Mercurial > repos > galaxyp > openms_openswathrtnormalizer

comparison OpenSwathRTNormalizer.xml @ 1:580a0a6ab12f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:46:32 -0400
parents 83818b56fd8c
children 13bfce690403
comparison
equal deleted inserted replaced
0:83818b56fd8c 1:580a0a6ab12f
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:
108 #end if 123 #end if
109 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff: 124 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
110 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff 125 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
111 #end if 126 #end if
112 #if $param_outlierDetection_outlierMethod: 127 #if $param_outlierDetection_outlierMethod:
113 -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod 128 -outlierDetection:outlierMethod
129 #if " " in str($param_outlierDetection_outlierMethod):
130 "$param_outlierDetection_outlierMethod"
131 #else
132 $param_outlierDetection_outlierMethod
133 #end if
114 #end if 134 #end if
115 #if $param_outlierDetection_useIterativeChauvenet: 135 #if $param_outlierDetection_useIterativeChauvenet:
116 -outlierDetection:useIterativeChauvenet 136 -outlierDetection:useIterativeChauvenet
117 #end if 137 #end if
118 #if $param_outlierDetection_RANSACMaxIterations: 138 #if $param_outlierDetection_RANSACMaxIterations:
157 #end if 177 #end if
158 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width: 178 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
159 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width 179 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
160 #end if 180 #end if
161 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction: 181 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
162 -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction 182 -algorithm:TransitionGroupPicker:background_subtraction
183 #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
184 "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
185 #else
186 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
187 #end if
163 #end if 188 #end if
164 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: 189 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
165 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks" 190 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
166 #end if 191 #end if
167 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: 192 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
187 #end if 212 #end if
188 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance: 213 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
189 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance 214 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
190 #end if 215 #end if
191 #if $adv_opts.param_algorithm_Scores_use_shape_score: 216 #if $adv_opts.param_algorithm_Scores_use_shape_score:
192 -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score 217 -algorithm:Scores:use_shape_score
218 #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
219 "$adv_opts.param_algorithm_Scores_use_shape_score"
220 #else
221 $adv_opts.param_algorithm_Scores_use_shape_score
222 #end if
193 #end if 223 #end if
194 #if $adv_opts.param_algorithm_Scores_use_coelution_score: 224 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
195 -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score 225 -algorithm:Scores:use_coelution_score
226 #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
227 "$adv_opts.param_algorithm_Scores_use_coelution_score"
228 #else
229 $adv_opts.param_algorithm_Scores_use_coelution_score
230 #end if
196 #end if 231 #end if
197 #if $adv_opts.param_algorithm_Scores_use_rt_score: 232 #if $adv_opts.param_algorithm_Scores_use_rt_score:
198 -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score 233 -algorithm:Scores:use_rt_score
234 #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
235 "$adv_opts.param_algorithm_Scores_use_rt_score"
236 #else
237 $adv_opts.param_algorithm_Scores_use_rt_score
238 #end if
199 #end if 239 #end if
200 #if $adv_opts.param_algorithm_Scores_use_library_score: 240 #if $adv_opts.param_algorithm_Scores_use_library_score:
201 -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score 241 -algorithm:Scores:use_library_score
242 #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
243 "$adv_opts.param_algorithm_Scores_use_library_score"
244 #else
245 $adv_opts.param_algorithm_Scores_use_library_score
246 #end if
202 #end if 247 #end if
203 #if $adv_opts.param_algorithm_Scores_use_elution_model_score: 248 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
204 -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score 249 -algorithm:Scores:use_elution_model_score
250 #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
251 "$adv_opts.param_algorithm_Scores_use_elution_model_score"
252 #else
253 $adv_opts.param_algorithm_Scores_use_elution_model_score
254 #end if
205 #end if 255 #end if
206 #if $adv_opts.param_algorithm_Scores_use_intensity_score: 256 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
207 -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score 257 -algorithm:Scores:use_intensity_score
258 #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
259 "$adv_opts.param_algorithm_Scores_use_intensity_score"
260 #else
261 $adv_opts.param_algorithm_Scores_use_intensity_score
262 #end if
208 #end if 263 #end if
209 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: 264 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
210 -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score 265 -algorithm:Scores:use_nr_peaks_score
266 #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
267 "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
268 #else
269 $adv_opts.param_algorithm_Scores_use_nr_peaks_score
270 #end if
211 #end if 271 #end if
212 #if $adv_opts.param_algorithm_Scores_use_total_xic_score: 272 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
213 -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score 273 -algorithm:Scores:use_total_xic_score
274 #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
275 "$adv_opts.param_algorithm_Scores_use_total_xic_score"
276 #else
277 $adv_opts.param_algorithm_Scores_use_total_xic_score
278 #end if
214 #end if 279 #end if
215 #if $adv_opts.param_algorithm_Scores_use_sn_score: 280 #if $adv_opts.param_algorithm_Scores_use_sn_score:
216 -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score 281 -algorithm:Scores:use_sn_score
282 #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
283 "$adv_opts.param_algorithm_Scores_use_sn_score"
284 #else
285 $adv_opts.param_algorithm_Scores_use_sn_score
286 #end if
217 #end if 287 #end if
218 #if $adv_opts.param_algorithm_Scores_use_dia_scores: 288 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
219 -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores 289 -algorithm:Scores:use_dia_scores
290 #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
291 "$adv_opts.param_algorithm_Scores_use_dia_scores"
292 #else
293 $adv_opts.param_algorithm_Scores_use_dia_scores
294 #end if
220 #end if 295 #end if
221 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: 296 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
222 -algorithm:Scores:use_ms1_correlation 297 -algorithm:Scores:use_ms1_correlation
223 #end if 298 #end if
224 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: 299 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: