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comparison OpenSwathRTNormalizer.xml @ 0:566046627ebf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:16:05 -0500
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.1.0">
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>
7 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathRTNormalizer
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_tr:
20 -tr $param_tr
21 #end if
22 #if $param_out:
23 -out $param_out
24 #end if
25 #if $param_rt_norm:
26 -rt_norm $param_rt_norm
27 #end if
28 #if $param_min_rsq:
29 -min_rsq $param_min_rsq
30 #end if
31 #if $param_min_coverage:
32 -min_coverage $param_min_coverage
33 #end if
34 #if $param_estimateBestPeptides:
35 -estimateBestPeptides
36 #end if
37 #if $param_algorithm_stop_report_after_feature:
38 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
39 #end if
40 #if $param_algorithm_rt_extraction_window:
41 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
42 #end if
43 #if $param_algorithm_rt_normalization_factor:
44 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
45 #end if
46 #if $param_algorithm_uis_threshold_sn:
47 -algorithm:uis_threshold_sn $param_algorithm_uis_threshold_sn
48 #end if
49 #if $param_algorithm_uis_threshold_peak_area:
50 -algorithm:uis_threshold_peak_area $param_algorithm_uis_threshold_peak_area
51 #end if
52 #if $param_algorithm_TransitionGroupPicker_stop_after_feature:
53 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
54 #end if
55 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
56 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
57 #end if
58 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
59 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
60 #end if
61 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
62 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
63 #end if
64 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
65 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
66 #end if
67 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
68 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
69 #end if
70 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
71 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
72 #end if
73 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
74 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
75 #end if
76 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
77 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
78 #end if
79 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
80 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
81 #end if
82 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
83 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
84 #end if
85 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
86 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
87 #end if
88 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
89 -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
90 #end if
91 #if $param_algorithm_DIAScoring_dia_extraction_window:
92 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
93 #end if
94 #if $param_algorithm_DIAScoring_dia_centroided:
95 -algorithm:DIAScoring:dia_centroided
96 #end if
97 #if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
98 -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
99 #end if
100 #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
101 -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
102 #end if
103 #if $param_algorithm_DIAScoring_dia_nr_isotopes:
104 -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
105 #end if
106 #if $param_algorithm_DIAScoring_dia_nr_charges:
107 -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
108 #end if
109 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
110 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
111 #end if
112 #if $param_outlierDetection_outlierMethod:
113 -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod
114 #end if
115 #if $param_outlierDetection_useIterativeChauvenet:
116 -outlierDetection:useIterativeChauvenet
117 #end if
118 #if $param_outlierDetection_RANSACMaxIterations:
119 -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations
120 #end if
121 #if $param_outlierDetection_RANSACMaxPercentRTThreshold:
122 -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold
123 #end if
124 #if $param_outlierDetection_RANSACSamplingSize:
125 -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize
126 #end if
127 #if $param_peptideEstimation_InitialQualityCutoff:
128 -peptideEstimation:InitialQualityCutoff $param_peptideEstimation_InitialQualityCutoff
129 #end if
130 #if $param_peptideEstimation_OverallQualityCutoff:
131 -peptideEstimation:OverallQualityCutoff $param_peptideEstimation_OverallQualityCutoff
132 #end if
133 #if $param_peptideEstimation_NrRTBins:
134 -peptideEstimation:NrRTBins $param_peptideEstimation_NrRTBins
135 #end if
136 #if $param_peptideEstimation_MinPeptidesPerBin:
137 -peptideEstimation:MinPeptidesPerBin $param_peptideEstimation_MinPeptidesPerBin
138 #end if
139 #if $param_peptideEstimation_MinBinsFilled:
140 -peptideEstimation:MinBinsFilled $param_peptideEstimation_MinBinsFilled
141 #end if
142 #if $adv_opts.adv_opts_selector=='advanced':
143 #if $adv_opts.param_force:
144 -force
145 #end if
146 #if $adv_opts.param_algorithm_quantification_cutoff:
147 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
148 #end if
149 #if $adv_opts.param_algorithm_write_convex_hull:
150 -algorithm:write_convex_hull
151 #end if
152 #if $adv_opts.param_algorithm_add_up_spectra:
153 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
154 #end if
155 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
156 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
157 #end if
158 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
159 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
160 #end if
161 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
162 -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
163 #end if
164 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
165 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
166 #end if
167 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
168 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
169 #end if
170 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
171 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
172 #end if
173 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
174 -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
175 #end if
176 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
177 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
178 #end if
179 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
180 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
181 #end if
182 #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
183 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
184 #end if
185 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
186 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
187 #end if
188 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
189 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
190 #end if
191 #if $adv_opts.param_algorithm_Scores_use_shape_score:
192 -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score
193 #end if
194 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
195 -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score
196 #end if
197 #if $adv_opts.param_algorithm_Scores_use_rt_score:
198 -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score
199 #end if
200 #if $adv_opts.param_algorithm_Scores_use_library_score:
201 -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score
202 #end if
203 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
204 -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score
205 #end if
206 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
207 -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score
208 #end if
209 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
210 -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score
211 #end if
212 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
213 -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score
214 #end if
215 #if $adv_opts.param_algorithm_Scores_use_sn_score:
216 -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score
217 #end if
218 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
219 -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores
220 #end if
221 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
222 -algorithm:Scores:use_ms1_correlation
223 #end if
224 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
225 -algorithm:Scores:use_ms1_fullscan
226 #end if
227 #if $adv_opts.param_algorithm_Scores_use_uis_scores:
228 -algorithm:Scores:use_uis_scores
229 #end if
230 #end if
231 </command>
232 <inputs>
233 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
234 <sanitizer>
235 <valid initial="string.printable">
236 <remove value="'"/>
237 <remove value="&quot;"/>
238 </valid>
239 </sanitizer>
240 </param>
241 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file with the RT peptides ('TraML' or 'csv')" help="(-tr) "/>
242 <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) "/>
243 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
244 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
245 <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)"/>
246 <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) "/>
247 <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"/>
248 <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)"/>
249 <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) "/>
250 <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) "/>
251 <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) "/>
252 <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) "/>
253 <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"/>
254 <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) "/>
255 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
256 <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) ">
257 <option value="false">false</option>
258 <option value="true" selected="true">true</option>
259 </param>
260 <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"/>
261 <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"/>
262 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
263 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
264 <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) ">
265 <option value="true" selected="true">true</option>
266 <option value="false">false</option>
267 </param>
268 <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) "/>
269 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
270 <option value="legacy" selected="true">legacy</option>
271 <option value="corrected">corrected</option>
272 <option value="crawdad">crawdad</option>
273 </param>
274 <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) "/>
275 <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) "/>
276 <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) "/>
277 <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) "/>
278 <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) "/>
279 <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) "/>
280 <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) "/>
281 <param name="param_outlierDetection_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)">
282 <option value="iter_residual" selected="true">iter_residual</option>
283 <option value="iter_jackknife">iter_jackknife</option>
284 <option value="ransac">ransac</option>
285 <option value="none">none</option>
286 </param>
287 <param name="param_outlierDetection_useIterativeChauvenet" display="radio" type="boolean" truevalue="-outlierDetection: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"/>
288 <param name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
289 <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"/>
290 <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) "/>
291 <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)"/>
292 <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)"/>
293 <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)"/>
294 <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) "/>
295 <param name="param_peptideEstimation_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
296 <expand macro="advanced_options">
297 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
298 <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) "/>
299 <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) "/>
300 <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) "/>
301 <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) "/>
302 <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) "/>
303 <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">
304 <option value="none" selected="true">none</option>
305 <option value="smoothed">smoothed</option>
306 <option value="original">original</option>
307 </param>
308 <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">
309 <sanitizer>
310 <valid initial="string.printable">
311 <remove value="'"/>
312 <remove value="&quot;"/>
313 </valid>
314 </sanitizer>
315 </param>
316 <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)"/>
317 <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) "/>
318 <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">
319 <sanitizer>
320 <valid initial="string.printable">
321 <remove value="'"/>
322 <remove value="&quot;"/>
323 </valid>
324 </sanitizer>
325 </param>
326 <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) "/>
327 <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) "/>
328 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
329 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
330 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
331 <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) ">
332 <option value="true" selected="true">true</option>
333 <option value="false">false</option>
334 </param>
335 <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) ">
336 <option value="true" selected="true">true</option>
337 <option value="false">false</option>
338 </param>
339 <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) ">
340 <option value="true" selected="true">true</option>
341 <option value="false">false</option>
342 </param>
343 <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) ">
344 <option value="true" selected="true">true</option>
345 <option value="false">false</option>
346 </param>
347 <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) ">
348 <option value="true" selected="true">true</option>
349 <option value="false">false</option>
350 </param>
351 <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) ">
352 <option value="true" selected="true">true</option>
353 <option value="false">false</option>
354 </param>
355 <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) ">
356 <option value="true" selected="true">true</option>
357 <option value="false">false</option>
358 </param>
359 <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) ">
360 <option value="true" selected="true">true</option>
361 <option value="false">false</option>
362 </param>
363 <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) ">
364 <option value="true" selected="true">true</option>
365 <option value="false">false</option>
366 </param>
367 <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) ">
368 <option value="true" selected="true">true</option>
369 <option value="false">false</option>
370 </param>
371 <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) "/>
372 <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) "/>
373 <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) "/>
374 </expand>
375 </inputs>
376 <outputs>
377 <data name="param_out" format="trafoxml"/>
378 </outputs>
379 <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.
380
381
382 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html</help>
383 </tool>