>
197 </section>
198 <section name="HPLC" title="" help="" expanded="false">
199 <param name="model_file" argument="-algorithm:MSSim:RT:HPLC:model_file" type="text" optional="true" value="examples/simulation/RTPredict.model" label="SVM model for retention time prediction" help="">
200 <expand macro="list_string_san"/>
201 </param>
202 </section>
203 <section name="CE" title="" help="" expanded="false">
204 <param name="pH" argument="-algorithm:MSSim:RT:CE:pH" type="float" optional="true" min="0.0" max="14.0" value="3.0" label="pH of buffe" help=""/>
205 <param name="alpha" argument="-algorithm:MSSim:RT:CE:alpha" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Exponent Alpha used to calculate mobility" help=""/>
206 <param name="mu_eo" argument="-algorithm:MSSim:RT:CE:mu_eo" type="float" optional="true" min="0.0" max="5.0" value="0.0" label="Electroosmotic flow" help=""/>
207 <param name="lenght_d" argument="-algorithm:MSSim:RT:CE:lenght_d" type="float" optional="true" min="0.0" max="1000.0" value="70.0" label="Length of capillary [cm] from injection site to MS" help=""/>
208 <param name="length_total" argument="-algorithm:MSSim:RT:CE:length_total" type="float" optional="true" min="0.0" max="1000.0" value="75.0" label="Total length of capillary [cm]" help=""/>
209 <param name="voltage" argument="-algorithm:MSSim:RT:CE:voltage" type="float" optional="true" min="0.0" value="1000.0" label="Voltage applied to capillary" help=""/>
210 </section>
211 </section>
212 <section name="Detectability" title="" help="" expanded="false">
213 <param name="dt_simulation_on" argument="-algorithm:MSSim:Detectability:dt_simulation_on" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Modelling detectibility enabled" help="This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count"/>
214 <param name="min_detect" argument="-algorithm:MSSim:Detectability:min_detect" type="float" optional="true" value="0.5" label="Minimum peptide detectability accepted" help="Peptides with a lower score will be removed"/>
215 <param name="dt_model_file" argument="-algorithm:MSSim:Detectability:dt_model_file" type="text" optional="true" value="examples/simulation/DTPredict.model" label="SVM model for peptide detectability prediction" help="">
216 <expand macro="list_string_san"/>
217 </param>
218 </section>
219 <section name="Ionization" title="" help="" expanded="false">
220 <section name="esi" title="" help="" expanded="false">
221 <param name="ionized_residues" argument="-algorithm:MSSim:Ionization:esi:ionized_residues" multiple="true" type="select" optional="true" label="List of residues (as three letter code) that will be considered during ES ionization" help="The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization">
222 <option value="Ala">Ala</option>
223 <option value="Cys">Cys</option>
224 <option value="Asp">Asp</option>
225 <option value="Glu">Glu</option>
226 <option value="Phe">Phe</option>
227 <option value="Gly">Gly</option>
228 <option value="His" selected="true">His</option>
229 <option value="Ile">Ile</option>
230 <option value="Lys" selected="true">Lys</option>
231 <option value="Leu">Leu</option>
232 <option value="Met">Met</option>
233 <option value="Asn">Asn</option>
234 <option value="Pro">Pro</option>
235 <option value="Gln">Gln</option>
236 <option value="Arg" selected="true">Arg</option>
237 <option value="Sec">Sec</option>
238 <option value="Ser">Ser</option>
239 <option value="Thr">Thr</option>
240 <option value="Val">Val</option>
241 <option value="Trp">Trp</option>
242 <option value="Tyr">Tyr</option>
243 <expand macro="list_string_san"/>
244 </param>
245 <param name="charge_impurity" argument="-algorithm:MSSim:Ionization:esi:charge_impurity" type="text" optional="true" value="H+:1" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally)" help="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']) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
246 <expand macro="list_string_val"/>
247 <expand macro="list_string_san"/>
248 </param>
249 <param name="max_impurity_set_size" argument="-algorithm:MSSim:Ionization:esi:max_impurity_set_size" type="integer" optional="true" value="3" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state" help="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+'"/>
250 <param name="ionization_probability" argument="-algorithm:MSSim:Ionization:esi:ionization_probability" type="float" optional="true" value="0.8" label="Probability for the binomial distribution of the ESI charge states" help=""/>
251 </section>
252 <section name="maldi" title="" help="" expanded="false">
253 <param name="ionization_probabilities" argument="-algorithm:MSSim:Ionization:maldi:ionization_probabilities" type="text" optional="true" value="0.9 0.1 0.0" label="List of probabilities for different charge states (starting at charge=1, 2, ...) during MALDI ionization (the list must sum up to 1.0)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
254 <expand macro="list_float_valsan"/>
255 </param>
256 </section>
257 <section name="mz" title="" help="" expanded="false">
258 <param name="lower_measurement_limit" argument="-algorithm:MSSim:Ionization:mz:lower_measurement_limit" type="float" optional="true" min="0.0" value="200.0" label="Lower m/z detector limit" help=""/>
259 <param name="upper_measurement_limit" argument="-algorithm:MSSim:Ionization:mz:upper_measurement_limit" type="float" optional="true" min="0.0" value="1200.0" label="Upper m/z detector limit" help=""/>
260 </section>
261 </section>
262 <section name="RawSignal" title="" help="" expanded="false">
263 <param name="enabled" argument="-algorithm:MSSim:RawSignal:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable RAW signal simulation" help="(select 'false' if you only need feature-maps)"/>
264 <param name="peak_shape" argument="-algorithm:MSSim:RawSignal:peak_shape" display="radio" type="select" optional="false" 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="">
265 <option value="Gaussian" selected="true">Gaussian</option>
266 <option value="Lorentzian">Lorentzian</option>
267 <expand macro="list_string_san"/>
268 </param>
269 <section name="resolution" title="" help="" expanded="false">
270 <param name="value" argument="-algorithm:MSSim:RawSignal:resolution:value" type="integer" optional="true" value="50000" label="Instrument resolution at 400 Th" help=""/>
271 <param name="type" argument="-algorithm:MSSim:RawSignal:resolution:type" display="radio" type="select" optional="false" label="How does resolution change with increasing m/z" help="QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass">
272 <option value="constant">constant</option>
273 <option value="linear" selected="true">linear</option>
274 <option value="sqrt">sqrt</option>
275 <expand macro="list_string_san"/>
276 </param>
277 </section>
278 <section name="baseline" title="Baseline modeling for MALDI ionization" help="" expanded="false">
279 <param name="scaling" argument="-algorithm:MSSim:RawSignal:baseline:scaling" type="float" optional="true" min="0.0" value="0.0" label="Scale of baseline" help="Set to 0 to disable simulation of baseline"/>
280 <param name="shape" argument="-algorithm:MSSim:RawSignal:baseline:shape" type="float" optional="true" min="0.0" value="0.5" label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)" help=""/>
281 </section>
282 <section name="mz" title="" help="" expanded="false">
283 <param name="sampling_points" argument="-algorithm:MSSim:RawSignal:mz:sampling_points" type="integer" optional="true" min="2" value="3" label="Number of raw data points per FWHM of the peak" help=""/>
284 </section>
285 <section name="contaminants" title="" help="" expanded="false">
286 <param name="file" argument="-algorithm:MSSim:RawSignal:contaminants:file" type="text" optional="true" value="examples/simulation/contaminants.csv" label="Contaminants file with sum formula and absolute RT interval" help="See 'OpenMS/examples/simulation/contaminants.txt' for details">
287 <expand macro="list_string_san"/>
288 </param>
289 </section>
290 <section name="variation" title="Random components that simulate biological and technical variations of the simulated data" help="" expanded="false">
291 <section name="mz" title="Shifts in mass to charge dimension of the simulated signals" help="" expanded="false">
292 <param name="error_mean" argument="-algorithm:MSSim:RawSignal:variation:mz:error_mean" type="float" optional="true" value="0.0" label="Average systematic m/z error (in Da)" help=""/>
293 <param name="error_stddev" argument="-algorithm:MSSim:RawSignal:variation:mz:error_stddev" type="float" optional="true" value="0.0" label="Standard deviation for m/z errors" help="Set to 0 to disable simulation of m/z errors"/>
294 </section>
295 <section name="intensity" title="Variations in intensity to model randomness in feature intensity" help="" expanded="false">
296 <param name="scale" argument="-algorithm:MSSim:RawSignal:variation:intensity:scale" type="float" optional="true" min="0.0" value="100.0" label="Constant scale factor of the feature intensity" help="Set to 1.0 to get the real intensity values provided in the FASTA file"/>
297 <param name="scale_stddev" argument="-algorithm:MSSim:RawSignal:variation:intensity:scale_stddev" type="float" optional="true" min="0.0" value="0.0" label="Standard deviation of peak intensity (relative to the scaled peak height)" help="Set to 0 to get simple rescaled intensities"/>
298 </section>
299 </section>
300 <section name="noise" title="Parameters modeling noise in mass spectrometry measurements" help="" expanded="false">
301 <section name="shot" title="Parameters of Poisson and Exponential for shot noise modeling (set :rate OR :mean = 0 to disable)" help="" expanded="false">
302 <param name="rate" argument="-algorithm:MSSim:RawSignal:noise:shot:rate" type="float" optional="true" min="0.0" value="0.0" label="Poisson rate of shot noise per unit m/z (random peaks in m/z, where the number of peaks per unit m/z follows a Poisson distribution)" help="Set this to 0 to disable simulation of shot noise"/>
303 <param name="intensity_mean" argument="-algorithm:MSSim:RawSignal:noise:shot:intensity-mean" type="float" optional="true" value="1.0" label="Shot noise intensity mean (exponentially distributed with given mean)" help=""/>
304 </section>
305 <section name="white" title="Parameters of Gaussian distribution for white noise modeling (set :mean AND :stddev = 0 to disable)" help="No new peaks are generated; only intensity of existing ones is changed" expanded="false">
306 <param name="mean" argument="-algorithm:MSSim:RawSignal:noise:white:mean" type="float" optional="true" value="0.0" label="Mean value of white noise (Gaussian) being added to each *measured* signal intensity" help=""/>
307 <param name="stddev" argument="-algorithm:MSSim:RawSignal:noise:white:stddev" type="float" optional="true" value="0.0" label="Standard deviation of white noise being added to each *measured* signal intensity" help=""/>
308 </section>
309 <section name="detector" title="Parameters of Gaussian distribution for detector noise modeling (set :mean AND :stddev = 0 to disable)" help="If enabled, ALL possible m/z positions (up to sampling frequency of detector) will receive an intensity increase/decrease according to the specified Gaussian intensity distribution (similar to a noisy baseline)" expanded="false">
310 <param name="mean" argument="-algorithm:MSSim:RawSignal:noise:detector:mean" type="float" optional="true" value="0.0" label="Mean intensity value of the detector noise (Gaussian distribution)" help=""/>
311 <param name="stddev" argument="-algorithm:MSSim:RawSignal:noise:detector:stddev" type="float" optional="true" value="0.0" label="Standard deviation of the detector noise (Gaussian distribution)" help=""/>
312 </section>
313 </section>
314 </section>
315 <section name="RawTandemSignal" title="" help="" expanded="false">
316 <param name="status" argument="-algorithm:MSSim:RawTandemSignal:status" display="radio" type="select" optional="false" label="Create Tandem-MS scans?" help="">
317 <option value="disabled" selected="true">disabled</option>
318 <option value="precursor">precursor</option>
319 <option value="MS^E">MS^E</option>
320 <expand macro="list_string_san"/>
321 </param>
322 <param name="tandem_mode" argument="-algorithm:MSSim:RawTandemSignal:tandem_mode" type="integer" optional="true" min="0" max="2" value="0" label="Algorithm to generate the tandem-MS spectra" help="0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity . "/>
323 <param name="svm_model_set_file" argument="-algorithm:MSSim:RawTandemSignal:svm_model_set_file" type="text" optional="true" value="examples/simulation/SvmModelSet.model" label="File containing the filenames of SVM Models for different charge variants" help="">
324 <expand macro="list_string_san"/>
325 </param>
326 <section name="Precursor" title="" help="" expanded="false">
327 <param name="ms2_spectra_per_rt_bin" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin" type="integer" optional="true" min="1" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help=""/>
328 <param name="min_mz_peak_distance" argument="-algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance" type="float" optional="true" min="0.0001" value="2.0" label="The minimal distance (in Th) between two peaks for concurrent selection for fragmentation" help="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"/>
329 <param name="mz_isolation_window" argument="-algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window" type="float" optional="true" min="0.0" value="2.0" label="All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation" help=""/>
330 <param name="exclude_overlapping_peaks" argument="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" help=""/>
331 <param name="charge_filter" argument="-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter" type="text" optional="true" value="2 3" label="Charges considered for MS2 fragmentation" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
332 <expand macro="list_integer_valsan">
333 <validator type="expression" message="a space separated list of integer values in the range 1:5 is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_) <= 5])
334 ]]></validator>
335 </expand>
336 </param>
337 <section name="Exclusion" title="" help="" expanded="false">
338 <param name="use_dynamic_exclusion" argument="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true dynamic exclusion is applied" help=""/>
339 <param name="exclusion_time" argument="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time" type="float" optional="true" min="0.0" value="100.0" label="The time (in seconds) a feature is excluded" help=""/>
340 </section>
341 <section name="ProteinBasedInclusion" title="" help="" expanded="false">
342 <param name="max_list_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size" type="integer" optional="true" min="1" value="1000" label="The maximal number of precursors in the inclusion list" help=""/>
343 <section name="rt" title="" help="" expanded="false">
344 <param name="min_rt" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt" type="float" optional="true" min="0.0" value="960.0" label="Minimal rt in seconds" help=""/>
345 <param name="max_rt" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt" type="float" optional="true" min="0.0" value="3840.0" label="Maximal rt in seconds" help=""/>
346 <param name="rt_step_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size" type="float" optional="true" min="1.0" value="30.0" label="rt step size in seconds" help=""/>
347 <param name="rt_window_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size" type="integer" optional="true" min="1" value="100" label="rt window size in seconds" help=""/>
348 </section>
349 <section name="thresholds" title="" help="" expanded="false">
350 <param name="min_protein_id_probability" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Minimal protein probability for a protein to be considered identified" help=""/>
351 <param name="min_pt_weight" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal pt weight of a precurso" help=""/>
352 <param name="min_mz" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz" type="float" optional="true" min="0.0" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
353 <param name="max_mz" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz" type="float" optional="true" min="0.0" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
354 <param name="use_peptide_rule" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use peptide rule instead of minimal protein id probability" help=""/>
355 <param name="min_peptide_ids" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids" type="integer" optional="true" min="1" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help=""/>
356 <param name="min_peptide_probability" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help=""/>
357 </section>
358 </section>
359 </section>
360 <section name="MS_E" title="" help="" expanded="false">
361 <param name="add_single_spectra" argument="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot)" help="They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead"/>
362 </section>
363 <section name="TandemSim" title="" help="" expanded="false">
364 <section name="Simple" title="" help="" expanded="false">
365 <param name="isotope_model" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:isotope_model" display="radio" type="select" optional="false" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
366 <option value="none" selected="true">none</option>
367 <option value="coarse">coarse</option>
368 <option value="fine">fine</option>
369 <expand macro="list_string_san"/>
370 </param>
371 <param name="max_isotope" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/>
372 <param name="max_isotope_probability" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope_probability" type="float" optional="true" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/>
373 <param name="add_metainfo" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
374 <param name="add_losses" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
375 <param name="sort_by_position" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:sort_by_position" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Sort output by position" help=""/>
376 <param name="add_precursor_peaks" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds peaks of the unfragmented precursor ion to the spectrum" help=""/>
377 <param name="add_all_precursor_charges" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds precursor peaks with all charges in the given range" help=""/>
378 <param name="add_abundant_immonium_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add most abundant immonium ions" help=""/>
379 <param name="add_first_prefix_ion" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
380 <param name="add_y_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of y-ions to the spectrum" help=""/>
381 <param name="add_b_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of b-ions to the spectrum" help=""/>
382 <param name="add_a_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
383 <param name="add_c_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
384 <param name="add_x_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of x-ions to the spectrum" help=""/>
385 <param name="add_z_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
386 <param name="y_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity" type="float" optional="true" value="1.0" label="Intensity of the y-ions" help=""/>
387 <param name="b_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity" type="float" optional="true" value="1.0" label="Intensity of the b-ions" help=""/>
388 <param name="a_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity" type="float" optional="true" value="1.0" label="Intensity of the a-ions" help=""/>
389 <param name="c_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity" type="float" optional="true" value="1.0" label="Intensity of the c-ions" help=""/>
390 <param name="x_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity" type="float" optional="true" value="1.0" label="Intensity of the x-ions" help=""/>
391 <param name="z_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity" type="float" optional="true" value="1.0" label="Intensity of the z-ions" help=""/>
392 <param name="relative_loss_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity" type="float" optional="true" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
393 <param name="precursor_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity" type="float" optional="true" value="1.0" label="Intensity of the precursor peak" help=""/>
394 <param name="precursor_H2O_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity" type="float" optional="true" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
395 <param name="precursor_NH3_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity" type="float" optional="true" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
396 </section>
397 <section name="SVM" title="" help="" expanded="false">
398 <param name="add_isotopes" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to 1 isotope peaks of the product ion peaks are added" help=""/>
399 <param name="max_isotope" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help=""/>
400 <param name="add_metainfo" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
401 <param name="add_first_prefix_ion" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
402 <param name="hide_y_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of y-ions to the spectrum" help=""/>
403 <param name="hide_y2_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of y-ions to the spectrum" help=""/>
404 <param name="hide_b_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of b-ions to the spectrum" help=""/>
405 <param name="hide_b2_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of b-ions to the spectrum" help=""/>
406 <param name="hide_a_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
407 <param name="hide_c_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
408 <param name="hide_x_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of x-ions to the spectrum" help=""/>
409 <param name="hide_z_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
410 <param name="hide_losses" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
411 <param name="y_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity" type="float" optional="true" value="1.0" label="Intensity of the y-ions" help=""/>
412 <param name="b_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity" type="float" optional="true" value="1.0" label="Intensity of the b-ions" help=""/>
413 <param name="a_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity" type="float" optional="true" value="1.0" label="Intensity of the a-ions" help=""/>
414 <param name="c_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity" type="float" optional="true" value="1.0" label="Intensity of the c-ions" help=""/>
415 <param name="x_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity" type="float" optional="true" value="1.0" label="Intensity of the x-ions" help=""/>
416 <param name="z_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity" type="float" optional="true" value="1.0" label="Intensity of the z-ions" help=""/>
417 <param name="relative_loss_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity" type="float" optional="true" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
418 </section>
419 </section>
420 </section>
421 <section name="Global" title="" help="" expanded="false">
422 <param name="ionization_type" argument="-algorithm:MSSim:Global:ionization_type" display="radio" type="select" optional="false" label="Type of Ionization (MALDI or ESI)" help="">
423 <option value="MALDI">MALDI</option>
424 <option value="ESI" selected="true">ESI</option>
425 <expand macro="list_string_san"/>
426 </param>
427 </section>
428 <section name="Labeling" title="" help="" expanded="false">
429 <param name="type" argument="-algorithm:MSSim:Labeling:type" type="select" optional="false" label="Select the labeling type you want for your experiment" help="">
430 <option value="ICPL">ICPL</option>
431 <option value="SILAC">SILAC</option>
432 <option value="itraq">itraq</option>
433 <option value="labelfree" selected="true">labelfree</option>
434 <option value="o18">o18</option>
435 <expand macro="list_string_san"/>
436 </param>
437 <section name="ICPL" title="ICPL labeling on MS1 level of lysines and n-term (on protein or peptide level) with either two or three channels" help="" expanded="false">
438 <param name="ICPL_fixed_rtshift" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift" type="float" optional="true" value="0.0" label="Fixed retention time shift between labeled pairs" help="If set to 0.0 only the retention times, computed by the RT model step are used"/>
439 <param name="label_proteins" argument="-algorithm:MSSim:Labeling:ICPL:label_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables protein-labeling" help="(select 'false' if you only need peptide-labeling)"/>
440 <param name="ICPL_light_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label" type="text" optional="true" value="UniMod:365" label="UniMod Id of the light channel ICPL label" help="">
441 <expand macro="list_string_san"/>
442 </param>
443 <param name="ICPL_medium_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label" type="text" optional="true" value="UniMod:687" label="UniMod Id of the medium channel ICPL label" help="">
444 <expand macro="list_string_san"/>
445 </param>
446 <param name="ICPL_heavy_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label" type="text" optional="true" value="UniMod:364" label="UniMod Id of the heavy channel ICPL label" help="">
447 <expand macro="list_string_san"/>
448 </param>
449 </section>
450 <section name="SILAC" title="SILAC labeling on MS1 level with up to 3 channels and custom modifications" help="" expanded="false">
451 <param name="fixed_rtshift" argument="-algorithm:MSSim:Labeling:SILAC:fixed_rtshift" type="float" optional="true" min="0.0" value="0.0001" label="Fixed retention time shift between labeled peptides" help="If set to 0.0 only the retention times computed by the RT model step are used"/>
452 <section name="medium_channel" title="Modifications for the medium SILAC channel" help="" expanded="false">
453 <param name="modification_lysine" argument="-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine" type="text" optional="true" value="UniMod:481" label="Modification of Lysine in the medium SILAC channel" help="">
454 <expand macro="list_string_san"/>
455 </param>
456 <param name="modification_arginine" argument="-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine" type="text" optional="true" value="UniMod:188" label="Modification of Arginine in the medium SILAC channel" help="">
457 <expand macro="list_string_san"/>
458 </param>
459 </section>
460 <section name="heavy_channel" title="Modifications for the heavy SILAC channel" help="If you want to use only 2 channels, just leave the Labels as they are and provide only 2 input files" expanded="false">
461 <param name="modification_lysine" argument="-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine" type="text" optional="true" value="UniMod:259" label="Modification of Lysine in the heavy SILAC channel" help="If left empty, two channelSILAC is assumed">
462 <expand macro="list_string_san"/>
463 </param>
464 <param name="modification_arginine" argument="-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine" type="text" optional="true" value="UniMod:267" label="Modification of Arginine in the heavy SILAC channel" help="If left empty, two-channel SILAC is assumed">
465 <expand macro="list_string_san"/>
466 </param>
467 </section>
468 </section>
469 <section name="itraq" title="iTRAQ labeling on MS2 level with up to 4 (4plex) or 8 (8plex) channels" help="" expanded="false">
470 <param name="iTRAQ" argument="-algorithm:MSSim:Labeling:itraq:iTRAQ" display="radio" type="select" optional="false" label="4plex or 8plex iTRAQ?" help="">
471 <option value="4plex" selected="true">4plex</option>
472 <option value="8plex">8plex</option>
473 <expand macro="list_string_san"/>
474 </param>
475 <param name="reporter_mass_shift" argument="-algorithm:MSSim:Labeling:itraq:reporter_mass_shift" type="float" optional="true" min="0.0" max="0.5" value="0.1" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of" help="e.g. 114.1, 115.1)"/>
476 <param name="channel_active_4plex" argument="-algorithm:MSSim:Labeling:itraq:channel_active_4plex" type="text" optional="true" 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" help="e.g. &quot;114:myref&quot;,&quot;115:liver&quot; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
477 <expand macro="list_string_val"/>
478 <expand macro="list_string_san"/>
479 </param>
480 <param name="channel_active_8plex" argument="-algorithm:MSSim:Labeling:itraq:channel_active_8plex" type="text" optional="true" 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" help="e.g. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
481 <expand macro="list_string_val"/>
482 <expand macro="list_string_san"/>
483 </param>
484 <param name="isotope_correction_values_4plex" argument="-algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex" type="text" optional="true" value="114:0.0/1.0/5.9/0.2 115:0.0/2.0/5.6/0.1 116:0.0/3.0/4.5/0.1 117:0.1/4.0/3.5/0.1" 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="e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
485 <expand macro="list_string_val"/>
486 <expand macro="list_string_san"/>
487 </param>
488 <param name="isotope_correction_values_8plex" argument="-algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex" type="text" optional="true" value="113:0.0/0.0/6.89/0.22 114:0.0/0.94/5.9/0.16 115:0.0/1.88/4.9/0.1 116:0.0/2.82/3.9/0.07 117:0.06/3.77/2.99/0.0 118:0.09/4.71/1.88/0.0 119:0.14/5.66/0.87/0.0 121:0.27/7.44/0.18/0.0" 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="e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
489 <expand macro="list_string_val"/>
490 <expand macro="list_string_san"/>
491 </param>
492 <param name="Y_contamination" argument="-algorithm:MSSim:Labeling:itraq:Y_contamination" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="Efficiency of labeling tyrosine ('Y') residues" help="0=off, 1=full labeling"/>
493 </section>
494 <section name="o18" title="18O labeling on MS1 level with 2 channels, requiring trypsin digestion" help="" expanded="false">
495 <param name="labeling_efficiency" argument="-algorithm:MSSim:Labeling:o18:labeling_efficiency" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" help=""/>
496 </section>
497 </section>
498 </section>
499 <section name="RandomNumberGenerators" title="Parameters for generating the random aspects" help="(e.g. noise) in the simulated data. The generation is separated into two parts, the technical part, like noise in the raw signal, and the biological part, like systematic deviations in the predicted retention times" expanded="false">
500 <param name="biological" argument="-algorithm:RandomNumberGenerators:biological" display="radio" type="select" optional="false" label="Controls the 'biological' randomness of the generated data" help="(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)">
501 <option value="reproducible">reproducible</option>
502 <option value="random" selected="true">random</option>
503 <expand macro="list_string_san"/>
504 </param>
505 <param name="technical" argument="-algorithm:RandomNumberGenerators:technical" display="radio" type="select" optional="false" label="Controls the 'technical' randomness of the generated data" help="(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)">
506 <option value="reproducible">reproducible</option>
507 <option value="random" selected="true">random</option>
508 <expand macro="list_string_san"/>
509 </param>
510 </section>
511 </section>
512 <expand macro="adv_opts_macro">
513 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
514 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
515 <expand macro="list_string_san"/>
516 </param>
517 </expand>
518 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
519 <option value="out_FLAG">out (Controls the 'technical' randomness of the generated data)</option>
520 <option value="out_pm_FLAG">out_pm (Controls the 'technical' randomness of the generated data)</option>
521 <option value="out_fm_FLAG">out_fm (Controls the 'technical' randomness of the generated data)</option>
522 <option value="out_cm_FLAG">out_cm (Controls the 'technical' randomness of the generated data)</option>
523 <option value="out_lcm_FLAG">out_lcm (Controls the 'technical' randomness of the generated data)</option>
524 <option value="out_cntm_FLAG">out_cntm (Controls the 'technical' randomness of the generated data)</option>
525 <option value="out_id_FLAG">out_id (Controls the 'technical' randomness of the generated data)</option>
526 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
627 </param> 527 </param>
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) ">
629 <option value="CNBr">CNBr</option>
630 <option value="Trypsin/P">Trypsin/P</option>
631 <option value="Lys-C">Lys-C</option>
632 <option value="Formic_acid">Formic_acid</option>
633 <option value="Arg-C/P">Arg-C/P</option>
634 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
635 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
636 <option value="proline endopeptidase">proline endopeptidase</option>
637 <option value="Arg-C">Arg-C</option>
638 <option value="unspecific cleavage">unspecific cleavage</option>
639 <option value="Trypsin" selected="true">Trypsin</option>
640 <option value="TrypChymo">TrypChymo</option>
641 <option value="V8-E">V8-E</option>
642 <option value="2-iodobenzoate">2-iodobenzoate</option>
643 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
644 <option value="no cleavage">no cleavage</option>
645 <option value="Asp-N_ambic">Asp-N_ambic</option>
646 <option value="PepsinA">PepsinA</option>
647 <option value="Chymotrypsin">Chymotrypsin</option>
648 <option value="V8-DE">V8-DE</option>
649 <option value="Asp-N/B">Asp-N/B</option>
650 <option value="Lys-N">Lys-N</option>
651 <option value="Lys-C/P">Lys-C/P</option>
652 <option value="leukocyte elastase">leukocyte elastase</option>
653 <option value="Asp-N">Asp-N</option>
654 </param>
655 <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)">
656 <option value="trained">trained</option>
657 <option value="naive" selected="true">naive</option>
658 </param>
659 <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) "/>
660 <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"/>
661 <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"/>
662 <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) ">
663 <option value="none">none</option>
664 <option value="HPLC" selected="true">HPLC</option>
665 <option value="CE">CE</option>
666 </param>
667 <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">
668 <option value="true" selected="true">true</option>
669 <option value="false">false</option>
670 </param>
671 <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) "/>
672 <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) "/>
673 <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) "/>
674 <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) "/>
675 <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) "/>
676 <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) "/>
677 <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) "/>
678 <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"/>
679 <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]"/>
680 <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)"/>
681 <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"/>
682 <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)"/>
683 <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) ">
684 <sanitizer>
685 <valid initial="string.printable">
686 <remove value="'"/>
687 <remove value="&quot;"/>
688 </valid>
689 </sanitizer>
690 </param>
691 <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) "/>
692 <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) "/>
693 <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) "/>
694 <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) "/>
695 <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) "/>
696 <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) "/>
697 <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"/>
698 <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"/>
699 <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) ">
700 <sanitizer>
701 <valid initial="string.printable">
702 <remove value="'"/>
703 <remove value="&quot;"/>
704 </valid>
705 </sanitizer>
706 </param>
707 <repeat name="rep_param_algorithm_MSSim_Ionization_esi_ionized_residues" min="0" max="1" title="param_algorithm_MSSim_Ionization_esi_ionized_residues">
708 <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">
709 <option value="Ala">Ala</option>
710 <option value="Cys">Cys</option>
711 <option value="Asp">Asp</option>
712 <option value="Glu">Glu</option>
713 <option value="Phe">Phe</option>
714 <option value="Gly">Gly</option>
715 <option value="His">His</option>
716 <option value="Ile">Ile</option>
717 <option value="Lys">Lys</option>
718 <option value="Leu">Leu</option>
719 <option value="Met">Met</option>
720 <option value="Asn">Asn</option>
721 <option value="Pro">Pro</option>
722 <option value="Gln">Gln</option>
723 <option value="Arg">Arg</option>
724 <option value="Sec">Sec</option>
725 <option value="Ser">Ser</option>
726 <option value="Thr">Thr</option>
727 <option value="Val">Val</option>
728 <option value="Trp">Trp</option>
729 <option value="Tyr">Tyr</option>
730 </param>
731 </repeat>
732 <repeat name="rep_param_algorithm_MSSim_Ionization_esi_charge_impurity" min="0" max="1" title="param_algorithm_MSSim_Ionization_esi_charge_impurity">
733 <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'])">
734 <sanitizer>
735 <valid initial="string.printable">
736 <remove value="'"/>
737 <remove value="&quot;"/>
738 </valid>
739 </sanitizer>
740 </param>
741 </repeat>
742 <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) "/>
743 <repeat name="rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" min="0" max="1" title="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities">
744 <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) ">
745 <sanitizer>
746 <valid initial="string.printable">
747 <remove value="'"/>
748 <remove value="&quot;"/>
749 </valid>
750 </sanitizer>
751 </param>
752 </repeat>
753 <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) "/>
754 <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) "/>
755 <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)">
756 <option value="true" selected="true">true</option>
757 <option value="false">false</option>
758 </param>
759 <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) ">
760 <option value="Gaussian" selected="true">Gaussian</option>
761 <option value="Lorentzian">Lorentzian</option>
762 </param>
763 <param name="param_algorithm_MSSim_RawSignal_resolution_value" type="integer" value="50000" label="Instrument resolution at 400 Th" help="(-value) "/>
764 <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) ">
765 <option value="constant">constant</option>
766 <option value="linear" selected="true">linear</option>
767 <option value="sqrt">sqrt</option>
768 </param>
769 <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"/>
770 <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) "/>
771 <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) "/>
772 <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">
773 <sanitizer>
774 <valid initial="string.printable">
775 <remove value="'"/>
776 <remove value="&quot;"/>
777 </valid>
778 </sanitizer>
779 </param>
780 <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"/>
781 <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) "/>
782 <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"/>
783 <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"/>
784 <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"/>
785 <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) "/>
786 <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) "/>
787 <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) "/>
788 <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) "/>
789 <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) "/>
790 <param name="param_algorithm_MSSim_RawTandemSignal_status" display="radio" type="select" optional="False" value="disabled" label="Create Tandem-MS scans?" help="(-status) ">
791 <option value="disabled" selected="true">disabled</option>
792 <option value="precursor">precursor</option>
793 <option value="MS^E">MS^E</option>
794 </param>
795 <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;"/>
796 <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) ">
797 <sanitizer>
798 <valid initial="string.printable">
799 <remove value="'"/>
800 <remove value="&quot;"/>
801 </valid>
802 </sanitizer>
803 </param>
804 <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) "/>
805 <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"/>
806 <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) "/>
807 <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) "/>
808 <repeat name="rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" min="0" max="1" title="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter">
809 <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) ">
810 <sanitizer>
811 <valid initial="string.printable">
812 <remove value="'"/>
813 <remove value="&quot;"/>
814 </valid>
815 </sanitizer>
816 </param>
817 </repeat>
818 <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) "/>
819 <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) "/>
820 <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) "/>
821 <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) "/>
822 <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) "/>
823 <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) "/>
824 <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) "/>
825 <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) "/>
826 <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) "/>
827 <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) "/>
828 <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) "/>
829 <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) "/>
830 <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) "/>
831 <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) "/>
832 <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"/>
833 <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) "/>
834 <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) "/>
835 <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) "/>
836 <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) "/>
837 <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) "/>
838 <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) "/>
839 <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) "/>
840 <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) "/>
841 <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) ">
842 <option value="true" selected="true">true</option>
843 <option value="false">false</option>
844 </param>
845 <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) ">
846 <option value="true" selected="true">true</option>
847 <option value="false">false</option>
848 </param>
849 <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) "/>
850 <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) "/>
851 <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) "/>
852 <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) "/>
853 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity) "/>
854 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity) "/>
855 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity) "/>
856 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity) "/>
857 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity) "/>
858 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity) "/>
859 <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) "/>
860 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity" type="float" value="1.0" label="Intensity of the precursor peak" help="(-precursor_intensity) "/>
861 <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) "/>
862 <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) "/>
863 <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) "/>
864 <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) "/>
865 <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) "/>
866 <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) "/>
867 <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) "/>
868 <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) "/>
869 <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) "/>
870 <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) "/>
871 <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) "/>
872 <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) "/>
873 <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) "/>
874 <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) "/>
875 <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) "/>
876 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity) "/>
877 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity) "/>
878 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity) "/>
879 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity) "/>
880 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity) "/>
881 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity) "/>
882 <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) "/>
883 <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) ">
884 <option value="MALDI">MALDI</option>
885 <option value="ESI" selected="true">ESI</option>
886 </param>
887 <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) ">
888 <option value="ICPL">ICPL</option>
889 <option value="SILAC">SILAC</option>
890 <option value="itraq">itraq</option>
891 <option value="labelfree" selected="true">labelfree</option>
892 <option value="o18">o18</option>
893 </param>
894 <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"/>
895 <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)">
896 <option value="true" selected="true">true</option>
897 <option value="false">false</option>
898 </param>
899 <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"/>
900 <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) ">
901 <sanitizer>
902 <valid initial="string.printable">
903 <remove value="'"/>
904 <remove value="&quot;"/>
905 </valid>
906 </sanitizer>
907 </param>
908 <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) ">
909 <sanitizer>
910 <valid initial="string.printable">
911 <remove value="'"/>
912 <remove value="&quot;"/>
913 </valid>
914 </sanitizer>
915 </param>
916 <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">
917 <sanitizer>
918 <valid initial="string.printable">
919 <remove value="'"/>
920 <remove value="&quot;"/>
921 </valid>
922 </sanitizer>
923 </param>
924 <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">
925 <sanitizer>
926 <valid initial="string.printable">
927 <remove value="'"/>
928 <remove value="&quot;"/>
929 </valid>
930 </sanitizer>
931 </param>
932 <param name="param_algorithm_MSSim_Labeling_itraq_iTRAQ" display="radio" type="select" optional="False" value="4plex" label="4plex or 8plex iTRAQ?" help="(-iTRAQ) ">
933 <option value="4plex" selected="true">4plex</option>
934 <option value="8plex">8plex</option>
935 </param>
936 <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)"/>
937 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex">
938 <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;">
939 <sanitizer>
940 <valid initial="string.printable">
941 <remove value="'"/>
942 <remove value="&quot;"/>
943 </valid>
944 </sanitizer>
945 </param>
946 </repeat>
947 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex">
948 <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;">
949 <sanitizer>
950 <valid initial="string.printable">
951 <remove value="'"/>
952 <remove value="&quot;"/>
953 </valid>
954 </sanitizer>
955 </param>
956 </repeat>
957 <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"/>
958 <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) "/>
959 <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)">
960 <option value="reproducible">reproducible</option>
961 <option value="random" selected="true">random</option>
962 </param>
963 <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)">
964 <option value="reproducible">reproducible</option>
965 <option value="random" selected="true">random</option>
966 </param>
967 <expand macro="advanced_options">
968 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
969 <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+'"/>
970 <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) ">
971 <sanitizer>
972 <valid initial="string.printable">
973 <remove value="'"/>
974 <remove value="&quot;"/>
975 </valid>
976 </sanitizer>
977 </param>
978 <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) ">
979 <sanitizer>
980 <valid initial="string.printable">
981 <remove value="'"/>
982 <remove value="&quot;"/>
983 </valid>
984 </sanitizer>
985 </param>
986 <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) ">
987 <sanitizer>
988 <valid initial="string.printable">
989 <remove value="'"/>
990 <remove value="&quot;"/>
991 </valid>
992 </sanitizer>
993 </param>
994 <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">
995 <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' ">
996 <sanitizer>
997 <valid initial="string.printable">
998 <remove value="'"/>
999 <remove value="&quot;"/>
1000 </valid>
1001 </sanitizer>
1002 </param>
1003 </repeat>
1004 <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">
1005 <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' ">
1006 <sanitizer>
1007 <valid initial="string.printable">
1008 <remove value="'"/>
1009 <remove value="&quot;"/>
1010 </valid>
1011 </sanitizer>
1012 </param>
1013 </repeat>
1014 </expand>
1015 </inputs> 528 </inputs>
1016 <outputs> 529 <outputs>
1017 <data name="param_out" format="mzml"/> 530 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml">
1018 <data name="param_out_pm" format="mzml"/> 531 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
1019 <data name="param_out_fm" format="featurexml"/> 532 </data>
1020 <data name="param_out_cm" format="consensusxml"/> 533 <data name="out_pm" label="${tool.name} on ${on_string}: out_pm" format="mzml">
1021 <data name="param_out_lcm" format="consensusxml"/> 534 <filter>OPTIONAL_OUTPUTS is not None and "out_pm_FLAG" in OPTIONAL_OUTPUTS</filter>
1022 <data name="param_out_cntm" format="featurexml"/> 535 </data>
1023 <data name="param_out_id" format="idxml"/> 536 <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
537 <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
538 </data>
539 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
540 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
541 </data>
542 <data name="out_lcm" label="${tool.name} on ${on_string}: out_lcm" format="consensusxml">
543 <filter>OPTIONAL_OUTPUTS is not None and "out_lcm_FLAG" in OPTIONAL_OUTPUTS</filter>
544 </data>
545 <data name="out_cntm" label="${tool.name} on ${on_string}: out_cntm" format="featurexml">
546 <filter>OPTIONAL_OUTPUTS is not None and "out_cntm_FLAG" in OPTIONAL_OUTPUTS</filter>
547 </data>
548 <data name="out_id" label="${tool.name} on ${on_string}: out_id" format="idxml">
549 <filter>OPTIONAL_OUTPUTS is not None and "out_id_FLAG" in OPTIONAL_OUTPUTS</filter>
550 </data>
551 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
552 <filter>OPTIONAL_OUTPUTS is None</filter>
553 </data>
554 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
555 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
556 </data>
1024 </outputs> 557 </outputs>
1025 <help>A highly configurable simulator for mass spectrometry experiments. 558 <tests>
559 <expand macro="autotest_MSSimulator"/>
560 <expand macro="manutest_MSSimulator"/>
561 </tests>
562 <help><![CDATA[A highly configurable simulator for mass spectrometry experiments.
1026 563
1027 564
1028 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MSSimulator.html</help> 565 For more information, visit http://www.openms.de/documentation/UTILS_MSSimulator.html]]></help>
566 <expand macro="references"/>
1029 </tool> 567 </tool>