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comparison OpenSwathRTNormalizer.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="1.12.0"> 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 <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> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token> 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 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathRTNormalizer 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathRTNormalizer
11 14
12 -in ${param_in} 15 -in
13 -tr ${param_tr} 16 #for token in $param_in:
14 -out ${param_out} 17 $token
15 -rt_norm ${param_rt_norm} 18 #end for
16 -min_rsq ${param_min_rsq} 19 #if $param_tr:
17 -min_coverage ${param_min_coverage} 20 -tr $param_tr
18 ${param_estimateBestPeptides} 21 #end if
19 -threads \${GALAXY_SLOTS:-24} 22 #if $param_out:
20 -algorithm:stop_report_after_feature ${param_stop_report_after_feature} 23 -out $param_out
21 -algorithm:rt_extraction_window ${param_rt_extraction_window} 24 #end if
22 -algorithm:rt_normalization_factor ${param_rt_normalization_factor} 25 #if $param_rt_norm:
23 -algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature} 26 -rt_norm $param_rt_norm
24 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio} 27 #end if
25 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length} 28 #if $param_min_rsq:
26 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order} 29 -min_rsq $param_min_rsq
27 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width} 30 #end if
28 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss} 31 #if $param_min_coverage:
29 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width} 32 -min_coverage $param_min_coverage
30 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise} 33 #end if
31 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len} 34 #if $param_estimateBestPeptides:
32 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count} 35 -estimateBestPeptides
33 ${param_remove_overlapping_peaks} 36 #end if
34 -algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method} 37 -threads \${GALAXY_SLOTS:-24}
35 -algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window} 38 #if $param_algorithm_stop_report_after_feature:
36 ${param_dia_centroided} 39 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
37 -algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min} 40 #end if
38 -algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff} 41 #if $param_algorithm_rt_extraction_window:
39 -algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes} 42 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
40 -algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges} 43 #end if
41 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff} 44 #if $param_algorithm_rt_normalization_factor:
42 -outlierDetection:outlierMethod ${param_outlierMethod} 45 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
43 -outlierDetection:useIterativeChauvenet ${param_useIterativeChauvenet} 46 #end if
44 -outlierDetection:RANSACMaxIterations ${param_RANSACMaxIterations} 47 #if $param_algorithm_TransitionGroupPicker_stop_after_feature:
45 -outlierDetection:RANSACMaxPercentRTThreshold ${param_RANSACMaxPercentRTThreshold} 48 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
46 -outlierDetection:RANSACSamplingSize ${param_RANSACSamplingSize} 49 #end if
47 -peptideEstimation:InitialQualityCutoff ${param_InitialQualityCutoff} 50 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
48 -peptideEstimation:OverallQualityCutoff ${param_OverallQualityCutoff} 51 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
49 -peptideEstimation:NrRTBins ${param_NrRTBins} 52 #end if
50 -peptideEstimation:MinPeptidesPerBin ${param_MinPeptidesPerBin} 53 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
51 -peptideEstimation:MinBinsFilled ${param_MinBinsFilled} 54 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
55 #end if
56 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
57 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
58 #end if
59 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
60 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
61 #end if
62 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
63 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
64 #end if
65 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
66 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
67 #end if
68 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
69 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
70 #end if
71 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
72 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
73 #end if
74 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
75 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
76 #end if
77 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
78 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
79 #end if
80 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
81 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
82 #end if
83 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
84 -algorithm:TransitionGroupPicker:PeakPickerMRM:method
85 #if &quot; &quot; in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
86 &quot;$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method&quot;
87 #else
88 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
89 #end if
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 $param_outlierDetection_outlierMethod:
113 -outlierDetection:outlierMethod
114 #if &quot; &quot; in str($param_outlierDetection_outlierMethod):
115 &quot;$param_outlierDetection_outlierMethod&quot;
116 #else
117 $param_outlierDetection_outlierMethod
118 #end if
119 #end if
120 #if $param_outlierDetection_useIterativeChauvenet:
121 -outlierDetection:useIterativeChauvenet
122 #end if
123 #if $param_outlierDetection_RANSACMaxIterations:
124 -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations
125 #end if
126 #if $param_outlierDetection_RANSACMaxPercentRTThreshold:
127 -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold
128 #end if
129 #if $param_outlierDetection_RANSACSamplingSize:
130 -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize
131 #end if
132 #if $param_peptideEstimation_InitialQualityCutoff:
133 -peptideEstimation:InitialQualityCutoff $param_peptideEstimation_InitialQualityCutoff
134 #end if
135 #if $param_peptideEstimation_OverallQualityCutoff:
136 -peptideEstimation:OverallQualityCutoff $param_peptideEstimation_OverallQualityCutoff
137 #end if
138 #if $param_peptideEstimation_NrRTBins:
139 -peptideEstimation:NrRTBins $param_peptideEstimation_NrRTBins
140 #end if
141 #if $param_peptideEstimation_MinPeptidesPerBin:
142 -peptideEstimation:MinPeptidesPerBin $param_peptideEstimation_MinPeptidesPerBin
143 #end if
144 #if $param_peptideEstimation_MinBinsFilled:
145 -peptideEstimation:MinBinsFilled $param_peptideEstimation_MinBinsFilled
146 #end if
52 #if $adv_opts.adv_opts_selector=='advanced': 147 #if $adv_opts.adv_opts_selector=='advanced':
53 -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff} 148 #if $adv_opts.param_force:
54 ${adv_opts.param_write_convex_hull} 149 -force
55 -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra} 150 #end if
56 -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling} 151 #if $adv_opts.param_algorithm_quantification_cutoff:
57 -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width} 152 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
58 -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction} 153 #end if
59 -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks} 154 #if $adv_opts.param_algorithm_write_convex_hull:
60 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z} 155 -algorithm:write_convex_hull
61 -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality} 156 #end if
62 -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality} 157 #if $adv_opts.param_algorithm_add_up_spectra:
63 -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step} 158 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
64 -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box} 159 #end if
65 -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration} 160 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
66 -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean} 161 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
67 -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance} 162 #end if
68 ${adv_opts.param_use_shape_score} 163 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
69 ${adv_opts.param_use_coelution_score} 164 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
70 ${adv_opts.param_use_rt_score} 165 #end if
71 ${adv_opts.param_use_library_score} 166 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
72 ${adv_opts.param_use_elution_model_score} 167 -algorithm:TransitionGroupPicker:background_subtraction
73 ${adv_opts.param_use_intensity_score} 168 #if &quot; &quot; in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
74 ${adv_opts.param_use_nr_peaks_score} 169 &quot;$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction&quot;
75 ${adv_opts.param_use_total_xic_score} 170 #else
76 ${adv_opts.param_use_sn_score} 171 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
77 ${adv_opts.param_use_dia_scores} 172 #end if
78 ${adv_opts.param_use_ms1_correlation} 173 #end if
79 ${adv_opts.param_use_ms1_fullscan} 174 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
175 -algorithm:TransitionGroupPicker:recalculate_peaks &quot;$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks&quot;
176 #end if
177 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
178 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
179 #end if
180 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
181 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
182 #end if
183 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
184 -algorithm:TransitionGroupPicker:compute_peak_quality &quot;$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality&quot;
185 #end if
186 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
187 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
188 #end if
189 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
190 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
191 #end if
192 #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
193 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
194 #end if
195 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
196 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
197 #end if
198 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
199 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
200 #end if
201 #if $adv_opts.param_algorithm_Scores_use_shape_score:
202 -algorithm:Scores:use_shape_score
203 #end if
204 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
205 -algorithm:Scores:use_coelution_score
206 #end if
207 #if $adv_opts.param_algorithm_Scores_use_rt_score:
208 -algorithm:Scores:use_rt_score
209 #end if
210 #if $adv_opts.param_algorithm_Scores_use_library_score:
211 -algorithm:Scores:use_library_score
212 #end if
213 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
214 -algorithm:Scores:use_elution_model_score
215 #end if
216 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
217 -algorithm:Scores:use_intensity_score
218 #end if
219 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
220 -algorithm:Scores:use_nr_peaks_score
221 #end if
222 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
223 -algorithm:Scores:use_total_xic_score
224 #end if
225 #if $adv_opts.param_algorithm_Scores_use_sn_score:
226 -algorithm:Scores:use_sn_score
227 #end if
228 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
229 -algorithm:Scores:use_dia_scores
230 #end if
231 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
232 -algorithm:Scores:use_ms1_correlation
233 #end if
234 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
235 -algorithm:Scores:use_ms1_fullscan
236 #end if
80 #end if 237 #end if
81 </command> 238 </command>
82 <inputs> 239 <inputs>
83 <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/> 240 <param format="mzml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
84 <param name="param_tr" type="data" format="tabular" optional="False" label="transition file with the RT peptides ('TraML' or 'csv')" help="(-tr)"/> 241 <sanitizer>
85 <param name="param_rt_norm" type="data" format="" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm)"/> 242 <valid initial="string.printable">
86 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq)"/> 243 <remove value="'"/>
87 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage)"/> 244 <remove value="&quot;"/>
88 <param name="param_estimateBestPeptides" type="boolean" truevalue="-estimateBestPeptides true" falsevalue="-estimateBestPeptides false" 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 (e.g. due to them being endogenous peptides or using a less curated list of peptides)." help="(-estimateBestPeptides)"/> 245 </valid>
89 <param name="param_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)"/> 246 </sanitizer>
90 <param name="param_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). For this to work, the TraML input file needs to contain normalized RT values." help="(-rt_extraction_window)"/> 247 </param>
91 <param name="param_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 (e.g. it goes from 0 to 100, set this value to 100)" help="(-rt_normalization_factor)"/> 248 <param format="tabular,traml" help="(-tr) " label="transition file with the RT peptides ('TraML' or 'csv')" name="param_tr" optional="False" type="data"/>
92 <param name="param_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)." help="(-stop_after_feature)"/> 249 <param format="trafoxml" help="(-rt_norm) " label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" name="param_rt_norm" optional="True" type="data"/>
93 <param name="param_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio)"/> 250 <param help="(-min_rsq) " label="Minimum r-squared of RT peptides regression" name="param_min_rsq" type="float" value="0.95"/>
94 <param name="param_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing.#br#This number has to be uneven. If it is not, 1 will be added." help="(-sgolay_frame_length)"/> 251 <param help="(-min_coverage) " label="Minimum relative amount of RT peptides to keep" name="param_min_coverage" type="float" value="0.6"/>
95 <param name="param_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted." help="(-sgolay_polynomial_order)"/> 252 <param checked="false" falsevalue="" help="(-estimateBestPeptides) e.g. due to them being endogenous peptides or using a less curated list of peptides)" 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 (" name="param_estimateBestPeptides" optional="True" truevalue="-estimateBestPeptides" type="boolean"/>
96 <param name="param_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size." help="(-gauss_width)"/> 253 <param help="(-stop_report_after_feature) " label="Stop reporting after feature (ordered by quality; -1 means do not stop)" name="param_algorithm_stop_report_after_feature" type="integer" value="-1"/>
97 <param name="param_use_gauss" type="text" size="20" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss)"/> 254 <param help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values" 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)" name="param_algorithm_rt_extraction_window" type="float" value="-1.0"/>
98 <param name="param_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off." help="(-peak_width)"/> 255 <param help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" name="param_algorithm_rt_normalization_factor" type="float" value="1.0"/>
99 <param name="param_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 (e.g. 1.0) can lead to peaks whose flanks are not fully captured." help="(-signal_to_noise)"/> 256 <param help="(-stop_after_feature) " label="Stop finding after feature (ordered by intensity; -1 means do not stop)" name="param_algorithm_TransitionGroupPicker_stop_after_feature" type="integer" value="-1"/>
100 <param name="param_sn_win_len" type="float" value="1000.0" label="Signal to noise window length." help="(-sn_win_len)"/> 257 <param help="(-stop_after_intensity_ratio) " label="Stop after reaching intensity ratio" name="param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001"/>
101 <param name="param_sn_bin_count" type="integer" value="30" label="Signal to noise bin count." help="(-sn_bin_count)"/> 258 <param help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added" label="The number of subsequent data points used for smoothing" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15"/>
102 <param name="param_remove_overlapping_peaks" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks true" falsevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks false" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks)"/> 259 <param help="(-sgolay_polynomial_order) " label="Order of the polynomial that is fitted" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3"/>
103 <param name="param_method" type="select" optional="True" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)." help="(-method)"> 260 <param help="(-gauss_width) " label="Gaussian width in seconds, estimated peak size" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0"/>
104 <option value="legacy">legacy</option> 261 <param checked="true" falsevalue="" help="(-use_gauss) " label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean"/>
105 <option value="corrected">corrected</option> 262 <param help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off" label="Force a certain minimal peak_width on the data (" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0"/>
106 <option value="crawdad">crawdad</option> 263 <param help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" min="0.0" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" optional="True" type="float" value="1.0"/>
107 </param> 264 <param help="(-sn_win_len) " label="Signal to noise window length" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0"/>
108 <param name="param_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th." help="(-dia_extraction_window)"/> 265 <param help="(-sn_bin_count) " label="Signal to noise bin count" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30"/>
109 <param name="param_dia_centroided" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided true" falsevalue="-algorithm:DIAScoring:dia_centroided false" checked="false" optional="True" label="Use centroded DIA data." help="(-dia_centroided)"/> 266 <param checked="true" falsevalue="" help="(-write_sn_log_messages) " label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean"/>
110 <param name="param_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to consider." help="(-dia_byseries_intensity_min)"/> 267 <param checked="false" falsevalue="" help="(-remove_overlapping_peaks) " label="Try to remove overlapping peaks during peak picking" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean"/>
111 <param name="param_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to consider." help="(-dia_byseries_ppm_diff)"/> 268 <param help="(-method) " label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" optional="True" type="select" value="legacy">
112 <param name="param_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to consider." help="(-dia_nr_isotopes)"/> 269 <option value="legacy">legacy</option>
113 <param name="param_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to consider." help="(-dia_nr_charges)"/> 270 <option value="corrected">corrected</option>
114 <param name="param_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)"/> 271 <option value="crawdad">crawdad</option>
115 <param name="param_outlierMethod" type="text" size="20" value="iter_residual" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none'). 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)." help="(-outlierMethod)"/> 272 </param>
116 <param name="param_useIterativeChauvenet" type="text" size="20" value="false" label="Whether to use Chauvenet's criterion when using iterative methods. This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained." help="(-useIterativeChauvenet)"/> 273 <param help="(-dia_extraction_window) " label="DIA extraction window in Th" min="0.0" name="param_algorithm_DIAScoring_dia_extraction_window" optional="True" type="float" value="0.05"/>
117 <param name="param_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm." help="(-RANSACMaxIterations)"/> 274 <param checked="false" falsevalue="" help="(-dia_centroided) " label="Use centroded DIA data" name="param_algorithm_DIAScoring_dia_centroided" optional="True" truevalue="-algorithm:DIAScoring:dia_centroided" type="boolean"/>
118 <param name="param_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient). Default is set to 3% which is around +/- 4 minutes on a 120 gradient." help="(-RANSACMaxPercentRTThreshold)"/> 275 <param help="(-dia_byseries_intensity_min) " label="DIA b/y series minimum intensity to conside" min="0.0" name="param_algorithm_DIAScoring_dia_byseries_intensity_min" optional="True" type="float" value="300.0"/>
119 <param name="param_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm." help="(-RANSACSamplingSize)"/> 276 <param help="(-dia_byseries_ppm_diff) " label="DIA b/y series minimal difference in ppm to conside" min="0.0" name="param_algorithm_DIAScoring_dia_byseries_ppm_diff" optional="True" type="float" value="10.0"/>
120 <param name="param_InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca. -2 to 2)" help="(-InitialQualityCutoff)"/> 277 <param help="(-dia_nr_isotopes) " label="DIA nr of isotopes to conside" min="0" name="param_algorithm_DIAScoring_dia_nr_isotopes" optional="True" type="integer" value="4"/>
121 <param name="param_OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca. 0 to 10)" help="(-OverallQualityCutoff)"/> 278 <param help="(-dia_nr_charges) " label="DIA nr of charges to conside" min="0" name="param_algorithm_DIAScoring_dia_nr_charges" optional="True" type="integer" value="4"/>
122 <param name="param_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage. 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)" help="(-NrRTBins)"/> 279 <param help="(-peak_before_mono_max_ppm_diff) " 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" min="0.0" name="param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff" optional="True" type="float" value="20.0"/>
123 <param name="param_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin)"/> 280 <param 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)" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" name="param_outlierDetection_outlierMethod" optional="True" type="select" value="iter_residual">
124 <param name="param_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled)"/> 281 <option value="iter_residual">iter_residual</option>
125 <expand macro="advanced_options"> 282 <option value="iter_jackknife">iter_jackknife</option>
126 <param name="param_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)"/> 283 <option value="ransac">ransac</option>
127 <param name="param_write_convex_hull" type="boolean" truevalue="-algorithm:write_convex_hull true" falsevalue="-algorithm:write_convex_hull false" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull)"/>
128 <param name="param_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)"/>
129 <param name="param_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)"/>
130 <param name="param_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)"/>
131 <param name="param_background_subtraction" type="select" optional="True" value="none" label="Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that." help="(-background_subtraction)">
132 <option value="none">none</option> 284 <option value="none">none</option>
133 <option value="smoothed">smoothed</option>
134 <option value="original">original</option>
135 </param> 285 </param>
136 <param name="param_recalculate_peaks" type="text" size="20" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large." help="(-recalculate_peaks)"/> 286 <param checked="false" falsevalue="" help="(-useIterativeChauvenet) This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained" label="Whether to use Chauvenet's criterion when using iterative methods" name="param_outlierDetection_useIterativeChauvenet" optional="True" truevalue="-outlierDetection:useIterativeChauvenet" type="boolean"/>
137 <param name="param_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. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)." help="(-recalculate_peaks_max_z)"/> 287 <param help="(-RANSACMaxIterations) " label="Maximum iterations for the RANSAC outlier detection algorithm" name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000"/>
138 <param name="param_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)"/> 288 <param help="(-RANSACMaxPercentRTThreshold) Default is set to 3% which is around +/- 4 minutes on a 120 gradient" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" name="param_outlierDetection_RANSACMaxPercentRTThreshold" type="integer" value="3"/>
139 <param name="param_compute_peak_quality" type="text" size="20" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad." help="(-compute_peak_quality)"/> 289 <param help="(-RANSACSamplingSize) " label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" name="param_outlierDetection_RANSACSamplingSize" type="integer" value="10"/>
140 <param name="param_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function." help="(-interpolation_step)"/> 290 <param help="(-InitialQualityCutoff) -2 to 2)" label="The initial overall quality cutoff for a peak to be scored (range ca" name="param_peptideEstimation_InitialQualityCutoff" type="float" value="0.5"/>
141 <param name="param_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)"/> 291 <param help="(-OverallQualityCutoff) 0 to 10)" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" name="param_peptideEstimation_OverallQualityCutoff" type="float" value="5.5"/>
142 <param name="param_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm." help="(-max_iteration)"/> 292 <param 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)" label="Number of RT bins to use to compute coverage" name="param_peptideEstimation_NrRTBins" type="integer" value="10"/>
143 <param name="param_mean" type="float" value="1.0" label="Centroid position of the model." help="(-mean)"/> 293 <param help="(-MinPeptidesPerBin) " label="Minimal number of peptides that are required for a bin to counted as 'covered'" name="param_peptideEstimation_MinPeptidesPerBin" type="integer" value="1"/>
144 <param name="param_variance" type="float" value="1.0" label="Variance of the model." help="(-variance)"/> 294 <param help="(-MinBinsFilled) " label="Minimal number of bins required to be covered" name="param_peptideEstimation_MinBinsFilled" type="integer" value="8"/>
145 <param name="param_use_shape_score" type="boolean" truevalue="-algorithm:Scores:use_shape_score true" falsevalue="-algorithm:Scores:use_shape_score false" 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)"/> 295 <expand macro="advanced_options">
146 <param name="param_use_coelution_score" type="boolean" truevalue="-algorithm:Scores:use_coelution_score true" falsevalue="-algorithm:Scores:use_coelution_score false" 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)"/> 296 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
147 <param name="param_use_rt_score" type="boolean" truevalue="-algorithm:Scores:use_rt_score true" falsevalue="-algorithm:Scores:use_rt_score false" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score)"/> 297 <param help="(-quantification_cutoff) " label="Cutoff in m/z below which peaks should not be used for quantification any more" min="0.0" name="param_algorithm_quantification_cutoff" optional="True" type="float" value="0.0"/>
148 <param name="param_use_library_score" type="boolean" truevalue="-algorithm:Scores:use_library_score true" falsevalue="-algorithm:Scores:use_library_score false" checked="true" optional="True" label="Use the library score" help="(-use_library_score)"/> 298 <param checked="false" falsevalue="" help="(-write_convex_hull) " label="Whether to write out all points of all features into the featureXML" name="param_algorithm_write_convex_hull" optional="True" truevalue="-algorithm:write_convex_hull" type="boolean"/>
149 <param name="param_use_elution_model_score" type="boolean" truevalue="-algorithm:Scores:use_elution_model_score true" falsevalue="-algorithm:Scores:use_elution_model_score false" 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)"/> 299 <param help="(-add_up_spectra) " label="Add up spectra around the peak apex (needs to be a non-even integer)" min="1" name="param_algorithm_add_up_spectra" optional="True" type="integer" value="1"/>
150 <param name="param_use_intensity_score" type="boolean" truevalue="-algorithm:Scores:use_intensity_score true" falsevalue="-algorithm:Scores:use_intensity_score false" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score)"/> 300 <param help="(-spacing_for_spectra_resampling) " label="If spectra are to be added, use this spacing to add them up" min="0.0" name="param_algorithm_spacing_for_spectra_resampling" optional="True" type="float" value="0.005"/>
151 <param name="param_use_nr_peaks_score" type="boolean" truevalue="-algorithm:Scores:use_nr_peaks_score true" falsevalue="-algorithm:Scores:use_nr_peaks_score false" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score)"/> 301 <param help="(-min_peak_width) " label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0"/>
152 <param name="param_use_total_xic_score" type="boolean" truevalue="-algorithm:Scores:use_total_xic_score true" falsevalue="-algorithm:Scores:use_total_xic_score false" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score)"/> 302 <param help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that" label="Try to apply a background subtraction to the peak (experimental)" name="param_algorithm_TransitionGroupPicker_background_subtraction" optional="True" type="select" value="none">
153 <param name="param_use_sn_score" type="boolean" truevalue="-algorithm:Scores:use_sn_score true" falsevalue="-algorithm:Scores:use_sn_score false" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score)"/> 303 <option value="none">none</option>
154 <param name="param_use_dia_scores" type="boolean" truevalue="-algorithm:Scores:use_dia_scores true" falsevalue="-algorithm:Scores:use_dia_scores false" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores)"/> 304 <option value="smoothed">smoothed</option>
155 <param name="param_use_ms1_correlation" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation true" falsevalue="-algorithm:Scores:use_ms1_correlation false" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation)"/> 305 <option value="original">original</option>
156 <param name="param_use_ms1_fullscan" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan true" falsevalue="-algorithm:Scores:use_ms1_fullscan false" 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)"/> 306 </param>
157 </expand> 307 <param help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" name="param_algorithm_TransitionGroupPicker_recalculate_peaks" size="30" type="text" value="false">
158 </inputs> 308 <sanitizer>
159 <outputs> 309 <valid initial="string.printable">
160 <data name="param_out" label="output file" format="data"/> 310 <remove value="'"/>
161 </outputs> 311 <remove value="&quot;"/>
162 <help>**What it does** 312 </valid>
163 313 </sanitizer>
164 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. 314 </param>
315 <param help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0"/>
316 <param help="(-minimal_quality) " label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0"/>
317 <param 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" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" name="param_algorithm_TransitionGroupPicker_compute_peak_quality" size="30" type="text" value="false">
318 <sanitizer>
319 <valid initial="string.printable">
320 <remove value="'"/>
321 <remove value="&quot;"/>
322 </valid>
323 </sanitizer>
324 </param>
325 <param help="(-interpolation_step) " label="Sampling rate for the interpolation of the model function" name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2"/>
326 <param help="(-tolerance_stdev_bounding_box) " label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0"/>
327 <param help="(-max_iteration) " label="Maximum number of iterations using by Levenberg-Marquardt algorithm" name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500"/>
328 <param help="(-mean) " label="Centroid position of the model" name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0"/>
329 <param help="(-variance) " label="Variance of the model" name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0"/>
330 <param checked="true" falsevalue="" help="(-use_shape_score) " label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" name="param_algorithm_Scores_use_shape_score" optional="True" truevalue="-algorithm:Scores:use_shape_score" type="boolean"/>
331 <param checked="true" falsevalue="" help="(-use_coelution_score) " label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" name="param_algorithm_Scores_use_coelution_score" optional="True" truevalue="-algorithm:Scores:use_coelution_score" type="boolean"/>
332 <param checked="true" falsevalue="" help="(-use_rt_score) " label="Use the retention time score (this score measure the difference in retention time)" name="param_algorithm_Scores_use_rt_score" optional="True" truevalue="-algorithm:Scores:use_rt_score" type="boolean"/>
333 <param checked="true" falsevalue="" help="(-use_library_score) " label="Use the library score" name="param_algorithm_Scores_use_library_score" optional="True" truevalue="-algorithm:Scores:use_library_score" type="boolean"/>
334 <param checked="true" falsevalue="" help="(-use_elution_model_score) " label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" name="param_algorithm_Scores_use_elution_model_score" optional="True" truevalue="-algorithm:Scores:use_elution_model_score" type="boolean"/>
335 <param checked="true" falsevalue="" help="(-use_intensity_score) " label="Use the intensity score" name="param_algorithm_Scores_use_intensity_score" optional="True" truevalue="-algorithm:Scores:use_intensity_score" type="boolean"/>
336 <param checked="true" falsevalue="" help="(-use_nr_peaks_score) " label="Use the number of peaks score" name="param_algorithm_Scores_use_nr_peaks_score" optional="True" truevalue="-algorithm:Scores:use_nr_peaks_score" type="boolean"/>
337 <param checked="true" falsevalue="" help="(-use_total_xic_score) " label="Use the total XIC score" name="param_algorithm_Scores_use_total_xic_score" optional="True" truevalue="-algorithm:Scores:use_total_xic_score" type="boolean"/>
338 <param checked="true" falsevalue="" help="(-use_sn_score) " label="Use the SN (signal to noise) score" name="param_algorithm_Scores_use_sn_score" optional="True" truevalue="-algorithm:Scores:use_sn_score" type="boolean"/>
339 <param checked="true" falsevalue="" help="(-use_dia_scores) " label="Use the DIA (SWATH) scores" name="param_algorithm_Scores_use_dia_scores" optional="True" truevalue="-algorithm:Scores:use_dia_scores" type="boolean"/>
340 <param checked="false" falsevalue="" help="(-use_ms1_correlation) " label="Use the correlation scores with the MS1 elution profiles" name="param_algorithm_Scores_use_ms1_correlation" optional="True" truevalue="-algorithm:Scores:use_ms1_correlation" type="boolean"/>
341 <param checked="false" falsevalue="" help="(-use_ms1_fullscan) " label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" name="param_algorithm_Scores_use_ms1_fullscan" optional="True" truevalue="-algorithm:Scores:use_ms1_fullscan" type="boolean"/>
342 </expand>
343 </inputs>
344 <outputs>
345 <data format="trafoxml" name="param_out"/>
346 </outputs>
347 <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.
165 348
166 349
167 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html 350 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html</help>
168 351 </tool>
169 @REFERENCES@
170 </help>
171 </tool>