Mercurial > repos > galaxyp > openms_openswathanalyzer

comparison OpenSwathAnalyzer.xml @ 1:7d2394730cdb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:44:33 -0400
parents addd804ac6c6
children ee58e9cf2d33
comparison
equal deleted inserted replaced
0:addd804ac6c6 1:7d2394730cdb
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 "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
142 #end if 167 #end if
143 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: 168 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
163 #end if 188 #end if
164 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance: 189 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
165 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance 190 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
166 #end if 191 #end if
167 #if $adv_opts.param_algorithm_Scores_use_shape_score: 192 #if $adv_opts.param_algorithm_Scores_use_shape_score:
168 -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score 193 -algorithm:Scores:use_shape_score
194 #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
195 "$adv_opts.param_algorithm_Scores_use_shape_score"
196 #else
197 $adv_opts.param_algorithm_Scores_use_shape_score
198 #end if
169 #end if 199 #end if
170 #if $adv_opts.param_algorithm_Scores_use_coelution_score: 200 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
171 -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score 201 -algorithm:Scores:use_coelution_score
202 #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
203 "$adv_opts.param_algorithm_Scores_use_coelution_score"
204 #else
205 $adv_opts.param_algorithm_Scores_use_coelution_score
206 #end if
172 #end if 207 #end if
173 #if $adv_opts.param_algorithm_Scores_use_rt_score: 208 #if $adv_opts.param_algorithm_Scores_use_rt_score:
174 -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score 209 -algorithm:Scores:use_rt_score
210 #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
211 "$adv_opts.param_algorithm_Scores_use_rt_score"
212 #else
213 $adv_opts.param_algorithm_Scores_use_rt_score
214 #end if
175 #end if 215 #end if
176 #if $adv_opts.param_algorithm_Scores_use_library_score: 216 #if $adv_opts.param_algorithm_Scores_use_library_score:
177 -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score 217 -algorithm:Scores:use_library_score
218 #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
219 "$adv_opts.param_algorithm_Scores_use_library_score"
220 #else
221 $adv_opts.param_algorithm_Scores_use_library_score
222 #end if
178 #end if 223 #end if
179 #if $adv_opts.param_algorithm_Scores_use_elution_model_score: 224 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
180 -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score 225 -algorithm:Scores:use_elution_model_score
226 #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
227 "$adv_opts.param_algorithm_Scores_use_elution_model_score"
228 #else
229 $adv_opts.param_algorithm_Scores_use_elution_model_score
230 #end if
181 #end if 231 #end if
182 #if $adv_opts.param_algorithm_Scores_use_intensity_score: 232 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
183 -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score 233 -algorithm:Scores:use_intensity_score
234 #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
235 "$adv_opts.param_algorithm_Scores_use_intensity_score"
236 #else
237 $adv_opts.param_algorithm_Scores_use_intensity_score
238 #end if
184 #end if 239 #end if
185 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: 240 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
186 -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score 241 -algorithm:Scores:use_nr_peaks_score
242 #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
243 "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
244 #else
245 $adv_opts.param_algorithm_Scores_use_nr_peaks_score
246 #end if
187 #end if 247 #end if
188 #if $adv_opts.param_algorithm_Scores_use_total_xic_score: 248 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
189 -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score 249 -algorithm:Scores:use_total_xic_score
250 #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
251 "$adv_opts.param_algorithm_Scores_use_total_xic_score"
252 #else
253 $adv_opts.param_algorithm_Scores_use_total_xic_score
254 #end if
190 #end if 255 #end if
191 #if $adv_opts.param_algorithm_Scores_use_sn_score: 256 #if $adv_opts.param_algorithm_Scores_use_sn_score:
192 -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score 257 -algorithm:Scores:use_sn_score
258 #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
259 "$adv_opts.param_algorithm_Scores_use_sn_score"
260 #else
261 $adv_opts.param_algorithm_Scores_use_sn_score
262 #end if
193 #end if 263 #end if
194 #if $adv_opts.param_algorithm_Scores_use_dia_scores: 264 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
195 -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores 265 -algorithm:Scores:use_dia_scores
266 #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
267 "$adv_opts.param_algorithm_Scores_use_dia_scores"
268 #else
269 $adv_opts.param_algorithm_Scores_use_dia_scores
270 #end if
196 #end if 271 #end if
197 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: 272 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
198 -algorithm:Scores:use_ms1_correlation 273 -algorithm:Scores:use_ms1_correlation
199 #end if 274 #end if
200 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: 275 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: