Mercurial > repos > galaxyp > openms_openswathanalyzer
comparison OpenSwathAnalyzer.xml @ 9:bc57c90ba60f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 20:14:25 +0000 |
parents | 9f0a3a6b5df6 |
children | 7ca917175b23 |
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8:a2a6e9551046 | 9:bc57c90ba60f |
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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: [Targeted Experiments]--> | 3 <!--Proposed Tool Section: [Targeted Experiments]--> |
4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.3.0"> | 4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description> | 5 <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token> | 7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <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[OpenSwathAnalyzer | 15 @EXT_FOO@ |
14 | 16 #import re |
15 #if $param_in: | 17 |
16 -in $param_in | 18 ## Preprocessing |
17 #end if | 19 mkdir in && |
18 #if $param_tr: | 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
19 -tr $param_tr | 21 mkdir tr && |
20 #end if | 22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && |
21 #if $param_rt_norm: | 23 #if $rt_norm: |
22 -rt_norm $param_rt_norm | 24 mkdir rt_norm && |
23 #end if | 25 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && |
24 #if $param_out: | 26 #end if |
25 -out $param_out | 27 mkdir out && |
26 #end if | 28 #if $swath_files: |
27 #if $param_no_strict: | 29 mkdir swath_files && |
28 -no-strict | 30 ${ ' '.join(["ln -s '%s' 'swath_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _]) } |
29 #end if | 31 #end if |
30 -swath_files | 32 |
31 #for token in $param_swath_files: | 33 ## Main program call |
32 $token | 34 |
33 #end for | 35 set -o pipefail && |
34 #if $param_min_upper_edge_dist: | 36 @EXECUTABLE@ -write_ctd ./ && |
35 -min_upper_edge_dist $param_min_upper_edge_dist | 37 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
36 #end if | 38 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
37 #if $param_algorithm_stop_report_after_feature: | 39 -in |
38 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature | 40 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
39 #end if | 41 -tr |
40 #if $param_algorithm_rt_extraction_window: | 42 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' |
41 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window | 43 #if $rt_norm: |
42 #end if | 44 -rt_norm |
43 #if $param_algorithm_rt_normalization_factor: | 45 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' |
44 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor | 46 #end if |
45 #end if | 47 -out |
46 #if $param_algorithm_uis_threshold_sn: | 48 'out/output.${gxy2omsext("featurexml")}' |
47 -algorithm:uis_threshold_sn $param_algorithm_uis_threshold_sn | 49 #if $swath_files: |
48 #end if | 50 -swath_files |
49 #if $param_algorithm_uis_threshold_peak_area: | 51 ${' '.join(["'swath_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])} |
50 -algorithm:uis_threshold_peak_area $param_algorithm_uis_threshold_peak_area | 52 #end if |
51 #end if | 53 |
52 #if $param_algorithm_TransitionGroupPicker_stop_after_feature: | 54 ## Postprocessing |
53 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature | 55 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' |
54 #end if | 56 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
55 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio: | 57 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
56 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio | 58 #end if]]></command> |
57 #end if | 59 <configfiles> |
58 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: | 60 <inputs name="args_json" data_style="paths"/> |
59 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length | 61 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
60 #end if | 62 </configfiles> |
61 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: | |
62 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order | |
63 #end if | |
64 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width: | |
65 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width | |
66 #end if | |
67 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss: | |
68 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss | |
69 #if " " in str($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 | |
74 #end if | |
75 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width: | |
76 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width | |
77 #end if | |
78 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise: | |
79 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise | |
80 #end if | |
81 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len: | |
82 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len | |
83 #end if | |
84 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count: | |
85 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count | |
86 #end if | |
87 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: | |
88 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages | |
89 #if " " in str($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 | |
94 #end if | |
95 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: | |
96 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks | |
97 #end if | |
98 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method: | |
99 -algorithm:TransitionGroupPicker:PeakPickerMRM:method | |
100 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method): | |
101 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" | |
102 #else | |
103 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method | |
104 #end if | |
105 #end if | |
106 #if $param_algorithm_DIAScoring_dia_extraction_window: | |
107 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window | |
108 #end if | |
109 #if $param_algorithm_DIAScoring_dia_centroided: | |
110 -algorithm:DIAScoring:dia_centroided | |
111 #end if | |
112 #if $param_algorithm_DIAScoring_dia_byseries_intensity_min: | |
113 -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min | |
114 #end if | |
115 #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff: | |
116 -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff | |
117 #end if | |
118 #if $param_algorithm_DIAScoring_dia_nr_isotopes: | |
119 -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes | |
120 #end if | |
121 #if $param_algorithm_DIAScoring_dia_nr_charges: | |
122 -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges | |
123 #end if | |
124 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff: | |
125 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff | |
126 #end if | |
127 #if $adv_opts.adv_opts_selector=='advanced': | |
128 #if $adv_opts.param_force: | |
129 -force | |
130 #end if | |
131 #if $adv_opts.param_model_type: | |
132 -model:type | |
133 #if " " in str($adv_opts.param_model_type): | |
134 "$adv_opts.param_model_type" | |
135 #else | |
136 $adv_opts.param_model_type | |
137 #end if | |
138 #end if | |
139 #if $adv_opts.param_model_symmetric_regression: | |
140 -model:symmetric_regression | |
141 #end if | |
142 #if $adv_opts.param_algorithm_quantification_cutoff: | |
143 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff | |
144 #end if | |
145 #if $adv_opts.param_algorithm_write_convex_hull: | |
146 -algorithm:write_convex_hull | |
147 #end if | |
148 #if $adv_opts.param_algorithm_add_up_spectra: | |
149 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra | |
150 #end if | |
151 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling: | |
152 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling | |
153 #end if | |
154 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width: | |
155 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width | |
156 #end if | |
157 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction: | |
158 -algorithm:TransitionGroupPicker:background_subtraction | |
159 #if " " in str($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 | |
164 #end if | |
165 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: | |
166 -algorithm:TransitionGroupPicker:recalculate_peaks | |
167 #end if | |
168 #if $adv_opts.param_algorithm_TransitionGroupPicker_use_precursors: | |
169 -algorithm:TransitionGroupPicker:use_precursors | |
170 #end if | |
171 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: | |
172 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z | |
173 #end if | |
174 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality: | |
175 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality | |
176 #end if | |
177 #if $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary: | |
178 -algorithm:TransitionGroupPicker:resample_boundary $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary | |
179 #end if | |
180 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality: | |
181 -algorithm:TransitionGroupPicker:compute_peak_quality | |
182 #end if | |
183 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step: | |
184 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step | |
185 #end if | |
186 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box: | |
187 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box | |
188 #end if | |
189 #if $adv_opts.param_algorithm_EMGScoring_max_iteration: | |
190 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration | |
191 #end if | |
192 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean: | |
193 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean | |
194 #end if | |
195 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance: | |
196 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance | |
197 #end if | |
198 #if $adv_opts.param_algorithm_Scores_use_shape_score: | |
199 -algorithm:Scores:use_shape_score | |
200 #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score): | |
201 "$adv_opts.param_algorithm_Scores_use_shape_score" | |
202 #else | |
203 $adv_opts.param_algorithm_Scores_use_shape_score | |
204 #end if | |
205 #end if | |
206 #if $adv_opts.param_algorithm_Scores_use_coelution_score: | |
207 -algorithm:Scores:use_coelution_score | |
208 #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score): | |
209 "$adv_opts.param_algorithm_Scores_use_coelution_score" | |
210 #else | |
211 $adv_opts.param_algorithm_Scores_use_coelution_score | |
212 #end if | |
213 #end if | |
214 #if $adv_opts.param_algorithm_Scores_use_rt_score: | |
215 -algorithm:Scores:use_rt_score | |
216 #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score): | |
217 "$adv_opts.param_algorithm_Scores_use_rt_score" | |
218 #else | |
219 $adv_opts.param_algorithm_Scores_use_rt_score | |
220 #end if | |
221 #end if | |
222 #if $adv_opts.param_algorithm_Scores_use_library_score: | |
223 -algorithm:Scores:use_library_score | |
224 #if " " in str($adv_opts.param_algorithm_Scores_use_library_score): | |
225 "$adv_opts.param_algorithm_Scores_use_library_score" | |
226 #else | |
227 $adv_opts.param_algorithm_Scores_use_library_score | |
228 #end if | |
229 #end if | |
230 #if $adv_opts.param_algorithm_Scores_use_elution_model_score: | |
231 -algorithm:Scores:use_elution_model_score | |
232 #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score): | |
233 "$adv_opts.param_algorithm_Scores_use_elution_model_score" | |
234 #else | |
235 $adv_opts.param_algorithm_Scores_use_elution_model_score | |
236 #end if | |
237 #end if | |
238 #if $adv_opts.param_algorithm_Scores_use_intensity_score: | |
239 -algorithm:Scores:use_intensity_score | |
240 #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score): | |
241 "$adv_opts.param_algorithm_Scores_use_intensity_score" | |
242 #else | |
243 $adv_opts.param_algorithm_Scores_use_intensity_score | |
244 #end if | |
245 #end if | |
246 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: | |
247 -algorithm:Scores:use_nr_peaks_score | |
248 #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score): | |
249 "$adv_opts.param_algorithm_Scores_use_nr_peaks_score" | |
250 #else | |
251 $adv_opts.param_algorithm_Scores_use_nr_peaks_score | |
252 #end if | |
253 #end if | |
254 #if $adv_opts.param_algorithm_Scores_use_total_xic_score: | |
255 -algorithm:Scores:use_total_xic_score | |
256 #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score): | |
257 "$adv_opts.param_algorithm_Scores_use_total_xic_score" | |
258 #else | |
259 $adv_opts.param_algorithm_Scores_use_total_xic_score | |
260 #end if | |
261 #end if | |
262 #if $adv_opts.param_algorithm_Scores_use_sn_score: | |
263 -algorithm:Scores:use_sn_score | |
264 #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score): | |
265 "$adv_opts.param_algorithm_Scores_use_sn_score" | |
266 #else | |
267 $adv_opts.param_algorithm_Scores_use_sn_score | |
268 #end if | |
269 #end if | |
270 #if $adv_opts.param_algorithm_Scores_use_dia_scores: | |
271 -algorithm:Scores:use_dia_scores | |
272 #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores): | |
273 "$adv_opts.param_algorithm_Scores_use_dia_scores" | |
274 #else | |
275 $adv_opts.param_algorithm_Scores_use_dia_scores | |
276 #end if | |
277 #end if | |
278 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: | |
279 -algorithm:Scores:use_ms1_correlation | |
280 #end if | |
281 #if $adv_opts.param_algorithm_Scores_use_sonar_scores: | |
282 -algorithm:Scores:use_sonar_scores | |
283 #end if | |
284 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: | |
285 -algorithm:Scores:use_ms1_fullscan | |
286 #end if | |
287 #if $adv_opts.param_algorithm_Scores_use_uis_scores: | |
288 -algorithm:Scores:use_uis_scores | |
289 #end if | |
290 #end if | |
291 ]]></command> | |
292 <inputs> | 63 <inputs> |
293 <param name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/> | 64 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file containing the chromatograms" help=" select mzml data sets(s)"/> |
294 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/> | 65 <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/> |
295 <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) "/> | 66 <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=" select trafoxml data sets(s)"/> |
296 <param name="param_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/> | 67 <param name="no_strict" argument="-no-strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="run in non-strict mode and allow some chromatograms to not be mapped" help=""/> |
297 <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be used"> | 68 <param name="swath_files" argument="-swath_files" type="data" format="mzml" multiple="true" optional="true" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be used select mzml data sets(s)"/> |
298 <sanitizer> | 69 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/> |
299 <valid initial="string.printable"> | 70 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false"> |
300 <remove value="'"/> | 71 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help=""> |
301 <remove value="""/> | |
302 </valid> | |
303 </sanitizer> | |
304 </param> | |
305 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/> | |
306 <param name="param_algorithm_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) "/> | |
307 <param name="param_algorithm_rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values"/> | |
308 <param name="param_algorithm_rt_normalization_factor" type="float" value="1.0" 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)"/> | |
309 <param name="param_algorithm_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) "/> | |
310 <param name="param_algorithm_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) "/> | |
311 <param name="param_algorithm_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) "/> | |
312 <param name="param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/> | |
313 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) <br>This number has to be uneven. If it is not, 1 will be added"/> | |
314 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/> | |
315 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> | |
316 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "> | |
317 <option value="false">false</option> | |
318 <option value="true" selected="true">true</option> | |
319 </param> | |
320 <param name="param_algorithm_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"/> | |
321 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" 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"/> | |
322 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/> | |
323 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/> | |
324 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="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) "> | |
325 <option value="true" selected="true">true</option> | |
326 <option value="false">false</option> | |
327 </param> | |
328 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/> | |
329 <param name="param_algorithm_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) "> | |
330 <option value="legacy">legacy</option> | |
331 <option value="corrected" selected="true">corrected</option> | |
332 <option value="crawdad">crawdad</option> | |
333 </param> | |
334 <param name="param_algorithm_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/> | |
335 <param name="param_algorithm_DIAScoring_dia_centroided" display="radio" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/> | |
336 <param name="param_algorithm_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) "/> | |
337 <param name="param_algorithm_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) "/> | |
338 <param name="param_algorithm_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/> | |
339 <param name="param_algorithm_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/> | |
340 <param name="param_algorithm_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) "/> | |
341 <expand macro="advanced_options"> | |
342 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
343 <param name="param_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) "> | |
344 <option value="linear" selected="true">linear</option> | 72 <option value="linear" selected="true">linear</option> |
345 <option value="b_spline">b_spline</option> | 73 <option value="b_spline">b_spline</option> |
346 <option value="interpolated">interpolated</option> | 74 <option value="interpolated">interpolated</option> |
347 <option value="lowess">lowess</option> | 75 <option value="lowess">lowess</option> |
348 </param> | 76 <expand macro="list_string_san"/> |
349 <param name="param_model_symmetric_regression" display="radio" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/> | 77 </param> |
350 <param name="param_algorithm_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) "/> | 78 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/> |
351 <param name="param_algorithm_write_convex_hull" display="radio" type="boolean" truevalue="-algorithm: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) "/> | 79 </section> |
352 <param name="param_algorithm_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra) "/> | 80 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
353 <param name="param_algorithm_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling) "/> | 81 <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" optional="true" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/> |
354 <param name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/> | 82 <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" optional="true" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="For this to work, the TraML input file needs to contain normalized RT values"/> |
355 <param name="param_algorithm_TransitionGroupPicker_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that"> | 83 <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" optional="true" value="1.0" 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)"/> |
356 <option value="none" selected="true">none</option> | 84 <param name="quantification_cutoff" argument="-algorithm: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=""/> |
357 <option value="smoothed">smoothed</option> | 85 <param name="write_convex_hull" argument="-algorithm: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=""/> |
358 <option value="original">original</option> | 86 <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" display="radio" type="select" optional="false" label="For spectrum addition, either use simple concatenation or use peak resampling" help=""> |
359 </param> | 87 <option value="simple" selected="true">simple</option> |
360 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/> | 88 <option value="resample">resample</option> |
361 <param name="param_algorithm_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/> | 89 <expand macro="list_string_san"/> |
362 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> | 90 </param> |
363 <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> | 91 <param name="add_up_spectra" argument="-algorithm: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=""/> |
364 <param name="param_algorithm_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) "/> | 92 <param name="spacing_for_spectra_resampling" argument="-algorithm: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=""/> |
365 <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/> | 93 <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" optional="true" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/> |
366 <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/> | 94 <param name="uis_threshold_peak_area" argument="-algorithm: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=""/> |
367 <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/> | 95 <param name="scoring_model" argument="-algorithm:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help=""> |
368 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/> | 96 <option value="default" selected="true">default</option> |
369 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/> | 97 <option value="single_transition">single_transition</option> |
370 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/> | 98 <expand macro="list_string_san"/> |
371 <param name="param_algorithm_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) "> | 99 </param> |
372 <option value="true" selected="true">true</option> | 100 <param name="im_extra_drift" argument="-algorithm: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)"/> |
373 <option value="false">false</option> | 101 <section name="TransitionGroupPicker" title="" help="" expanded="false"> |
374 </param> | 102 <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/> |
375 <param name="param_algorithm_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) "> | 103 <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/> |
376 <option value="true" selected="true">true</option> | 104 <param name="min_peak_width" argument="-algorithm: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=""/> |
377 <option value="false">false</option> | 105 <param name="peak_integration" argument="-algorithm: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=""> |
378 </param> | 106 <option value="original" selected="true">original</option> |
379 <param name="param_algorithm_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) "> | 107 <option value="smoothed">smoothed</option> |
380 <option value="true" selected="true">true</option> | 108 <expand macro="list_string_san"/> |
381 <option value="false">false</option> | 109 </param> |
382 </param> | 110 <param name="background_subtraction" argument="-algorithm: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"> |
383 <param name="param_algorithm_Scores_use_library_score" display="radio" type="select" optional="False" value="true" label="Use the library score" help="(-use_library_score) "> | 111 <option value="none" selected="true">none</option> |
384 <option value="true" selected="true">true</option> | 112 <option value="original">original</option> |
385 <option value="false">false</option> | 113 <option value="exact">exact</option> |
386 </param> | 114 <expand macro="list_string_san"/> |
387 <param name="param_algorithm_Scores_use_elution_model_score" display="radio" type="select" optional="False" value="true" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score) "> | 115 </param> |
388 <option value="true" selected="true">true</option> | 116 <param name="recalculate_peaks" argument="-algorithm:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" 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"/> |
389 <option value="false">false</option> | 117 <param name="use_precursors" argument="-algorithm: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=""/> |
390 </param> | 118 <param name="use_consensus" argument="-algorithm: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=""/> |
391 <param name="param_algorithm_Scores_use_intensity_score" display="radio" type="select" optional="False" value="true" label="Use the intensity score" help="(-use_intensity_score) "> | 119 <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="1.0" 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)"/> |
392 <option value="true" selected="true">true</option> | 120 <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/> |
393 <option value="false">false</option> | 121 <param name="resample_boundary" argument="-algorithm: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=""/> |
394 </param> | 122 <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" 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"/> |
395 <param name="param_algorithm_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) "> | 123 <param name="compute_peak_shape_metrics" argument="-algorithm: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"/> |
396 <option value="true" selected="true">true</option> | 124 <param name="compute_total_mi" argument="-algorithm: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=""/> |
397 <option value="false">false</option> | 125 <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help=""> |
398 </param> | 126 <option value="largest" selected="true">largest</option> |
399 <param name="param_algorithm_Scores_use_total_xic_score" display="radio" type="select" optional="False" value="true" label="Use the total XIC score" help="(-use_total_xic_score) "> | 127 <option value="widest">widest</option> |
400 <option value="true" selected="true">true</option> | 128 <expand macro="list_string_san"/> |
401 <option value="false">false</option> | 129 </param> |
402 </param> | 130 <section name="PeakPickerMRM" title="" help="" expanded="false"> |
403 <param name="param_algorithm_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) "> | 131 <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" 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"/> |
404 <option value="true" selected="true">true</option> | 132 <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/> |
405 <option value="false">false</option> | 133 <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/> |
406 </param> | 134 <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/> |
407 <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) If turned off, will not use fragment ion spectra for scoring"> | 135 <param name="peak_width" argument="-algorithm: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"/> |
408 <option value="true" selected="true">true</option> | 136 <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" 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"/> |
409 <option value="false">false</option> | 137 <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/> |
410 </param> | 138 <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/> |
411 <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/> | 139 <param name="write_sn_log_messages" argument="-algorithm: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=""/> |
412 <param name="param_algorithm_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/> | 140 <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/> |
413 <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/> | 141 <param name="method" argument="-algorithm: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=""> |
414 <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/> | 142 <option value="legacy">legacy</option> |
143 <option value="corrected" selected="true">corrected</option> | |
144 <option value="crawdad">crawdad</option> | |
145 <expand macro="list_string_san"/> | |
146 </param> | |
147 </section> | |
148 <section name="PeakIntegrator" title="" help="" expanded="false"> | |
149 <param name="integration_type" argument="-algorithm: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=""> | |
150 <option value="intensity_sum" selected="true">intensity_sum</option> | |
151 <option value="simpson">simpson</option> | |
152 <option value="trapezoid">trapezoid</option> | |
153 <expand macro="list_string_san"/> | |
154 </param> | |
155 <param name="baseline_type" argument="-algorithm: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)"> | |
156 <option value="base_to_base" selected="true">base_to_base</option> | |
157 <option value="vertical_division">vertical_division</option> | |
158 <option value="vertical_division_min">vertical_division_min</option> | |
159 <option value="vertical_division_max">vertical_division_max</option> | |
160 <expand macro="list_string_san"/> | |
161 </param> | |
162 <param name="fit_EMG" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/> | |
163 </section> | |
164 </section> | |
165 <section name="DIAScoring" title="" help="" expanded="false"> | |
166 <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/> | |
167 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" display="radio" type="select" optional="false" label="DIA extraction window unit" help=""> | |
168 <option value="Th" selected="true">Th</option> | |
169 <option value="ppm">ppm</option> | |
170 <expand macro="list_string_san"/> | |
171 </param> | |
172 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/> | |
173 <param name="dia_byseries_intensity_min" argument="-algorithm: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=""/> | |
174 <param name="dia_byseries_ppm_diff" argument="-algorithm: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=""/> | |
175 <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" optional="true" min="0" value="4" label="DIA number of isotopes to conside" help=""/> | |
176 <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/> | |
177 <param name="peak_before_mono_max_ppm_diff" argument="-algorithm: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=""/> | |
178 </section> | |
179 <section name="EMGScoring" title="" help="" expanded="false"> | |
180 <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" optional="true" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/> | |
181 <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" optional="true" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help=""/> | |
182 <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" optional="true" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/> | |
183 <section name="statistics" title="" help="" expanded="false"> | |
184 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/> | |
185 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/> | |
186 </section> | |
187 </section> | |
188 <section name="Scores" title="" help="" expanded="false"> | |
189 <param name="use_shape_score" argument="-algorithm: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=""/> | |
190 <param name="use_coelution_score" argument="-algorithm: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=""/> | |
191 <param name="use_rt_score" argument="-algorithm: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=""/> | |
192 <param name="use_library_score" argument="-algorithm:Scores:use_library_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the library score" help=""/> | |
193 <param name="use_elution_model_score" argument="-algorithm:Scores:use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help=""/> | |
194 <param name="use_intensity_score" argument="-algorithm:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/> | |
195 <param name="use_nr_peaks_score" argument="-algorithm:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/> | |
196 <param name="use_total_xic_score" argument="-algorithm:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/> | |
197 <param name="use_total_mi_score" argument="-algorithm:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/> | |
198 <param name="use_sn_score" argument="-algorithm:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/> | |
199 <param name="use_mi_score" argument="-algorithm:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/> | |
200 <param name="use_dia_scores" argument="-algorithm: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"/> | |
201 <param name="use_ms1_correlation" argument="-algorithm:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/> | |
202 <param name="use_sonar_scores" argument="-algorithm:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/> | |
203 <param name="use_ion_mobility_scores" argument="-algorithm:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/> | |
204 <param name="use_ms1_fullscan" argument="-algorithm: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=""/> | |
205 <param name="use_ms1_mi" argument="-algorithm:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/> | |
206 <param name="use_uis_scores" argument="-algorithm:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/> | |
207 </section> | |
208 </section> | |
209 <expand macro="adv_opts_macro"> | |
210 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
211 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
212 <expand macro="list_string_san"/> | |
213 </param> | |
415 </expand> | 214 </expand> |
215 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
216 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
217 </param> | |
416 </inputs> | 218 </inputs> |
417 <outputs> | 219 <outputs> |
418 <data name="param_out" format="featurexml"/> | 220 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> |
221 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
222 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
223 </data> | |
419 </outputs> | 224 </outputs> |
420 <help>Picks peaks and finds features in an SWATH-MS or SRM experiment. | 225 <tests> |
421 | 226 <expand macro="autotest_OpenSwathAnalyzer"/> |
422 | 227 <expand macro="manutest_OpenSwathAnalyzer"/> |
423 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathAnalyzer.html</help> | 228 </tests> |
229 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment. | |
230 | |
231 | |
232 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathAnalyzer.html]]></help> | |
233 <expand macro="references"/> | |
424 </tool> | 234 </tool> |