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comparison OpenSwathRTNormalizer.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.0.0">
3 <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>
4 <macros>
5 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>OpenSwathRTNormalizer
11
12 -in
13 #for token in $param_in:
14 $token
15 #end for
16 #if $param_tr:
17 -tr $param_tr
18 #end if
19 #if $param_out:
20 -out $param_out
21 #end if
22 #if $param_rt_norm:
23 -rt_norm $param_rt_norm
24 #end if
25 #if $param_min_rsq:
26 -min_rsq $param_min_rsq
27 #end if
28 #if $param_min_coverage:
29 -min_coverage $param_min_coverage
30 #end if
31 #if $param_estimateBestPeptides:
32 -estimateBestPeptides
33 #end if
34 -threads \${GALAXY_SLOTS:-24}
35 #if $param_algorithm_stop_report_after_feature:
36 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
37 #end if
38 #if $param_algorithm_rt_extraction_window:
39 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
40 #end if
41 #if $param_algorithm_rt_normalization_factor:
42 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
43 #end if
44 #if $param_algorithm_TransitionGroupPicker_stop_after_feature:
45 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
46 #end if
47 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
48 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
49 #end if
50 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
51 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
52 #end if
53 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
54 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
55 #end if
56 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
57 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
58 #end if
59 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
60 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
61 #end if
62 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
63 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
64 #end if
65 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
66 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
67 #end if
68 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
69 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
70 #end if
71 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
72 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
73 #end if
74 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
75 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
76 #end if
77 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
78 -algorithm:TransitionGroupPicker:PeakPickerMRM:method
79 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
80 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
81 #else
82 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
83 #end if
84 #end if
85 #if $param_algorithm_DIAScoring_dia_extraction_window:
86 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
87 #end if
88 #if $param_algorithm_DIAScoring_dia_centroided:
89 -algorithm:DIAScoring:dia_centroided
90 #end if
91 #if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
92 -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
93 #end if
94 #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
95 -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
96 #end if
97 #if $param_algorithm_DIAScoring_dia_nr_isotopes:
98 -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
99 #end if
100 #if $param_algorithm_DIAScoring_dia_nr_charges:
101 -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
102 #end if
103 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
104 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
105 #end if
106 #if $param_outlierDetection_outlierMethod:
107 -outlierDetection:outlierMethod "$param_outlierDetection_outlierMethod"
108 #end if
109 #if $param_outlierDetection_useIterativeChauvenet:
110 -outlierDetection:useIterativeChauvenet "$param_outlierDetection_useIterativeChauvenet"
111 #end if
112 #if $param_outlierDetection_RANSACMaxIterations:
113 -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations
114 #end if
115 #if $param_outlierDetection_RANSACMaxPercentRTThreshold:
116 -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold
117 #end if
118 #if $param_outlierDetection_RANSACSamplingSize:
119 -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize
120 #end if
121 #if $param_peptideEstimation_InitialQualityCutoff:
122 -peptideEstimation:InitialQualityCutoff $param_peptideEstimation_InitialQualityCutoff
123 #end if
124 #if $param_peptideEstimation_OverallQualityCutoff:
125 -peptideEstimation:OverallQualityCutoff $param_peptideEstimation_OverallQualityCutoff
126 #end if
127 #if $param_peptideEstimation_NrRTBins:
128 -peptideEstimation:NrRTBins $param_peptideEstimation_NrRTBins
129 #end if
130 #if $param_peptideEstimation_MinPeptidesPerBin:
131 -peptideEstimation:MinPeptidesPerBin $param_peptideEstimation_MinPeptidesPerBin
132 #end if
133 #if $param_peptideEstimation_MinBinsFilled:
134 -peptideEstimation:MinBinsFilled $param_peptideEstimation_MinBinsFilled
135 #end if
136 #if $adv_opts.adv_opts_selector=='advanced':
137 #if $adv_opts.param_force:
138 -force
139 #end if
140 #if $adv_opts.param_algorithm_quantification_cutoff:
141 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
142 #end if
143 #if $adv_opts.param_algorithm_write_convex_hull:
144 -algorithm:write_convex_hull
145 #end if
146 #if $adv_opts.param_algorithm_add_up_spectra:
147 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
148 #end if
149 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
150 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
151 #end if
152 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
153 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
154 #end if
155 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
156 -algorithm:TransitionGroupPicker:background_subtraction
157 #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
158 "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
159 #else
160 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
161 #end if
162 #end if
163 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
164 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
165 #end if
166 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
167 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
168 #end if
169 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
170 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
171 #end if
172 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
173 -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
174 #end if
175 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
176 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
177 #end if
178 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
179 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
180 #end if
181 #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
182 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
183 #end if
184 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
185 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
186 #end if
187 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
188 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
189 #end if
190 #if $adv_opts.param_algorithm_Scores_use_shape_score:
191 -algorithm:Scores:use_shape_score
192 #end if
193 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
194 -algorithm:Scores:use_coelution_score
195 #end if
196 #if $adv_opts.param_algorithm_Scores_use_rt_score:
197 -algorithm:Scores:use_rt_score
198 #end if
199 #if $adv_opts.param_algorithm_Scores_use_library_score:
200 -algorithm:Scores:use_library_score
201 #end if
202 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
203 -algorithm:Scores:use_elution_model_score
204 #end if
205 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
206 -algorithm:Scores:use_intensity_score
207 #end if
208 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
209 -algorithm:Scores:use_nr_peaks_score
210 #end if
211 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
212 -algorithm:Scores:use_total_xic_score
213 #end if
214 #if $adv_opts.param_algorithm_Scores_use_sn_score:
215 -algorithm:Scores:use_sn_score
216 #end if
217 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
218 -algorithm:Scores:use_dia_scores
219 #end if
220 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
221 -algorithm:Scores:use_ms1_correlation
222 #end if
223 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
224 -algorithm:Scores:use_ms1_fullscan
225 #end if
226 #end if
227 </command>
228 <inputs>
229 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
230 <sanitizer>
231 <valid initial="string.printable">
232 <remove value="'"/>
233 <remove value="&quot;"/>
234 </valid>
235 </sanitizer>
236 </param>
237 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file with the RT peptides ('TraML' or 'csv')" help="(-tr) "/>
238 <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) "/>
239 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
240 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
241 <param name="param_estimateBestPeptides" 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)"/>
242 <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) "/>
243 <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"/>
244 <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)"/>
245 <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) "/>
246 <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) "/>
247 <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"/>
248 <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) "/>
249 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
250 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" type="text" size="30" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
251 <sanitizer>
252 <valid initial="string.printable">
253 <remove value="'"/>
254 <remove value="&quot;"/>
255 </valid>
256 </sanitizer>
257 </param>
258 <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"/>
259 <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"/>
260 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
261 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
262 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" 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) "/>
263 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" type="select" optional="True" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
264 <option value="legacy">legacy</option>
265 <option value="corrected">corrected</option>
266 <option value="crawdad">crawdad</option>
267 </param>
268 <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) "/>
269 <param name="param_algorithm_DIAScoring_dia_centroided" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
270 <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) "/>
271 <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) "/>
272 <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) "/>
273 <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) "/>
274 <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) "/>
275 <param name="param_outlierDetection_outlierMethod" type="text" size="30" 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)">
276 <sanitizer>
277 <valid initial="string.printable">
278 <remove value="'"/>
279 <remove value="&quot;"/>
280 </valid>
281 </sanitizer>
282 </param>
283 <param name="param_outlierDetection_useIterativeChauvenet" type="text" size="30" value="false" 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">
284 <sanitizer>
285 <valid initial="string.printable">
286 <remove value="'"/>
287 <remove value="&quot;"/>
288 </valid>
289 </sanitizer>
290 </param>
291 <param name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
292 <param name="param_outlierDetection_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"/>
293 <param name="param_outlierDetection_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help="(-RANSACSamplingSize) "/>
294 <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)"/>
295 <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)"/>
296 <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)"/>
297 <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) "/>
298 <param name="param_peptideEstimation_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
299 <expand macro="advanced_options">
300 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
301 <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) "/>
302 <param name="param_algorithm_write_convex_hull" 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) "/>
303 <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) "/>
304 <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) "/>
305 <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) "/>
306 <param name="param_algorithm_TransitionGroupPicker_background_subtraction" type="select" optional="True" 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">
307 <option value="none">none</option>
308 <option value="smoothed">smoothed</option>
309 <option value="original">original</option>
310 </param>
311 <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">
312 <sanitizer>
313 <valid initial="string.printable">
314 <remove value="'"/>
315 <remove value="&quot;"/>
316 </valid>
317 </sanitizer>
318 </param>
319 <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)"/>
320 <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) "/>
321 <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">
322 <sanitizer>
323 <valid initial="string.printable">
324 <remove value="'"/>
325 <remove value="&quot;"/>
326 </valid>
327 </sanitizer>
328 </param>
329 <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) "/>
330 <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) "/>
331 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
332 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
333 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
334 <param name="param_algorithm_Scores_use_shape_score" type="boolean" truevalue="-algorithm:Scores:use_shape_score" falsevalue="" checked="true" optional="True" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) "/>
335 <param name="param_algorithm_Scores_use_coelution_score" type="boolean" truevalue="-algorithm:Scores:use_coelution_score" falsevalue="" checked="true" optional="True" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) "/>
336 <param name="param_algorithm_Scores_use_rt_score" type="boolean" truevalue="-algorithm:Scores:use_rt_score" falsevalue="" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score) "/>
337 <param name="param_algorithm_Scores_use_library_score" type="boolean" truevalue="-algorithm:Scores:use_library_score" falsevalue="" checked="true" optional="True" label="Use the library score" help="(-use_library_score) "/>
338 <param name="param_algorithm_Scores_use_elution_model_score" type="boolean" truevalue="-algorithm:Scores:use_elution_model_score" falsevalue="" checked="true" optional="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) "/>
339 <param name="param_algorithm_Scores_use_intensity_score" type="boolean" truevalue="-algorithm:Scores:use_intensity_score" falsevalue="" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score) "/>
340 <param name="param_algorithm_Scores_use_nr_peaks_score" type="boolean" truevalue="-algorithm:Scores:use_nr_peaks_score" falsevalue="" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score) "/>
341 <param name="param_algorithm_Scores_use_total_xic_score" type="boolean" truevalue="-algorithm:Scores:use_total_xic_score" falsevalue="" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score) "/>
342 <param name="param_algorithm_Scores_use_sn_score" type="boolean" truevalue="-algorithm:Scores:use_sn_score" falsevalue="" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score) "/>
343 <param name="param_algorithm_Scores_use_dia_scores" type="boolean" truevalue="-algorithm:Scores:use_dia_scores" falsevalue="" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "/>
344 <param name="param_algorithm_Scores_use_ms1_correlation" 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) "/>
345 <param name="param_algorithm_Scores_use_ms1_fullscan" 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) "/>
346 </expand>
347 </inputs>
348 <outputs>
349 <data name="param_out" format="trafoxml"/>
350 </outputs>
351 <help>**What it does**
352
353 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.
354
355
356 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html</help>
357 <expand macro="references"/>
358 </tool>