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comparison OpenSwathAnalyzer.xml @ 0:addd804ac6c6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 10:20:07 -0500
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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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.1.0">
5 <description>Picks peaks and finds features in an SRM experiment.</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathAnalyzer
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_tr:
19 -tr $param_tr
20 #end if
21 #if $param_rt_norm:
22 -rt_norm $param_rt_norm
23 #end if
24 #if $param_out:
25 -out $param_out
26 #end if
27 #if $param_no_strict:
28 -no-strict
29 #end if
30 -swath_files
31 #for token in $param_swath_files:
32 $token
33 #end for
34 #if $param_min_upper_edge_dist:
35 -min_upper_edge_dist $param_min_upper_edge_dist
36 #end if
37 #if $param_algorithm_stop_report_after_feature:
38 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
39 #end if
40 #if $param_algorithm_rt_extraction_window:
41 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
42 #end if
43 #if $param_algorithm_rt_normalization_factor:
44 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
45 #end if
46 #if $param_algorithm_uis_threshold_sn:
47 -algorithm:uis_threshold_sn $param_algorithm_uis_threshold_sn
48 #end if
49 #if $param_algorithm_uis_threshold_peak_area:
50 -algorithm:uis_threshold_peak_area $param_algorithm_uis_threshold_peak_area
51 #end if
52 #if $param_algorithm_TransitionGroupPicker_stop_after_feature:
53 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
54 #end if
55 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
56 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
57 #end if
58 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
59 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
60 #end if
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 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
69 #end if
70 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
71 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
72 #end if
73 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
74 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
75 #end if
76 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
77 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
78 #end if
79 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
80 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
81 #end if
82 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
83 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
84 #end if
85 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
86 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
87 #end if
88 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
89 -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
90 #end if
91 #if $param_algorithm_DIAScoring_dia_extraction_window:
92 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
93 #end if
94 #if $param_algorithm_DIAScoring_dia_centroided:
95 -algorithm:DIAScoring:dia_centroided
96 #end if
97 #if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
98 -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
99 #end if
100 #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
101 -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
102 #end if
103 #if $param_algorithm_DIAScoring_dia_nr_isotopes:
104 -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
105 #end if
106 #if $param_algorithm_DIAScoring_dia_nr_charges:
107 -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
108 #end if
109 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
110 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
111 #end if
112 #if $adv_opts.adv_opts_selector=='advanced':
113 #if $adv_opts.param_force:
114 -force
115 #end if
116 #if $adv_opts.param_model_type:
117 -model:type $adv_opts.param_model_type
118 #end if
119 #if $adv_opts.param_model_symmetric_regression:
120 -model:symmetric_regression
121 #end if
122 #if $adv_opts.param_algorithm_quantification_cutoff:
123 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
124 #end if
125 #if $adv_opts.param_algorithm_write_convex_hull:
126 -algorithm:write_convex_hull
127 #end if
128 #if $adv_opts.param_algorithm_add_up_spectra:
129 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
130 #end if
131 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
132 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
133 #end if
134 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
135 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
136 #end if
137 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
138 -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
139 #end if
140 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
141 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
142 #end if
143 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
144 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
145 #end if
146 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
147 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
148 #end if
149 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
150 -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
151 #end if
152 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
153 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
154 #end if
155 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
156 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
157 #end if
158 #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
159 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
160 #end if
161 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
162 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
163 #end if
164 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
165 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
166 #end if
167 #if $adv_opts.param_algorithm_Scores_use_shape_score:
168 -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score
169 #end if
170 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
171 -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score
172 #end if
173 #if $adv_opts.param_algorithm_Scores_use_rt_score:
174 -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score
175 #end if
176 #if $adv_opts.param_algorithm_Scores_use_library_score:
177 -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score
178 #end if
179 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
180 -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score
181 #end if
182 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
183 -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score
184 #end if
185 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
186 -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score
187 #end if
188 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
189 -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score
190 #end if
191 #if $adv_opts.param_algorithm_Scores_use_sn_score:
192 -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score
193 #end if
194 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
195 -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores
196 #end if
197 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
198 -algorithm:Scores:use_ms1_correlation
199 #end if
200 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
201 -algorithm:Scores:use_ms1_fullscan
202 #end if
203 #if $adv_opts.param_algorithm_Scores_use_uis_scores:
204 -algorithm:Scores:use_uis_scores
205 #end if
206 #end if
207 </command>
208 <inputs>
209 <param name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/>
210 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
211 <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) "/>
212 <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) "/>
213 <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">
214 <sanitizer>
215 <valid initial="string.printable">
216 <remove value="'"/>
217 <remove value="&quot;"/>
218 </valid>
219 </sanitizer>
220 </param>
221 <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) "/>
222 <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) "/>
223 <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"/>
224 <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)"/>
225 <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) "/>
226 <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) "/>
227 <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) "/>
228 <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) "/>
229 <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"/>
230 <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) "/>
231 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
232 <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) ">
233 <option value="false">false</option>
234 <option value="true" selected="true">true</option>
235 </param>
236 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0" 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"/>
237 <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"/>
238 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
239 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
240 <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) ">
241 <option value="true" selected="true">true</option>
242 <option value="false">false</option>
243 </param>
244 <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) "/>
245 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
246 <option value="legacy" selected="true">legacy</option>
247 <option value="corrected">corrected</option>
248 <option value="crawdad">crawdad</option>
249 </param>
250 <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) "/>
251 <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) "/>
252 <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) "/>
253 <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) "/>
254 <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) "/>
255 <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) "/>
256 <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) "/>
257 <expand macro="advanced_options">
258 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
259 <param name="param_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) ">
260 <option value="linear" selected="true">linear</option>
261 <option value="b_spline">b_spline</option>
262 <option value="interpolated">interpolated</option>
263 <option value="lowess">lowess</option>
264 </param>
265 <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'"/>
266 <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) "/>
267 <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) "/>
268 <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) "/>
269 <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) "/>
270 <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) "/>
271 <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">
272 <option value="none" selected="true">none</option>
273 <option value="smoothed">smoothed</option>
274 <option value="original">original</option>
275 </param>
276 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" 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">
277 <sanitizer>
278 <valid initial="string.printable">
279 <remove value="'"/>
280 <remove value="&quot;"/>
281 </valid>
282 </sanitizer>
283 </param>
284 <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)"/>
285 <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) "/>
286 <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" 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">
287 <sanitizer>
288 <valid initial="string.printable">
289 <remove value="'"/>
290 <remove value="&quot;"/>
291 </valid>
292 </sanitizer>
293 </param>
294 <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) "/>
295 <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) "/>
296 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
297 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
298 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
299 <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) ">
300 <option value="true" selected="true">true</option>
301 <option value="false">false</option>
302 </param>
303 <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) ">
304 <option value="true" selected="true">true</option>
305 <option value="false">false</option>
306 </param>
307 <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) ">
308 <option value="true" selected="true">true</option>
309 <option value="false">false</option>
310 </param>
311 <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) ">
312 <option value="true" selected="true">true</option>
313 <option value="false">false</option>
314 </param>
315 <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) ">
316 <option value="true" selected="true">true</option>
317 <option value="false">false</option>
318 </param>
319 <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) ">
320 <option value="true" selected="true">true</option>
321 <option value="false">false</option>
322 </param>
323 <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) ">
324 <option value="true" selected="true">true</option>
325 <option value="false">false</option>
326 </param>
327 <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) ">
328 <option value="true" selected="true">true</option>
329 <option value="false">false</option>
330 </param>
331 <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) ">
332 <option value="true" selected="true">true</option>
333 <option value="false">false</option>
334 </param>
335 <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) ">
336 <option value="true" selected="true">true</option>
337 <option value="false">false</option>
338 </param>
339 <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) "/>
340 <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) "/>
341 <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) "/>
342 </expand>
343 </inputs>
344 <outputs>
345 <data name="param_out" format="featurexml"/>
346 </outputs>
347 <help>Picks peaks and finds features in an SRM experiment.
348
349
350 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html</help>
351 </tool>