Mercurial > repos > galaxyp > openms_openswathworkflow

comparison OpenSwathWorkflow.xml @ 9:3967f7cf35b9 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 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:46:48 +0000
parents 091d4e82839a
children 887be35bc42e
comparison
equal deleted inserted replaced
8:bc63b4d12779 9:3967f7cf35b9
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="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.3.0"> 4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Complete workflow to run OpenSWATH</description> 5 <description>Complete workflow to run OpenSWATH</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathWorkflow</token> 7 <token name="@EXECUTABLE@">OpenSwathWorkflow</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[OpenSwathWorkflow 15 @EXT_FOO@
14 16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir tr &&
22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
23 #if $tr_irt:
24 mkdir tr_irt &&
25 ln -s '$tr_irt' 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)' &&
26 #end if
27 #if $tr_irt_nonlinear:
28 mkdir tr_irt_nonlinear &&
29 ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
30 #end if
31 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 mkdir out_features &&
33 #end if
34 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
35 mkdir out_tsv &&
36 #end if
37 #if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
38 mkdir out_osw &&
39 #end if
40 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
41 mkdir out_chrom &&
42 #end if
43 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
44 mkdir out_qc &&
45 #end if
46 #if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 mkdir Debugging_irt_mzml &&
48 #end if
49 #if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
50 mkdir Debugging_irt_trafo &&
51 #end if
52 #if $adv_opts_cond.adv_opts_selector=='advanced':
53 #if $adv_opts_cond.rt_norm:
54 mkdir adv_opts_cond.rt_norm &&
55 ln -s '$adv_opts_cond.rt_norm' 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)' &&
56 #end if
57 #if $adv_opts_cond.swath_windows_file:
58 mkdir adv_opts_cond.swath_windows_file &&
59 ln -s '$adv_opts_cond.swath_windows_file' 'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)' &&
60 #end if
61 #end if
62
63 ## Main program call
64
65 set -o pipefail &&
66 @EXECUTABLE@ -write_ctd ./ &&
67 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
68 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
15 -in 69 -in
16 #for token in $param_in: 70 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
17 $token 71 -tr
18 #end for 72 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
19 #if $param_tr: 73 #if $tr_irt:
20 -tr $param_tr 74 -tr_irt
21 #end if 75 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)'
22 #if $param_tr_type: 76 #end if
23 -tr_type 77 #if $tr_irt_nonlinear:
24 #if " " in str($param_tr_type): 78 -tr_irt_nonlinear
25 "$param_tr_type" 79 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)'
26 #else 80 #end if
27 $param_tr_type 81 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
82 -out_features
83 'out_features/output.${gxy2omsext("featurexml")}'
84 #end if
85 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
86 -out_tsv
87 'out_tsv/output.${gxy2omsext("tabular")}'
88 #end if
89 #if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
90 -out_osw
91 'out_osw/output.${gxy2omsext("osw")}'
92 #end if
93 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
94 -out_chrom
95 'out_chrom/output.${adv_opts_cond.out_chrom_type}'
96 #end if
97 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98 -out_qc
99 'out_qc/output.${gxy2omsext("json")}'
100 #end if
101 #if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
102 -Debugging:irt_mzml
103 'Debugging_irt_mzml/output.${gxy2omsext("mzml")}'
104 #end if
105 #if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
106 -Debugging:irt_trafo
107 'Debugging_irt_trafo/output.${gxy2omsext("trafoxml")}'
108 #end if
109 #if $adv_opts_cond.adv_opts_selector=='advanced':
110 #if $adv_opts_cond.rt_norm:
111 -rt_norm
112 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)'
28 #end if 113 #end if
29 #end if 114 #if $adv_opts_cond.swath_windows_file:
30 #if $param_tr_irt: 115 -swath_windows_file
31 -tr_irt $param_tr_irt 116 'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)'
32 #end if
33 #if $param_out_features:
34 -out_features $param_out_features
35 #end if
36 #if $param_out_tsv:
37 -out_tsv $param_out_tsv
38 #end if
39 #if $param_out_osw:
40 -out_osw $param_out_osw
41 #end if
42 #if $param_out_chrom:
43 -out_chrom $param_out_chrom
44 #end if
45 #if $param_rt_extraction_window:
46 -rt_extraction_window $param_rt_extraction_window
47 #end if
48 #if $param_mz_extraction_window:
49 -mz_extraction_window $param_mz_extraction_window
50 #end if
51 #if $param_ppm:
52 -ppm
53 #end if
54 #if $param_sonar:
55 -sonar
56 #end if
57 #if $param_RTNormalization_alignmentMethod:
58 -RTNormalization:alignmentMethod
59 #if " " in str($param_RTNormalization_alignmentMethod):
60 "$param_RTNormalization_alignmentMethod"
61 #else
62 $param_RTNormalization_alignmentMethod
63 #end if 117 #end if
64 #end if 118 #end if
65 #if $param_RTNormalization_outlierMethod: 119 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
66 -RTNormalization:outlierMethod 120 | tee '$stdout'
67 #if " " in str($param_RTNormalization_outlierMethod): 121 #end if
68 "$param_RTNormalization_outlierMethod" 122
69 #else 123 ## Postprocessing
70 $param_RTNormalization_outlierMethod 124 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
71 #end if 125 && mv 'out_features/output.${gxy2omsext("featurexml")}' '$out_features'
72 #end if 126 #end if
73 #if $param_RTNormalization_useIterativeChauvenet: 127 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
74 -RTNormalization:useIterativeChauvenet 128 && mv 'out_tsv/output.${gxy2omsext("tabular")}' '$out_tsv'
75 #end if 129 #end if
76 #if $param_RTNormalization_RANSACMaxIterations: 130 #if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
77 -RTNormalization:RANSACMaxIterations $param_RTNormalization_RANSACMaxIterations 131 && mv 'out_osw/output.${gxy2omsext("osw")}' '$out_osw'
78 #end if 132 #end if
79 #if $param_RTNormalization_RANSACMaxPercentRTThreshold: 133 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
80 -RTNormalization:RANSACMaxPercentRTThreshold $param_RTNormalization_RANSACMaxPercentRTThreshold 134 && mv 'out_chrom/output.${adv_opts_cond.out_chrom_type}' '$out_chrom'
81 #end if 135 #end if
82 #if $param_RTNormalization_RANSACSamplingSize: 136 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
83 -RTNormalization:RANSACSamplingSize $param_RTNormalization_RANSACSamplingSize 137 && mv 'out_qc/output.${gxy2omsext("json")}' '$out_qc'
84 #end if 138 #end if
85 #if $param_RTNormalization_estimateBestPeptides: 139 #if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
86 -RTNormalization:estimateBestPeptides 140 && mv 'Debugging_irt_mzml/output.${gxy2omsext("mzml")}' '$Debugging_irt_mzml'
87 #end if 141 #end if
88 #if $param_RTNormalization_InitialQualityCutoff: 142 #if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
89 -RTNormalization:InitialQualityCutoff $param_RTNormalization_InitialQualityCutoff 143 && mv 'Debugging_irt_trafo/output.${gxy2omsext("trafoxml")}' '$Debugging_irt_trafo'
90 #end if 144 #end if
91 #if $param_RTNormalization_OverallQualityCutoff: 145 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
92 -RTNormalization:OverallQualityCutoff $param_RTNormalization_OverallQualityCutoff 146 && mv '@EXECUTABLE@.ctd' '$ctd_out'
93 #end if 147 #end if]]></command>
94 #if $param_RTNormalization_NrRTBins: 148 <configfiles>
95 -RTNormalization:NrRTBins $param_RTNormalization_NrRTBins 149 <inputs name="args_json" data_style="paths"/>
96 #end if 150 <configfile name="hardcoded_json"><![CDATA[{"tempDirectory": "\$TMP_DIR", "outer_loop_threads": "1", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
97 #if $param_RTNormalization_MinPeptidesPerBin: 151 </configfiles>
98 -RTNormalization:MinPeptidesPerBin $param_RTNormalization_MinPeptidesPerBin
99 #end if
100 #if $param_RTNormalization_MinBinsFilled:
101 -RTNormalization:MinBinsFilled $param_RTNormalization_MinBinsFilled
102 #end if
103 #if $param_RTNormalization_lowess_span:
104 -RTNormalization:lowess:span $param_RTNormalization_lowess_span
105 #end if
106 #if $param_RTNormalization_b_spline_num_nodes:
107 -RTNormalization:b_spline:num_nodes $param_RTNormalization_b_spline_num_nodes
108 #end if
109 #if $param_Scoring_stop_report_after_feature:
110 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
111 #end if
112 #if $param_Scoring_rt_normalization_factor:
113 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
114 #end if
115 #if $param_Scoring_uis_threshold_sn:
116 -Scoring:uis_threshold_sn $param_Scoring_uis_threshold_sn
117 #end if
118 #if $param_Scoring_uis_threshold_peak_area:
119 -Scoring:uis_threshold_peak_area $param_Scoring_uis_threshold_peak_area
120 #end if
121 #if $param_Scoring_TransitionGroupPicker_stop_after_feature:
122 -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature
123 #end if
124 #if $param_Scoring_TransitionGroupPicker_min_peak_width:
125 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
126 #end if
127 #if $param_Scoring_TransitionGroupPicker_background_subtraction:
128 -Scoring:TransitionGroupPicker:background_subtraction
129 #if " " in str($param_Scoring_TransitionGroupPicker_background_subtraction):
130 "$param_Scoring_TransitionGroupPicker_background_subtraction"
131 #else
132 $param_Scoring_TransitionGroupPicker_background_subtraction
133 #end if
134 #end if
135 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
136 -Scoring:TransitionGroupPicker:recalculate_peaks
137 #if " " in str($param_Scoring_TransitionGroupPicker_recalculate_peaks):
138 "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
139 #else
140 $param_Scoring_TransitionGroupPicker_recalculate_peaks
141 #end if
142 #end if
143 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
144 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
145 #end if
146 #if $param_Scoring_TransitionGroupPicker_minimal_quality:
147 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
148 #end if
149 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
150 -Scoring:TransitionGroupPicker:compute_peak_quality
151 #if " " in str($param_Scoring_TransitionGroupPicker_compute_peak_quality):
152 "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
153 #else
154 $param_Scoring_TransitionGroupPicker_compute_peak_quality
155 #end if
156 #end if
157 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
158 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
159 #end if
160 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
161 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
162 #end if
163 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width:
164 -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width
165 #end if
166 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss:
167 -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss
168 #end if
169 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width:
170 -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width
171 #end if
172 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
173 -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
174 #end if
175 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
176 -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
177 #end if
178 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
179 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
180 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks):
181 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks"
182 #else
183 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
184 #end if
185 #end if
186 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
187 -Scoring:TransitionGroupPicker:PeakPickerMRM:method
188 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method):
189 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method"
190 #else
191 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
192 #end if
193 #end if
194 #if $param_Scoring_DIAScoring_dia_extraction_window:
195 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
196 #end if
197 #if $param_Scoring_DIAScoring_dia_centroided:
198 -Scoring:DIAScoring:dia_centroided
199 #end if
200 #if $param_Scoring_DIAScoring_dia_byseries_intensity_min:
201 -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min
202 #end if
203 #if $param_Scoring_DIAScoring_dia_byseries_ppm_diff:
204 -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff
205 #end if
206 #if $param_Scoring_DIAScoring_dia_nr_isotopes:
207 -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes
208 #end if
209 #if $param_Scoring_DIAScoring_dia_nr_charges:
210 -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges
211 #end if
212 #if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff:
213 -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff
214 #end if
215 #if $param_Scoring_EMGScoring_max_iteration:
216 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
217 #end if
218 #if $adv_opts.adv_opts_selector=='advanced':
219 #if $adv_opts.param_rt_norm:
220 -rt_norm $adv_opts.param_rt_norm
221 #end if
222 #if $adv_opts.param_swath_windows_file:
223 -swath_windows_file $adv_opts.param_swath_windows_file
224 #end if
225 #if $adv_opts.param_sort_swath_maps:
226 -sort_swath_maps
227 #end if
228 #if $adv_opts.param_use_ms1_traces:
229 -use_ms1_traces
230 #end if
231 #if $adv_opts.param_enable_uis_scoring:
232 -enable_uis_scoring
233 #end if
234 #if $adv_opts.param_min_upper_edge_dist:
235 -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist
236 #end if
237 #if $adv_opts.param_extra_rt_extraction_window:
238 -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window
239 #end if
240 #if $adv_opts.param_min_rsq:
241 -min_rsq $adv_opts.param_min_rsq
242 #end if
243 #if $adv_opts.param_min_coverage:
244 -min_coverage $adv_opts.param_min_coverage
245 #end if
246 #if $adv_opts.param_split_file_input:
247 -split_file_input
248 #end if
249 #if $adv_opts.param_use_elution_model_score:
250 -use_elution_model_score
251 #end if
252 #if $adv_opts.param_readOptions:
253 -readOptions
254 #if " " in str($adv_opts.param_readOptions):
255 "$adv_opts.param_readOptions"
256 #else
257 $adv_opts.param_readOptions
258 #end if
259 #end if
260 #if $adv_opts.param_mz_correction_function:
261 -mz_correction_function
262 #if " " in str($adv_opts.param_mz_correction_function):
263 "$adv_opts.param_mz_correction_function"
264 #else
265 $adv_opts.param_mz_correction_function
266 #end if
267 #end if
268 #if $adv_opts.param_irt_mz_extraction_window:
269 -irt_mz_extraction_window $adv_opts.param_irt_mz_extraction_window
270 #end if
271 #if $adv_opts.param_ppm_irtwindow:
272 -ppm_irtwindow
273 #end if
274 #if $adv_opts.param_tempDirectory:
275 -tempDirectory "$adv_opts.param_tempDirectory"
276 #end if
277 #if $adv_opts.param_extraction_function:
278 -extraction_function
279 #if " " in str($adv_opts.param_extraction_function):
280 "$adv_opts.param_extraction_function"
281 #else
282 $adv_opts.param_extraction_function
283 #end if
284 #end if
285 #if $adv_opts.param_batchSize:
286 -batchSize $adv_opts.param_batchSize
287 #end if
288 #if $adv_opts.param_force:
289 -force
290 #end if
291 #if $adv_opts.param_Library_retentionTimeInterpretation:
292 -Library:retentionTimeInterpretation
293 #if " " in str($adv_opts.param_Library_retentionTimeInterpretation):
294 "$adv_opts.param_Library_retentionTimeInterpretation"
295 #else
296 $adv_opts.param_Library_retentionTimeInterpretation
297 #end if
298 #end if
299 #if $adv_opts.param_Library_override_group_label_check:
300 -Library:override_group_label_check
301 #end if
302 #if $adv_opts.param_Library_force_invalid_mods:
303 -Library:force_invalid_mods
304 #end if
305 #if $adv_opts.param_Scoring_quantification_cutoff:
306 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
307 #end if
308 #if $adv_opts.param_Scoring_write_convex_hull:
309 -Scoring:write_convex_hull
310 #end if
311 #if $adv_opts.param_Scoring_TransitionGroupPicker_use_precursors:
312 -Scoring:TransitionGroupPicker:use_precursors
313 #end if
314 #if $adv_opts.param_Scoring_TransitionGroupPicker_resample_boundary:
315 -Scoring:TransitionGroupPicker:resample_boundary $adv_opts.param_Scoring_TransitionGroupPicker_resample_boundary
316 #end if
317 #if $adv_opts.param_Scoring_Scores_use_shape_score:
318 -Scoring:Scores:use_shape_score
319 #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score):
320 "$adv_opts.param_Scoring_Scores_use_shape_score"
321 #else
322 $adv_opts.param_Scoring_Scores_use_shape_score
323 #end if
324 #end if
325 #if $adv_opts.param_Scoring_Scores_use_coelution_score:
326 -Scoring:Scores:use_coelution_score
327 #if " " in str($adv_opts.param_Scoring_Scores_use_coelution_score):
328 "$adv_opts.param_Scoring_Scores_use_coelution_score"
329 #else
330 $adv_opts.param_Scoring_Scores_use_coelution_score
331 #end if
332 #end if
333 #if $adv_opts.param_Scoring_Scores_use_rt_score:
334 -Scoring:Scores:use_rt_score
335 #if " " in str($adv_opts.param_Scoring_Scores_use_rt_score):
336 "$adv_opts.param_Scoring_Scores_use_rt_score"
337 #else
338 $adv_opts.param_Scoring_Scores_use_rt_score
339 #end if
340 #end if
341 #if $adv_opts.param_Scoring_Scores_use_library_score:
342 -Scoring:Scores:use_library_score
343 #if " " in str($adv_opts.param_Scoring_Scores_use_library_score):
344 "$adv_opts.param_Scoring_Scores_use_library_score"
345 #else
346 $adv_opts.param_Scoring_Scores_use_library_score
347 #end if
348 #end if
349 #if $adv_opts.param_Scoring_Scores_use_intensity_score:
350 -Scoring:Scores:use_intensity_score
351 #if " " in str($adv_opts.param_Scoring_Scores_use_intensity_score):
352 "$adv_opts.param_Scoring_Scores_use_intensity_score"
353 #else
354 $adv_opts.param_Scoring_Scores_use_intensity_score
355 #end if
356 #end if
357 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
358 -Scoring:Scores:use_nr_peaks_score
359 #if " " in str($adv_opts.param_Scoring_Scores_use_nr_peaks_score):
360 "$adv_opts.param_Scoring_Scores_use_nr_peaks_score"
361 #else
362 $adv_opts.param_Scoring_Scores_use_nr_peaks_score
363 #end if
364 #end if
365 #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
366 -Scoring:Scores:use_total_xic_score
367 #if " " in str($adv_opts.param_Scoring_Scores_use_total_xic_score):
368 "$adv_opts.param_Scoring_Scores_use_total_xic_score"
369 #else
370 $adv_opts.param_Scoring_Scores_use_total_xic_score
371 #end if
372 #end if
373 #if $adv_opts.param_Scoring_Scores_use_sn_score:
374 -Scoring:Scores:use_sn_score
375 #if " " in str($adv_opts.param_Scoring_Scores_use_sn_score):
376 "$adv_opts.param_Scoring_Scores_use_sn_score"
377 #else
378 $adv_opts.param_Scoring_Scores_use_sn_score
379 #end if
380 #end if
381 #if $adv_opts.param_Scoring_Scores_use_dia_scores:
382 -Scoring:Scores:use_dia_scores
383 #if " " in str($adv_opts.param_Scoring_Scores_use_dia_scores):
384 "$adv_opts.param_Scoring_Scores_use_dia_scores"
385 #else
386 $adv_opts.param_Scoring_Scores_use_dia_scores
387 #end if
388 #end if
389 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
390 -Scoring:Scores:use_ms1_correlation
391 #end if
392 #if $adv_opts.param_Scoring_Scores_use_sonar_scores:
393 -Scoring:Scores:use_sonar_scores
394 #end if
395 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
396 -Scoring:Scores:use_ms1_fullscan
397 #end if
398 #if $adv_opts.param_Scoring_Scores_use_uis_scores:
399 -Scoring:Scores:use_uis_scores
400 #end if
401 #end if
402 ]]></command>
403 <inputs> 152 <inputs>
404 <param name="param_in" type="data" format="mzml,mzxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> 153 <param name="in" argument="-in" type="data" format="mzml,mzxml,sqmass" optional="false" label="Input files separated by blank" help=" select mzml,mzxml,sqmass data sets(s)"/>
405 <sanitizer> 154 <param name="tr" argument="-tr" type="data" format="pqp,tabular,traml" optional="false" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/>
406 <valid initial="string.printable"> 155 <param name="tr_irt" argument="-tr_irt" type="data" format="pqp,tabular,traml" optional="true" label="transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
407 <remove value="'"/> 156 <param name="tr_irt_nonlinear" argument="-tr_irt_nonlinear" type="data" format="pqp,tabular,traml" optional="true" label="additional nonlinear transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
408 <remove value="&quot;"/> 157 <param name="sonar" argument="-sonar" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is scanning SWATH data" help=""/>
409 </valid> 158 <param name="rt_extraction_window" argument="-rt_extraction_window" type="float" optional="true" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help=""/>
410 </sanitizer> 159 <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
411 </param> 160 <param name="mz_extraction_window" argument="-mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
412 <param name="param_tr" type="data" format="traml,tabular,pqp" optional="False" label="transition file ('TraML','tsv','pqp')" help="(-tr) "/> 161 <param name="mz_extraction_window_ms1" argument="-mz_extraction_window_ms1" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
413 <param name="param_tr_type" display="radio" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) "> 162 <param name="im_extraction_window_ms1" argument="-im_extraction_window_ms1" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in milliseconds)" help=""/>
414 <option value="traML">traML</option> 163 <section name="Debugging" title="Debugging" help="" expanded="false"/>
415 <option value="tsv">tsv</option> 164 <section name="Calibration" title="Parameters for the m/z and ion mobility calibration" help="" expanded="false">
416 <option value="pqp">pqp</option> 165 <param name="ms1_im_calibration" argument="-Calibration:ms1_im_calibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)" help=""/>
417 </param> 166 <param name="im_correction_function" argument="-Calibration:im_correction_function" display="radio" type="select" optional="false" label="Type of normalization function for IM calibration" help="">
418 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/> 167 <option value="none">none</option>
419 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/> 168 <option value="linear" selected="true">linear</option>
420 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/> 169 <expand macro="list_string_san"/>
421 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/> 170 </param>
422 <param name="param_sonar" display="radio" type="boolean" truevalue="-sonar" falsevalue="" checked="false" optional="True" label="data is scanning SWATH data" help="(-sonar) "/> 171 <param name="debug_im_file" argument="-Calibration:debug_im_file" type="text" optional="true" value="" label="Debug file for Ion Mobility calibration" help="">
423 <param name="param_RTNormalization_alignmentMethod" display="radio" type="select" optional="False" value="linear" label="How to perform the alignment to the normalized RT space using anchor points" help="(-alignmentMethod) 'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing"> 172 <expand macro="list_string_san"/>
424 <option value="linear" selected="true">linear</option> 173 </param>
425 <option value="interpolated">interpolated</option> 174 <param name="debug_mz_file" argument="-Calibration:debug_mz_file" type="text" optional="true" value="" label="Debug file for m/z calibration" help="">
426 <option value="lowess">lowess</option> 175 <expand macro="list_string_san"/>
427 <option value="b_spline">b_spline</option> 176 </param>
428 </param> 177 </section>
429 <param name="param_RTNormalization_outlierMethod" display="radio" type="select" optional="False" value="iter_residual" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="(-outlierMethod) Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)"> 178 <section name="Library" title="Library parameters section" help="" expanded="false">
430 <option value="iter_residual" selected="true">iter_residual</option> 179 <param name="retentionTimeInterpretation" argument="-Library:retentionTimeInterpretation" display="radio" type="select" optional="false" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
431 <option value="iter_jackknife">iter_jackknife</option> 180 <option value="iRT" selected="true">iRT</option>
432 <option value="ransac">ransac</option> 181 <option value="seconds">seconds</option>
433 <option value="none">none</option> 182 <option value="minutes">minutes</option>
434 </param> 183 <expand macro="list_string_san"/>
435 <param name="param_RTNormalization_useIterativeChauvenet" display="radio" type="boolean" truevalue="-RTNormalization:useIterativeChauvenet" falsevalue="" checked="false" optional="True" label="Whether to use Chauvenet's criterion when using iterative methods" help="(-useIterativeChauvenet) This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/> 184 </param>
436 <param name="param_RTNormalization_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/> 185 <param name="override_group_label_check" argument="-Library:override_group_label_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="Only turn this off if you know what you are doing"/>
437 <param name="param_RTNormalization_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="(-RANSACMaxPercentRTThreshold) Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/> 186 <param name="force_invalid_mods" argument="-Library:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>
438 <param name="param_RTNormalization_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help="(-RANSACSamplingSize) "/> 187 </section>
439 <param name="param_RTNormalization_estimateBestPeptides" display="radio" type="boolean" truevalue="-RTNormalization:estimateBestPeptides" falsevalue="" checked="false" optional="True" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization. Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (" help="(-estimateBestPeptides) e.g. due to them being endogenous peptides or using a less curated list of peptides)"/> 188 <section name="RTNormalization" title="Parameters for the RTNormalization for iRT petides" help="This specifies how the RT alignment is performed and how outlier detection is applied. Outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
440 <param name="param_RTNormalization_InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="(-InitialQualityCutoff) -2 to 2)"/> 189 <param name="alignmentMethod" argument="-RTNormalization:alignmentMethod" display="radio" type="select" optional="false" label="How to perform the alignment to the normalized RT space using anchor points" help="'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing">
441 <param name="param_RTNormalization_OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="(-OverallQualityCutoff) 0 to 10)"/> 190 <option value="linear" selected="true">linear</option>
442 <param name="param_RTNormalization_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="(-NrRTBins) This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/> 191 <option value="interpolated">interpolated</option>
443 <param name="param_RTNormalization_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/> 192 <option value="lowess">lowess</option>
444 <param name="param_RTNormalization_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/> 193 <option value="b_spline">b_spline</option>
445 <param name="param_RTNormalization_lowess_span" type="float" min="0.0" max="1.0" optional="True" value="0.666666666667" label="Span parameter for lowess" help="(-span) "/> 194 <expand macro="list_string_san"/>
446 <param name="param_RTNormalization_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for b spline" help="(-num_nodes) "/> 195 </param>
447 <param name="param_Scoring_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/> 196 <param name="outlierMethod" argument="-RTNormalization:outlierMethod" display="radio" type="select" optional="false" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
448 <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)"/> 197 <option value="iter_residual" selected="true">iter_residual</option>
449 <param name="param_Scoring_uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_sn) "/> 198 <option value="iter_jackknife">iter_jackknife</option>
450 <param name="param_Scoring_uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_peak_area) "/> 199 <option value="ransac">ransac</option>
451 <param name="param_Scoring_TransitionGroupPicker_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/> 200 <option value="none">none</option>
452 <param name="param_Scoring_TransitionGroupPicker_min_peak_width" type="float" value="14.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/> 201 <expand macro="list_string_san"/>
453 <param name="param_Scoring_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"> 202 </param>
454 <option value="none" selected="true">none</option> 203 <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
455 <option value="smoothed">smoothed</option> 204 <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" optional="true" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
456 <option value="original">original</option> 205 <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" optional="true" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
457 </param> 206 <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" optional="true" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
458 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" display="radio" type="select" optional="False" value="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"> 207 <param name="estimateBestPeptides" argument="-RTNormalization:estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
459 <option value="true" selected="true">true</option> 208 <param name="InitialQualityCutoff" argument="-RTNormalization:InitialQualityCutoff" type="float" optional="true" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
460 <option value="false">false</option> 209 <param name="OverallQualityCutoff" argument="-RTNormalization:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
461 </param> 210 <param name="NrRTBins" argument="-RTNormalization:NrRTBins" type="integer" optional="true" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
462 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="0.75" 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)"/> 211 <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
463 <param name="param_Scoring_TransitionGroupPicker_minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> 212 <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/>
464 <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" display="radio" type="select" optional="False" value="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"> 213 <section name="lowess" title="" help="" expanded="false">
465 <option value="true" selected="true">true</option> 214 <param name="span" argument="-RTNormalization:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Span parameter for lowess" help=""/>
466 <option value="false">false</option> 215 </section>
467 </param> 216 <section name="b_spline" title="" help="" expanded="false">
468 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/> 217 <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for b spline" help=""/>
469 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/> 218 </section>
470 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> 219 </section>
471 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" falsevalue="" checked="false" optional="True" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "/> 220 <section name="Scoring" title="Scoring parameters section" help="" expanded="false">
472 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/> 221 <param name="stop_report_after_feature" argument="-Scoring:stop_report_after_feature" type="integer" optional="true" value="5" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
473 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/> 222 <param name="rt_normalization_factor" argument="-Scoring:rt_normalization_factor" type="float" optional="true" value="100.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
474 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" falsevalue="" checked="false" optional="True" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help="(-write_sn_log_messages) "/> 223 <param name="quantification_cutoff" argument="-Scoring:quantification_cutoff" type="float" optional="true" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
475 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="select" optional="False" value="true" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "> 224 <param name="write_convex_hull" argument="-Scoring:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
476 <option value="false">false</option> 225 <param name="spectrum_addition_method" argument="-Scoring:spectrum_addition_method" display="radio" type="select" optional="false" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
477 <option value="true" selected="true">true</option> 226 <option value="simple" selected="true">simple</option>
478 </param> 227 <option value="resample">resample</option>
479 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="(-method) "> 228 <expand macro="list_string_san"/>
480 <option value="legacy">legacy</option> 229 </param>
481 <option value="corrected" selected="true">corrected</option> 230 <param name="add_up_spectra" argument="-Scoring:add_up_spectra" type="integer" optional="true" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
482 <option value="crawdad">crawdad</option> 231 <param name="spacing_for_spectra_resampling" argument="-Scoring:spacing_for_spectra_resampling" type="float" optional="true" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
483 </param> 232 <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="true" value="0" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
484 <param name="param_Scoring_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/> 233 <param name="uis_threshold_peak_area" argument="-Scoring:uis_threshold_peak_area" type="integer" optional="true" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
485 <param name="param_Scoring_DIAScoring_dia_centroided" display="radio" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/> 234 <param name="scoring_model" argument="-Scoring:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help="">
486 <param name="param_Scoring_DIAScoring_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to conside" help="(-dia_byseries_intensity_min) "/> 235 <option value="default" selected="true">default</option>
487 <param name="param_Scoring_DIAScoring_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help="(-dia_byseries_ppm_diff) "/> 236 <option value="single_transition">single_transition</option>
488 <param name="param_Scoring_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/> 237 <expand macro="list_string_san"/>
489 <param name="param_Scoring_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/> 238 </param>
490 <param name="param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff" type="float" min="0.0" optional="True" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help="(-peak_before_mono_max_ppm_diff) "/> 239 <param name="im_extra_drift" argument="-Scoring:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
491 <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/> 240 <section name="TransitionGroupPicker" title="" help="" expanded="false">
492 <expand macro="advanced_options"> 241 <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
493 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) If set, tr_irt may be omitted"/> 242 <param name="min_peak_width" argument="-Scoring:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
494 <param name="param_swath_windows_file" type="data" format="txt" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/> 243 <param name="peak_integration" argument="-Scoring:TransitionGroupPicker:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
495 <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/> 244 <option value="original" selected="true">original</option>
496 <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/> 245 <option value="smoothed">smoothed</option>
497 <param name="param_enable_uis_scoring" display="radio" type="boolean" truevalue="-enable_uis_scoring" falsevalue="" checked="false" optional="True" label="Enable additional scoring of identification assays" help="(-enable_uis_scoring) "/> 246 <expand macro="list_string_san"/>
498 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/> 247 </param>
499 <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/> 248 <param name="background_subtraction" argument="-Scoring:TransitionGroupPicker:background_subtraction" display="radio" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
500 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/> 249 <option value="none" selected="true">none</option>
501 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/> 250 <option value="original">original</option>
502 <param name="param_split_file_input" display="radio" type="boolean" truevalue="-split_file_input" falsevalue="" checked="false" optional="True" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help="(-split_file_input) "/> 251 <option value="exact">exact</option>
503 <param name="param_use_elution_model_score" display="radio" type="boolean" truevalue="-use_elution_model_score" falsevalue="" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score) "/> 252 <expand macro="list_string_san"/>
504 <param name="param_readOptions" display="radio" type="select" optional="False" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="(-readOptions) If you choose cache, make sure to also set tempDirectory"> 253 </param>
254 <param name="recalculate_peaks" argument="-Scoring:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
255 <param name="use_precursors" argument="-Scoring:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
256 <param name="use_consensus" argument="-Scoring:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
257 <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
258 <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
259 <param name="resample_boundary" argument="-Scoring:TransitionGroupPicker:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
260 <param name="compute_peak_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
261 <param name="compute_peak_shape_metrics" argument="-Scoring:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
262 <param name="compute_total_mi" argument="-Scoring:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
263 <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
264 <option value="largest" selected="true">largest</option>
265 <option value="widest">widest</option>
266 <expand macro="list_string_san"/>
267 </param>
268 <section name="PeakPickerMRM" title="" help="" expanded="false">
269 <param name="sgolay_frame_length" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
270 <param name="sgolay_polynomial_order" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
271 <param name="gauss_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" optional="true" value="30.0" label="Gaussian width in seconds, estimated peak size" help=""/>
272 <param name="use_gauss" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
273 <param name="peak_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
274 <param name="signal_to_noise" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
275 <param name="write_sn_log_messages" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
276 <param name="remove_overlapping_peaks" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Try to remove overlapping peaks during peak picking" help=""/>
277 <param name="method" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:method" display="radio" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
278 <option value="legacy">legacy</option>
279 <option value="corrected" selected="true">corrected</option>
280 <option value="crawdad">crawdad</option>
281 <expand macro="list_string_san"/>
282 </param>
283 </section>
284 <section name="PeakIntegrator" title="" help="" expanded="false">
285 <param name="integration_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" display="radio" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
286 <option value="intensity_sum" selected="true">intensity_sum</option>
287 <option value="simpson">simpson</option>
288 <option value="trapezoid">trapezoid</option>
289 <expand macro="list_string_san"/>
290 </param>
291 <param name="baseline_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" display="radio" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
292 <option value="base_to_base" selected="true">base_to_base</option>
293 <option value="vertical_division">vertical_division</option>
294 <option value="vertical_division_min">vertical_division_min</option>
295 <option value="vertical_division_max">vertical_division_max</option>
296 <expand macro="list_string_san"/>
297 </param>
298 <param name="fit_EMG" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/>
299 </section>
300 </section>
301 <section name="DIAScoring" title="" help="" expanded="false">
302 <param name="dia_extraction_window" argument="-Scoring:DIAScoring:dia_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
303 <param name="dia_extraction_unit" argument="-Scoring:DIAScoring:dia_extraction_unit" display="radio" type="select" optional="false" label="DIA extraction window unit" help="">
304 <option value="Th" selected="true">Th</option>
305 <option value="ppm">ppm</option>
306 <expand macro="list_string_san"/>
307 </param>
308 <param name="dia_centroided" argument="-Scoring:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
309 <param name="dia_byseries_intensity_min" argument="-Scoring:DIAScoring:dia_byseries_intensity_min" type="float" optional="true" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
310 <param name="dia_byseries_ppm_diff" argument="-Scoring:DIAScoring:dia_byseries_ppm_diff" type="float" optional="true" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
311 <param name="dia_nr_isotopes" argument="-Scoring:DIAScoring:dia_nr_isotopes" type="integer" optional="true" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
312 <param name="dia_nr_charges" argument="-Scoring:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/>
313 <param name="peak_before_mono_max_ppm_diff" argument="-Scoring:DIAScoring:peak_before_mono_max_ppm_diff" type="float" optional="true" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
314 </section>
315 <section name="EMGScoring" title="" help="" expanded="false">
316 <param name="max_iteration" argument="-Scoring:EMGScoring:max_iteration" type="integer" optional="true" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
317 </section>
318 <section name="Scores" title="" help="" expanded="false">
319 <param name="use_shape_score" argument="-Scoring:Scores:use_shape_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help=""/>
320 <param name="use_coelution_score" argument="-Scoring:Scores:use_coelution_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help=""/>
321 <param name="use_rt_score" argument="-Scoring:Scores:use_rt_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the retention time score (this score measure the difference in retention time)" help=""/>
322 <param name="use_library_score" argument="-Scoring:Scores:use_library_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the library score" help=""/>
323 <param name="use_intensity_score" argument="-Scoring:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/>
324 <param name="use_nr_peaks_score" argument="-Scoring:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/>
325 <param name="use_total_xic_score" argument="-Scoring:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/>
326 <param name="use_total_mi_score" argument="-Scoring:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/>
327 <param name="use_sn_score" argument="-Scoring:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/>
328 <param name="use_mi_score" argument="-Scoring:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/>
329 <param name="use_dia_scores" argument="-Scoring:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/>
330 <param name="use_ms1_correlation" argument="-Scoring:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/>
331 <param name="use_sonar_scores" argument="-Scoring:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/>
332 <param name="use_ion_mobility_scores" argument="-Scoring:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/>
333 <param name="use_ms1_fullscan" argument="-Scoring:Scores:use_ms1_fullscan" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help=""/>
334 <param name="use_ms1_mi" argument="-Scoring:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/>
335 <param name="use_uis_scores" argument="-Scoring:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
336 </section>
337 </section>
338 <expand macro="adv_opts_macro">
339 <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="If set, tr_irt may be omitted select trafoxml data sets(s)"/>
340 <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
341 <param name="sort_swath_maps" argument="-sort_swath_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort input SWATH files when matching to SWATH windows from swath_windows_file" help=""/>
342 <param name="use_ms1_traces" argument="-use_ms1_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the precursor ion trace(s) and use for scoring" help=""/>
343 <param name="enable_uis_scoring" argument="-enable_uis_scoring" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable additional scoring of identification assays" help=""/>
344 <param name="out_chrom_type" type="select" optional="false" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))">
345 <option value="mzML">mzml</option>
346 <option value="sqMass">sqmass</option>
347 </param>
348 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
349 <param name="extra_rt_extraction_window" argument="-extra_rt_extraction_window" type="float" optional="true" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/>
350 <param name="mz_extraction_window_unit" argument="-mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
351 <option value="Th" selected="true">Th</option>
352 <option value="ppm">ppm</option>
353 <expand macro="list_string_san"/>
354 </param>
355 <param name="mz_extraction_window_ms1_unit" argument="-mz_extraction_window_ms1_unit" display="radio" type="select" optional="false" label="Unit of the MS1 m/z extraction window" help="">
356 <option value="ppm">ppm</option>
357 <option value="Th" selected="true">Th</option>
358 <expand macro="list_string_san"/>
359 </param>
360 <param name="use_ms1_ion_mobility" argument="-use_ms1_ion_mobility" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Also perform precursor extraction using the same ion mobility window as for fragment ion extraction" help=""/>
361 <param name="matching_window_only" argument="-matching_window_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows" help="Will only attempt to extract each assay from the *best* matching DIA window (instead of all matching windows)"/>
362 <param name="irt_mz_extraction_window" argument="-irt_mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
363 <param name="irt_mz_extraction_window_unit" argument="-irt_mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
364 <option value="Th" selected="true">Th</option>
365 <option value="ppm">ppm</option>
366 <expand macro="list_string_san"/>
367 </param>
368 <param name="irt_im_extraction_window" argument="-irt_im_extraction_window" type="float" optional="true" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds)" help=""/>
369 <param name="min_rsq" argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
370 <param name="min_coverage" argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
371 <param name="split_file_input" argument="-split_file_input" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help=""/>
372 <param name="use_elution_model_score" argument="-use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Turn on elution model score (EMG fit to peak)" help=""/>
373 <param name="readOptions" argument="-readOptions" display="radio" type="select" optional="false" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="If you choose cache, make sure to also set tempDirectory">
505 <option value="normal" selected="true">normal</option> 374 <option value="normal" selected="true">normal</option>
506 <option value="cache">cache</option> 375 <option value="cache">cache</option>
507 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option> 376 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
508 <option value="workingInMemory">workingInMemory</option> 377 <option value="workingInMemory">workingInMemory</option>
509 </param> 378 <expand macro="list_string_san"/>
510 <param name="param_mz_correction_function" type="select" optional="False" value="none" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="(-mz_correction_function) "> 379 </param>
380 <param name="mz_correction_function" argument="-mz_correction_function" type="select" optional="false" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="">
511 <option value="none" selected="true">none</option> 381 <option value="none" selected="true">none</option>
382 <option value="regression_delta_ppm">regression_delta_ppm</option>
512 <option value="unweighted_regression">unweighted_regression</option> 383 <option value="unweighted_regression">unweighted_regression</option>
513 <option value="weighted_regression">weighted_regression</option> 384 <option value="weighted_regression">weighted_regression</option>
514 <option value="quadratic_regression">quadratic_regression</option> 385 <option value="quadratic_regression">quadratic_regression</option>
515 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option> 386 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option>
516 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option> 387 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option>
517 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option> 388 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
518 </param> 389 <expand macro="list_string_san"/>
519 <param name="param_irt_mz_extraction_window" type="float" value="0.05" label="Extraction window used for iRT and m/z correction (in Thomson, use ppm use -ppm flag)" help="(-irt_mz_extraction_window) "/> 390 </param>
520 <param name="param_ppm_irtwindow" display="radio" type="boolean" truevalue="-ppm_irtwindow" falsevalue="" checked="false" optional="True" label="iRT m/z extraction_window is in ppm" help="(-ppm_irtwindow) "/> 391 <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help="">
521 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
522 <sanitizer>
523 <valid initial="string.printable">
524 <remove value="'"/>
525 <remove value="&quot;"/>
526 </valid>
527 </sanitizer>
528 </param>
529 <param name="param_extraction_function" display="radio" type="select" optional="False" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
530 <option value="tophat" selected="true">tophat</option> 392 <option value="tophat" selected="true">tophat</option>
531 <option value="bartlett">bartlett</option> 393 <option value="bartlett">bartlett</option>
532 </param> 394 <expand macro="list_string_san"/>
533 <param name="param_batchSize" type="integer" min="0" optional="True" value="0" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 500-1000)" help="(-batchSize) "/> 395 </param>
534 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 396 <param name="batchSize" argument="-batchSize" type="integer" optional="true" min="0" value="250" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
535 <param name="param_Library_retentionTimeInterpretation" display="radio" type="select" optional="False" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) "> 397 <param name="ms1_isotopes" argument="-ms1_isotopes" type="integer" optional="true" min="0" value="0" label="The number of MS1 isotopes used for extraction" help=""/>
536 <option value="iRT" selected="true">iRT</option> 398 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
537 <option value="seconds">seconds</option> 399 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
538 <option value="minutes">minutes</option> 400 <expand macro="list_string_san"/>
539 </param> 401 </param>
540 <param name="param_Library_override_group_label_check" display="radio" type="boolean" truevalue="-Library:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
541 <param name="param_Library_force_invalid_mods" display="radio" type="boolean" truevalue="-Library:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/>
542 <param name="param_Scoring_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff) "/>
543 <param name="param_Scoring_write_convex_hull" display="radio" type="boolean" truevalue="-Scoring:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/>
544 <param name="param_Scoring_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
545 <param name="param_Scoring_TransitionGroupPicker_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>
546 <param name="param_Scoring_Scores_use_shape_score" display="radio" type="select" optional="False" value="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) ">
547 <option value="true" selected="true">true</option>
548 <option value="false">false</option>
549 </param>
550 <param name="param_Scoring_Scores_use_coelution_score" display="radio" type="select" optional="False" value="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) ">
551 <option value="true" selected="true">true</option>
552 <option value="false">false</option>
553 </param>
554 <param name="param_Scoring_Scores_use_rt_score" display="radio" type="select" optional="False" value="true" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score) ">
555 <option value="true" selected="true">true</option>
556 <option value="false">false</option>
557 </param>
558 <param name="param_Scoring_Scores_use_library_score" display="radio" type="select" optional="False" value="true" label="Use the library score" help="(-use_library_score) ">
559 <option value="true" selected="true">true</option>
560 <option value="false">false</option>
561 </param>
562 <param name="param_Scoring_Scores_use_intensity_score" display="radio" type="select" optional="False" value="true" label="Use the intensity score" help="(-use_intensity_score) ">
563 <option value="true" selected="true">true</option>
564 <option value="false">false</option>
565 </param>
566 <param name="param_Scoring_Scores_use_nr_peaks_score" display="radio" type="select" optional="False" value="true" label="Use the number of peaks score" help="(-use_nr_peaks_score) ">
567 <option value="true" selected="true">true</option>
568 <option value="false">false</option>
569 </param>
570 <param name="param_Scoring_Scores_use_total_xic_score" display="radio" type="select" optional="False" value="true" label="Use the total XIC score" help="(-use_total_xic_score) ">
571 <option value="true" selected="true">true</option>
572 <option value="false">false</option>
573 </param>
574 <param name="param_Scoring_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) ">
575 <option value="true" selected="true">true</option>
576 <option value="false">false</option>
577 </param>
578 <param name="param_Scoring_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">
579 <option value="true" selected="true">true</option>
580 <option value="false">false</option>
581 </param>
582 <param name="param_Scoring_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
583 <param name="param_Scoring_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>
584 <param name="param_Scoring_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-Scoring: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) "/>
585 <param name="param_Scoring_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
586 </expand> 402 </expand>
403 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
404 <option value="out_features_FLAG">out_features (Use UIS scores for peptidoform identification)</option>
405 <option value="out_tsv_FLAG">out_tsv (Use UIS scores for peptidoform identification)</option>
406 <option value="out_osw_FLAG">out_osw (Use UIS scores for peptidoform identification)</option>
407 <option value="out_chrom_FLAG">out_chrom (Use UIS scores for peptidoform identification)</option>
408 <option value="out_qc_FLAG">out_qc (Use UIS scores for peptidoform identification)</option>
409 <option value="irt_mzml_FLAG">irt_mzml (Use UIS scores for peptidoform identification)</option>
410 <option value="irt_trafo_FLAG">irt_trafo (Use UIS scores for peptidoform identification)</option>
411 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
412 </param>
587 </inputs> 413 </inputs>
588 <outputs> 414 <outputs>
589 <data name="param_out_features" format="featurexml"/> 415 <data name="out_features" label="${tool.name} on ${on_string}: out_features" format="featurexml">
590 <data name="param_out_tsv" format="tabular"/> 416 <filter>OPTIONAL_OUTPUTS is not None and "out_features_FLAG" in OPTIONAL_OUTPUTS</filter>
591 <data name="param_out_osw" format="osw"/> 417 </data>
592 <data name="param_out_chrom" format="mzml"/> 418 <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="tabular">
419 <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter>
420 </data>
421 <data name="out_osw" label="${tool.name} on ${on_string}: out_osw" format="osw">
422 <filter>OPTIONAL_OUTPUTS is not None and "out_osw_FLAG" in OPTIONAL_OUTPUTS</filter>
423 </data>
424 <data name="out_chrom" label="${tool.name} on ${on_string}: out_chrom">
425 <change_format>
426 <when input="adv_opts_cond.out_chrom_type" value="mzML" format="mzml"/>
427 <when input="adv_opts_cond.out_chrom_type" value="sqMass" format="sqmass"/>
428 </change_format>
429 <filter>OPTIONAL_OUTPUTS is not None and "out_chrom_FLAG" in OPTIONAL_OUTPUTS</filter>
430 </data>
431 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
432 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
433 </data>
434 <data name="Debugging_irt_mzml" label="${tool.name} on ${on_string}: Debugging:irt_mzml" format="mzml">
435 <filter>OPTIONAL_OUTPUTS is not None and "irt_mzml_FLAG" in OPTIONAL_OUTPUTS</filter>
436 </data>
437 <data name="Debugging_irt_trafo" label="${tool.name} on ${on_string}: Debugging:irt_trafo" format="trafoxml">
438 <filter>OPTIONAL_OUTPUTS is not None and "irt_trafo_FLAG" in OPTIONAL_OUTPUTS</filter>
439 </data>
440 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
441 <filter>OPTIONAL_OUTPUTS is None</filter>
442 </data>
443 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
444 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
445 </data>
593 </outputs> 446 </outputs>
594 <help>Complete workflow to run OpenSWATH 447 <tests>
595 448 <expand macro="autotest_OpenSwathWorkflow"/>
596 449 <expand macro="manutest_OpenSwathWorkflow"/>
597 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathWorkflow.html</help> 450 </tests>
451 <help><![CDATA[Complete workflow to run OpenSWATH
452
453
454 For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathWorkflow.html]]></help>
455 <expand macro="references"/>
598 </tool> 456 </tool>