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comparison OpenSwathAnalyzer.xml @ 9:bc57c90ba60f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:14:25 +0000
parents 9f0a3a6b5df6
children 7ca917175b23
comparison
equal deleted inserted replaced
8:a2a6e9551046 9:bc57c90ba60f
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="&quot;"/>
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) &lt;br&gt;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>