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comparison OpenSwathAnalyzer.xml @ 1:2473b7efa9d1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:57:31 -0400
parents f9ead04f81ef
children de254355ce13
comparison
equal deleted inserted replaced
0:f9ead04f81ef 1:2473b7efa9d1
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.1.0"> 4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.2.0">
5 <description>Picks peaks and finds features in an SRM experiment.</description> 5 <description>Picks peaks and finds features in an SRM experiment.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token> 7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
63 #end if 63 #end if
64 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width: 64 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
65 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width 65 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
66 #end if 66 #end if
67 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss: 67 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
68 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss 68 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
69 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss):
70 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
71 #else
72 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
73 #end if
69 #end if 74 #end if
70 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width: 75 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
71 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width 76 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
72 #end if 77 #end if
73 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise: 78 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
78 #end if 83 #end if
79 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count: 84 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
80 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count 85 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
81 #end if 86 #end if
82 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: 87 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
83 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages 88 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
89 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages):
90 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages"
91 #else
92 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
93 #end if
84 #end if 94 #end if
85 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: 95 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
86 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks 96 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
87 #end if 97 #end if
88 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method: 98 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
89 -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method 99 -algorithm:TransitionGroupPicker:PeakPickerMRM:method
100 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
101 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
102 #else
103 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
104 #end if
90 #end if 105 #end if
91 #if $param_algorithm_DIAScoring_dia_extraction_window: 106 #if $param_algorithm_DIAScoring_dia_extraction_window:
92 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window 107 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
93 #end if 108 #end if
94 #if $param_algorithm_DIAScoring_dia_centroided: 109 #if $param_algorithm_DIAScoring_dia_centroided:
112 #if $adv_opts.adv_opts_selector=='advanced': 127 #if $adv_opts.adv_opts_selector=='advanced':
113 #if $adv_opts.param_force: 128 #if $adv_opts.param_force:
114 -force 129 -force
115 #end if 130 #end if
116 #if $adv_opts.param_model_type: 131 #if $adv_opts.param_model_type:
117 -model:type $adv_opts.param_model_type 132 -model:type
133 #if " " in str($adv_opts.param_model_type):
134 "$adv_opts.param_model_type"
135 #else
136 $adv_opts.param_model_type
137 #end if
118 #end if 138 #end if
119 #if $adv_opts.param_model_symmetric_regression: 139 #if $adv_opts.param_model_symmetric_regression:
120 -model:symmetric_regression 140 -model:symmetric_regression
121 #end if 141 #end if
122 #if $adv_opts.param_algorithm_quantification_cutoff: 142 #if $adv_opts.param_algorithm_quantification_cutoff:
133 #end if 153 #end if
134 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width: 154 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
135 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width 155 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
136 #end if 156 #end if
137 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction: 157 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
138 -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction 158 -algorithm:TransitionGroupPicker:background_subtraction
159 #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
160 "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
161 #else
162 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
163 #end if
139 #end if 164 #end if
140 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: 165 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
141 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks" 166 -algorithm:TransitionGroupPicker:recalculate_peaks
167 #end if
168 #if $adv_opts.param_algorithm_TransitionGroupPicker_use_precursors:
169 -algorithm:TransitionGroupPicker:use_precursors
142 #end if 170 #end if
143 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: 171 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
144 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z 172 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
145 #end if 173 #end if
146 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality: 174 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
147 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality 175 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
148 #end if 176 #end if
149 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality: 177 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
150 -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality" 178 -algorithm:TransitionGroupPicker:compute_peak_quality
151 #end if 179 #end if
152 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step: 180 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
153 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step 181 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
154 #end if 182 #end if
155 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box: 183 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
163 #end if 191 #end if
164 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance: 192 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
165 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance 193 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
166 #end if 194 #end if
167 #if $adv_opts.param_algorithm_Scores_use_shape_score: 195 #if $adv_opts.param_algorithm_Scores_use_shape_score:
168 -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score 196 -algorithm:Scores:use_shape_score
197 #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
198 "$adv_opts.param_algorithm_Scores_use_shape_score"
199 #else
200 $adv_opts.param_algorithm_Scores_use_shape_score
201 #end if
169 #end if 202 #end if
170 #if $adv_opts.param_algorithm_Scores_use_coelution_score: 203 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
171 -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score 204 -algorithm:Scores:use_coelution_score
205 #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
206 "$adv_opts.param_algorithm_Scores_use_coelution_score"
207 #else
208 $adv_opts.param_algorithm_Scores_use_coelution_score
209 #end if
172 #end if 210 #end if
173 #if $adv_opts.param_algorithm_Scores_use_rt_score: 211 #if $adv_opts.param_algorithm_Scores_use_rt_score:
174 -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score 212 -algorithm:Scores:use_rt_score
213 #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
214 "$adv_opts.param_algorithm_Scores_use_rt_score"
215 #else
216 $adv_opts.param_algorithm_Scores_use_rt_score
217 #end if
175 #end if 218 #end if
176 #if $adv_opts.param_algorithm_Scores_use_library_score: 219 #if $adv_opts.param_algorithm_Scores_use_library_score:
177 -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score 220 -algorithm:Scores:use_library_score
221 #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
222 "$adv_opts.param_algorithm_Scores_use_library_score"
223 #else
224 $adv_opts.param_algorithm_Scores_use_library_score
225 #end if
178 #end if 226 #end if
179 #if $adv_opts.param_algorithm_Scores_use_elution_model_score: 227 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
180 -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score 228 -algorithm:Scores:use_elution_model_score
229 #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
230 "$adv_opts.param_algorithm_Scores_use_elution_model_score"
231 #else
232 $adv_opts.param_algorithm_Scores_use_elution_model_score
233 #end if
181 #end if 234 #end if
182 #if $adv_opts.param_algorithm_Scores_use_intensity_score: 235 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
183 -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score 236 -algorithm:Scores:use_intensity_score
237 #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
238 "$adv_opts.param_algorithm_Scores_use_intensity_score"
239 #else
240 $adv_opts.param_algorithm_Scores_use_intensity_score
241 #end if
184 #end if 242 #end if
185 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: 243 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
186 -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score 244 -algorithm:Scores:use_nr_peaks_score
245 #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
246 "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
247 #else
248 $adv_opts.param_algorithm_Scores_use_nr_peaks_score
249 #end if
187 #end if 250 #end if
188 #if $adv_opts.param_algorithm_Scores_use_total_xic_score: 251 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
189 -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score 252 -algorithm:Scores:use_total_xic_score
253 #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
254 "$adv_opts.param_algorithm_Scores_use_total_xic_score"
255 #else
256 $adv_opts.param_algorithm_Scores_use_total_xic_score
257 #end if
190 #end if 258 #end if
191 #if $adv_opts.param_algorithm_Scores_use_sn_score: 259 #if $adv_opts.param_algorithm_Scores_use_sn_score:
192 -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score 260 -algorithm:Scores:use_sn_score
261 #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
262 "$adv_opts.param_algorithm_Scores_use_sn_score"
263 #else
264 $adv_opts.param_algorithm_Scores_use_sn_score
265 #end if
193 #end if 266 #end if
194 #if $adv_opts.param_algorithm_Scores_use_dia_scores: 267 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
195 -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores 268 -algorithm:Scores:use_dia_scores
269 #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
270 "$adv_opts.param_algorithm_Scores_use_dia_scores"
271 #else
272 $adv_opts.param_algorithm_Scores_use_dia_scores
273 #end if
196 #end if 274 #end if
197 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: 275 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
198 -algorithm:Scores:use_ms1_correlation 276 -algorithm:Scores:use_ms1_correlation
277 #end if
278 #if $adv_opts.param_algorithm_Scores_use_sonar_scores:
279 -algorithm:Scores:use_sonar_scores
199 #end if 280 #end if
200 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: 281 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
201 -algorithm:Scores:use_ms1_fullscan 282 -algorithm:Scores:use_ms1_fullscan
202 #end if 283 #end if
203 #if $adv_opts.param_algorithm_Scores_use_uis_scores: 284 #if $adv_opts.param_algorithm_Scores_use_uis_scores:
271 <param name="param_algorithm_TransitionGroupPicker_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that"> 352 <param name="param_algorithm_TransitionGroupPicker_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
272 <option value="none" selected="true">none</option> 353 <option value="none" selected="true">none</option>
273 <option value="smoothed">smoothed</option> 354 <option value="smoothed">smoothed</option>
274 <option value="original">original</option> 355 <option value="original">original</option>
275 </param> 356 </param>
276 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"> 357 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
277 <sanitizer> 358 <param name="param_algorithm_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
278 <valid initial="string.printable">
279 <remove value="'"/>
280 <remove value="&quot;"/>
281 </valid>
282 </sanitizer>
283 </param>
284 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> 359 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
285 <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> 360 <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
286 <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"> 361 <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
287 <sanitizer>
288 <valid initial="string.printable">
289 <remove value="'"/>
290 <remove value="&quot;"/>
291 </valid>
292 </sanitizer>
293 </param>
294 <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/> 362 <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>
295 <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/> 363 <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>
296 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/> 364 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
297 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/> 365 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
298 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/> 366 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
330 </param> 398 </param>
331 <param name="param_algorithm_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) "> 399 <param name="param_algorithm_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) ">
332 <option value="true" selected="true">true</option> 400 <option value="true" selected="true">true</option>
333 <option value="false">false</option> 401 <option value="false">false</option>
334 </param> 402 </param>
335 <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "> 403 <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) If turned off, will not use fragment ion spectra for scoring">
336 <option value="true" selected="true">true</option> 404 <option value="true" selected="true">true</option>
337 <option value="false">false</option> 405 <option value="false">false</option>
338 </param> 406 </param>
339 <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/> 407 <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
408 <param name="param_algorithm_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>
340 <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/> 409 <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/>
341 <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/> 410 <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
342 </expand> 411 </expand>
343 </inputs> 412 </inputs>
344 <outputs> 413 <outputs>