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comparison OpenSwathRTNormalizer.xml @ 13:3a841eba4877 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 22:44:31 +0000
parents 672d03a9794b
children 0200289da8e1
comparison
equal deleted inserted replaced
12:672d03a9794b 13:3a841eba4877
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="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.3.0"> 4 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description> 5 <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token> 7 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</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[OpenSwathRTNormalizer 15 @EXT_FOO@
14 16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
21 mkdir tr &&
22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
23 mkdir out &&
24 #if $rt_norm:
25 mkdir rt_norm &&
26 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
27 #end if
28
29 ## Main program call
30
31 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
15 -in 35 -in
16 #for token in $param_in: 36 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
17 $token 37 -tr
18 #end for 38 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
19 #if $param_tr: 39 -out
20 -tr $param_tr 40 'out/output.${gxy2omsext("trafoxml")}'
41 #if $rt_norm:
42 -rt_norm
43 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
21 #end if 44 #end if
22 #if $param_out: 45
23 -out $param_out 46 ## Postprocessing
24 #end if 47 && mv 'out/output.${gxy2omsext("trafoxml")}' '$out'
25 #if $param_rt_norm: 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
26 -rt_norm $param_rt_norm 49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
27 #end if 50 #end if]]></command>
28 #if $param_min_rsq: 51 <configfiles>
29 -min_rsq $param_min_rsq 52 <inputs name="args_json" data_style="paths"/>
30 #end if 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
31 #if $param_min_coverage: 54 </configfiles>
32 -min_coverage $param_min_coverage
33 #end if
34 #if $param_estimateBestPeptides:
35 -estimateBestPeptides
36 #end if
37 #if $param_RTNormalization_outlierMethod:
38 -RTNormalization:outlierMethod
39 #if " " in str($param_RTNormalization_outlierMethod):
40 "$param_RTNormalization_outlierMethod"
41 #else
42 $param_RTNormalization_outlierMethod
43 #end if
44 #end if
45 #if $param_RTNormalization_useIterativeChauvenet:
46 -RTNormalization:useIterativeChauvenet
47 #end if
48 #if $param_RTNormalization_RANSACMaxIterations:
49 -RTNormalization:RANSACMaxIterations $param_RTNormalization_RANSACMaxIterations
50 #end if
51 #if $param_RTNormalization_RANSACMaxPercentRTThreshold:
52 -RTNormalization:RANSACMaxPercentRTThreshold $param_RTNormalization_RANSACMaxPercentRTThreshold
53 #end if
54 #if $param_RTNormalization_RANSACSamplingSize:
55 -RTNormalization:RANSACSamplingSize $param_RTNormalization_RANSACSamplingSize
56 #end if
57 #if $param_algorithm_stop_report_after_feature:
58 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
59 #end if
60 #if $param_algorithm_rt_extraction_window:
61 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
62 #end if
63 #if $param_algorithm_rt_normalization_factor:
64 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
65 #end if
66 #if $param_algorithm_uis_threshold_sn:
67 -algorithm:uis_threshold_sn $param_algorithm_uis_threshold_sn
68 #end if
69 #if $param_algorithm_uis_threshold_peak_area:
70 -algorithm:uis_threshold_peak_area $param_algorithm_uis_threshold_peak_area
71 #end if
72 #if $param_algorithm_TransitionGroupPicker_stop_after_feature:
73 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
74 #end if
75 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
76 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
77 #end if
78 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
79 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
80 #end if
81 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
82 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
83 #end if
84 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
85 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
86 #end if
87 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
88 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
89 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss):
90 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
91 #else
92 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
93 #end if
94 #end if
95 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
96 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
97 #end if
98 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
99 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
100 #end if
101 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
102 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
103 #end if
104 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
105 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
106 #end if
107 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
108 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
109 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages):
110 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages"
111 #else
112 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
113 #end if
114 #end if
115 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
116 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
117 #end if
118 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
119 -algorithm:TransitionGroupPicker:PeakPickerMRM:method
120 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
121 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
122 #else
123 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
124 #end if
125 #end if
126 #if $param_algorithm_DIAScoring_dia_extraction_window:
127 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
128 #end if
129 #if $param_algorithm_DIAScoring_dia_centroided:
130 -algorithm:DIAScoring:dia_centroided
131 #end if
132 #if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
133 -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
134 #end if
135 #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
136 -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
137 #end if
138 #if $param_algorithm_DIAScoring_dia_nr_isotopes:
139 -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
140 #end if
141 #if $param_algorithm_DIAScoring_dia_nr_charges:
142 -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
143 #end if
144 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
145 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
146 #end if
147 #if $param_peptideEstimation_InitialQualityCutoff:
148 -peptideEstimation:InitialQualityCutoff $param_peptideEstimation_InitialQualityCutoff
149 #end if
150 #if $param_peptideEstimation_OverallQualityCutoff:
151 -peptideEstimation:OverallQualityCutoff $param_peptideEstimation_OverallQualityCutoff
152 #end if
153 #if $param_peptideEstimation_NrRTBins:
154 -peptideEstimation:NrRTBins $param_peptideEstimation_NrRTBins
155 #end if
156 #if $param_peptideEstimation_MinPeptidesPerBin:
157 -peptideEstimation:MinPeptidesPerBin $param_peptideEstimation_MinPeptidesPerBin
158 #end if
159 #if $param_peptideEstimation_MinBinsFilled:
160 -peptideEstimation:MinBinsFilled $param_peptideEstimation_MinBinsFilled
161 #end if
162 #if $adv_opts.adv_opts_selector=='advanced':
163 #if $adv_opts.param_force:
164 -force
165 #end if
166 #if $adv_opts.param_algorithm_quantification_cutoff:
167 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
168 #end if
169 #if $adv_opts.param_algorithm_write_convex_hull:
170 -algorithm:write_convex_hull
171 #end if
172 #if $adv_opts.param_algorithm_add_up_spectra:
173 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
174 #end if
175 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
176 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
177 #end if
178 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
179 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
180 #end if
181 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
182 -algorithm:TransitionGroupPicker:background_subtraction
183 #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
184 "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
185 #else
186 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
187 #end if
188 #end if
189 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
190 -algorithm:TransitionGroupPicker:recalculate_peaks
191 #end if
192 #if $adv_opts.param_algorithm_TransitionGroupPicker_use_precursors:
193 -algorithm:TransitionGroupPicker:use_precursors
194 #end if
195 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
196 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
197 #end if
198 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
199 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
200 #end if
201 #if $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary:
202 -algorithm:TransitionGroupPicker:resample_boundary $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary
203 #end if
204 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
205 -algorithm:TransitionGroupPicker:compute_peak_quality
206 #end if
207 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
208 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
209 #end if
210 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
211 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
212 #end if
213 #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
214 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
215 #end if
216 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
217 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
218 #end if
219 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
220 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
221 #end if
222 #if $adv_opts.param_algorithm_Scores_use_shape_score:
223 -algorithm:Scores:use_shape_score
224 #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
225 "$adv_opts.param_algorithm_Scores_use_shape_score"
226 #else
227 $adv_opts.param_algorithm_Scores_use_shape_score
228 #end if
229 #end if
230 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
231 -algorithm:Scores:use_coelution_score
232 #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
233 "$adv_opts.param_algorithm_Scores_use_coelution_score"
234 #else
235 $adv_opts.param_algorithm_Scores_use_coelution_score
236 #end if
237 #end if
238 #if $adv_opts.param_algorithm_Scores_use_rt_score:
239 -algorithm:Scores:use_rt_score
240 #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
241 "$adv_opts.param_algorithm_Scores_use_rt_score"
242 #else
243 $adv_opts.param_algorithm_Scores_use_rt_score
244 #end if
245 #end if
246 #if $adv_opts.param_algorithm_Scores_use_library_score:
247 -algorithm:Scores:use_library_score
248 #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
249 "$adv_opts.param_algorithm_Scores_use_library_score"
250 #else
251 $adv_opts.param_algorithm_Scores_use_library_score
252 #end if
253 #end if
254 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
255 -algorithm:Scores:use_elution_model_score
256 #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
257 "$adv_opts.param_algorithm_Scores_use_elution_model_score"
258 #else
259 $adv_opts.param_algorithm_Scores_use_elution_model_score
260 #end if
261 #end if
262 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
263 -algorithm:Scores:use_intensity_score
264 #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
265 "$adv_opts.param_algorithm_Scores_use_intensity_score"
266 #else
267 $adv_opts.param_algorithm_Scores_use_intensity_score
268 #end if
269 #end if
270 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
271 -algorithm:Scores:use_nr_peaks_score
272 #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
273 "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
274 #else
275 $adv_opts.param_algorithm_Scores_use_nr_peaks_score
276 #end if
277 #end if
278 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
279 -algorithm:Scores:use_total_xic_score
280 #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
281 "$adv_opts.param_algorithm_Scores_use_total_xic_score"
282 #else
283 $adv_opts.param_algorithm_Scores_use_total_xic_score
284 #end if
285 #end if
286 #if $adv_opts.param_algorithm_Scores_use_sn_score:
287 -algorithm:Scores:use_sn_score
288 #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
289 "$adv_opts.param_algorithm_Scores_use_sn_score"
290 #else
291 $adv_opts.param_algorithm_Scores_use_sn_score
292 #end if
293 #end if
294 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
295 -algorithm:Scores:use_dia_scores
296 #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
297 "$adv_opts.param_algorithm_Scores_use_dia_scores"
298 #else
299 $adv_opts.param_algorithm_Scores_use_dia_scores
300 #end if
301 #end if
302 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
303 -algorithm:Scores:use_ms1_correlation
304 #end if
305 #if $adv_opts.param_algorithm_Scores_use_sonar_scores:
306 -algorithm:Scores:use_sonar_scores
307 #end if
308 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
309 -algorithm:Scores:use_ms1_fullscan
310 #end if
311 #if $adv_opts.param_algorithm_Scores_use_uis_scores:
312 -algorithm:Scores:use_uis_scores
313 #end if
314 #end if
315 ]]></command>
316 <inputs> 55 <inputs>
317 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> 56 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
318 <sanitizer> 57 <param name="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file with the RT peptides ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
319 <valid initial="string.printable"> 58 <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)"/>
320 <remove value="'"/> 59 <param name="min_rsq" argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
321 <remove value="&quot;"/> 60 <param name="min_coverage" argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
322 </valid> 61 <param name="estimateBestPeptides" argument="-estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
323 </sanitizer> 62 <section name="RTNormalization" title="Parameters for the RTNormalization" help="RT normalization and outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
63 <param name="outlierMethod" argument="-RTNormalization:outlierMethod" display="radio" type="select" optional="false" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
64 <option value="iter_residual" selected="true">iter_residual</option>
65 <option value="iter_jackknife">iter_jackknife</option>
66 <option value="ransac">ransac</option>
67 <option value="none">none</option>
68 <expand macro="list_string_san"/>
69 </param>
70 <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
71 <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" optional="true" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
72 <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" optional="true" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
73 <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" optional="true" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
74 </section>
75 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
76 <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=""/>
77 <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"/>
78 <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)"/>
79 <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=""/>
80 <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=""/>
81 <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="">
82 <option value="simple" selected="true">simple</option>
83 <option value="resample">resample</option>
84 <expand macro="list_string_san"/>
85 </param>
86 <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=""/>
87 <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=""/>
88 <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=""/>
89 <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=""/>
90 <param name="scoring_model" argument="-algorithm:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help="">
91 <option value="default" selected="true">default</option>
92 <option value="single_transition">single_transition</option>
93 <expand macro="list_string_san"/>
94 </param>
95 <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)"/>
96 <section name="TransitionGroupPicker" title="" help="" expanded="false">
97 <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=""/>
98 <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=""/>
99 <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=""/>
100 <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="">
101 <option value="original" selected="true">original</option>
102 <option value="smoothed">smoothed</option>
103 <expand macro="list_string_san"/>
104 </param>
105 <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">
106 <option value="none" selected="true">none</option>
107 <option value="original">original</option>
108 <option value="exact">exact</option>
109 <expand macro="list_string_san"/>
110 </param>
111 <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"/>
112 <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=""/>
113 <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=""/>
114 <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)"/>
115 <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=""/>
116 <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=""/>
117 <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"/>
118 <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"/>
119 <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=""/>
120 <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="">
121 <option value="largest" selected="true">largest</option>
122 <option value="widest">widest</option>
123 <expand macro="list_string_san"/>
124 </param>
125 <section name="PeakPickerMRM" title="" help="" expanded="false">
126 <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"/>
127 <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=""/>
128 <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=""/>
129 <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=""/>
130 <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"/>
131 <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"/>
132 <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=""/>
133 <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=""/>
134 <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=""/>
135 <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=""/>
136 <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="">
137 <option value="legacy">legacy</option>
138 <option value="corrected" selected="true">corrected</option>
139 <option value="crawdad">crawdad</option>
140 <expand macro="list_string_san"/>
141 </param>
142 </section>
143 <section name="PeakIntegrator" title="" help="" expanded="false">
144 <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="">
145 <option value="intensity_sum" selected="true">intensity_sum</option>
146 <option value="simpson">simpson</option>
147 <option value="trapezoid">trapezoid</option>
148 <expand macro="list_string_san"/>
149 </param>
150 <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)">
151 <option value="base_to_base" selected="true">base_to_base</option>
152 <option value="vertical_division">vertical_division</option>
153 <option value="vertical_division_min">vertical_division_min</option>
154 <option value="vertical_division_max">vertical_division_max</option>
155 <expand macro="list_string_san"/>
156 </param>
157 <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=""/>
158 </section>
159 </section>
160 <section name="DIAScoring" title="" help="" expanded="false">
161 <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=""/>
162 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" display="radio" type="select" optional="false" label="DIA extraction window unit" help="">
163 <option value="Th" selected="true">Th</option>
164 <option value="ppm">ppm</option>
165 <expand macro="list_string_san"/>
166 </param>
167 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
168 <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=""/>
169 <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=""/>
170 <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=""/>
171 <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=""/>
172 <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=""/>
173 </section>
174 <section name="EMGScoring" title="" help="" expanded="false">
175 <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=""/>
176 <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=""/>
177 <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=""/>
178 <section name="statistics" title="" help="" expanded="false">
179 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/>
180 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/>
181 </section>
182 </section>
183 <section name="Scores" title="" help="" expanded="false">
184 <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=""/>
185 <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=""/>
186 <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=""/>
187 <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=""/>
188 <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=""/>
189 <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=""/>
190 <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=""/>
191 <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=""/>
192 <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=""/>
193 <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=""/>
194 <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=""/>
195 <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"/>
196 <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=""/>
197 <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=""/>
198 <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=""/>
199 <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=""/>
200 <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=""/>
201 <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=""/>
202 </section>
203 </section>
204 <section name="peptideEstimation" title="Parameters for the peptide estimation (use -estimateBestPeptides to enable)" help="" expanded="false">
205 <param name="InitialQualityCutoff" argument="-peptideEstimation:InitialQualityCutoff" type="float" optional="true" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
206 <param name="OverallQualityCutoff" argument="-peptideEstimation:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
207 <param name="NrRTBins" argument="-peptideEstimation:NrRTBins" type="integer" optional="true" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
208 <param name="MinPeptidesPerBin" argument="-peptideEstimation:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
209 <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/>
210 </section>
211 <expand macro="adv_opts_macro">
212 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
213 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
214 <expand macro="list_string_san"/>
215 </param>
216 </expand>
217 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
218 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
324 </param> 219 </param>
325 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file with the RT peptides ('TraML' or 'csv')" help="(-tr) "/>
326 <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) "/>
327 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
328 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
329 <param name="param_estimateBestPeptides" display="radio" type="boolean" truevalue="-estimateBestPeptides" falsevalue="" checked="false" optional="True" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization. Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (" help="(-estimateBestPeptides) e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
330 <param name="param_RTNormalization_outlierMethod" display="radio" type="select" optional="False" value="iter_residual" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="(-outlierMethod) Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
331 <option value="iter_residual" selected="true">iter_residual</option>
332 <option value="iter_jackknife">iter_jackknife</option>
333 <option value="ransac">ransac</option>
334 <option value="none">none</option>
335 </param>
336 <param name="param_RTNormalization_useIterativeChauvenet" display="radio" type="boolean" truevalue="-RTNormalization:useIterativeChauvenet" falsevalue="" checked="false" optional="True" label="Whether to use Chauvenet's criterion when using iterative methods" help="(-useIterativeChauvenet) This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
337 <param name="param_RTNormalization_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
338 <param name="param_RTNormalization_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="(-RANSACMaxPercentRTThreshold) Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
339 <param name="param_RTNormalization_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help="(-RANSACSamplingSize) "/>
340 <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) "/>
341 <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"/>
342 <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)"/>
343 <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) "/>
344 <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) "/>
345 <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) "/>
346 <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) "/>
347 <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"/>
348 <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) "/>
349 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
350 <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) ">
351 <option value="false">false</option>
352 <option value="true" selected="true">true</option>
353 </param>
354 <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"/>
355 <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"/>
356 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
357 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
358 <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) ">
359 <option value="true" selected="true">true</option>
360 <option value="false">false</option>
361 </param>
362 <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) "/>
363 <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) ">
364 <option value="legacy">legacy</option>
365 <option value="corrected" selected="true">corrected</option>
366 <option value="crawdad">crawdad</option>
367 </param>
368 <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) "/>
369 <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) "/>
370 <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) "/>
371 <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) "/>
372 <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) "/>
373 <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) "/>
374 <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) "/>
375 <param name="param_peptideEstimation_InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="(-InitialQualityCutoff) -2 to 2)"/>
376 <param name="param_peptideEstimation_OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="(-OverallQualityCutoff) 0 to 10)"/>
377 <param name="param_peptideEstimation_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="(-NrRTBins) This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
378 <param name="param_peptideEstimation_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/>
379 <param name="param_peptideEstimation_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
380 <expand macro="advanced_options">
381 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
382 <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) "/>
383 <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) "/>
384 <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) "/>
385 <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) "/>
386 <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) "/>
387 <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">
388 <option value="none" selected="true">none</option>
389 <option value="smoothed">smoothed</option>
390 <option value="original">original</option>
391 </param>
392 <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"/>
393 <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) "/>
394 <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)"/>
395 <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) "/>
396 <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) "/>
397 <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"/>
398 <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) "/>
399 <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) "/>
400 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
401 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
402 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
403 <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) ">
404 <option value="true" selected="true">true</option>
405 <option value="false">false</option>
406 </param>
407 <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) ">
408 <option value="true" selected="true">true</option>
409 <option value="false">false</option>
410 </param>
411 <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) ">
412 <option value="true" selected="true">true</option>
413 <option value="false">false</option>
414 </param>
415 <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) ">
416 <option value="true" selected="true">true</option>
417 <option value="false">false</option>
418 </param>
419 <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) ">
420 <option value="true" selected="true">true</option>
421 <option value="false">false</option>
422 </param>
423 <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) ">
424 <option value="true" selected="true">true</option>
425 <option value="false">false</option>
426 </param>
427 <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) ">
428 <option value="true" selected="true">true</option>
429 <option value="false">false</option>
430 </param>
431 <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) ">
432 <option value="true" selected="true">true</option>
433 <option value="false">false</option>
434 </param>
435 <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) ">
436 <option value="true" selected="true">true</option>
437 <option value="false">false</option>
438 </param>
439 <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">
440 <option value="true" selected="true">true</option>
441 <option value="false">false</option>
442 </param>
443 <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) "/>
444 <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) "/>
445 <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) "/>
446 <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) "/>
447 </expand>
448 </inputs> 220 </inputs>
449 <outputs> 221 <outputs>
450 <data name="param_out" format="trafoxml"/> 222 <data name="out" label="${tool.name} on ${on_string}: out" format="trafoxml"/>
223 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
224 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
225 </data>
451 </outputs> 226 </outputs>
452 <help>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. 227 <tests>
453 228 <expand macro="autotest_OpenSwathRTNormalizer"/>
454 229 <expand macro="manutest_OpenSwathRTNormalizer"/>
455 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathRTNormalizer.html</help> 230 </tests>
231 <help><![CDATA[This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.
232
233
234 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathRTNormalizer.html]]></help>
235 <expand macro="references"/>
456 </tool> 236 </tool>