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comparison OpenSwathWorkflow.xml @ 5:56988709dec6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:02:55 -0500
parents 190554cf2195
children 091d4e82839a
comparison
equal deleted inserted replaced
4:1734e2933b2b 5:56988709dec6
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.2.0.1"> 4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.3.0">
5 <description>Complete workflow to run OpenSWATH</description> 5 <description>Complete workflow to run OpenSWATH</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathWorkflow</token> 7 <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
52 -ppm 52 -ppm
53 #end if 53 #end if
54 #if $param_sonar: 54 #if $param_sonar:
55 -sonar 55 -sonar
56 #end if 56 #end if
57 #if $param_RTNormalization_alignmentMethod:
58 -RTNormalization:alignmentMethod
59 #if " " in str($param_RTNormalization_alignmentMethod):
60 "$param_RTNormalization_alignmentMethod"
61 #else
62 $param_RTNormalization_alignmentMethod
63 #end if
64 #end if
65 #if $param_RTNormalization_outlierMethod:
66 -RTNormalization:outlierMethod
67 #if " " in str($param_RTNormalization_outlierMethod):
68 "$param_RTNormalization_outlierMethod"
69 #else
70 $param_RTNormalization_outlierMethod
71 #end if
72 #end if
73 #if $param_RTNormalization_useIterativeChauvenet:
74 -RTNormalization:useIterativeChauvenet
75 #end if
76 #if $param_RTNormalization_RANSACMaxIterations:
77 -RTNormalization:RANSACMaxIterations $param_RTNormalization_RANSACMaxIterations
78 #end if
79 #if $param_RTNormalization_RANSACMaxPercentRTThreshold:
80 -RTNormalization:RANSACMaxPercentRTThreshold $param_RTNormalization_RANSACMaxPercentRTThreshold
81 #end if
82 #if $param_RTNormalization_RANSACSamplingSize:
83 -RTNormalization:RANSACSamplingSize $param_RTNormalization_RANSACSamplingSize
84 #end if
85 #if $param_RTNormalization_estimateBestPeptides:
86 -RTNormalization:estimateBestPeptides
87 #end if
88 #if $param_RTNormalization_InitialQualityCutoff:
89 -RTNormalization:InitialQualityCutoff $param_RTNormalization_InitialQualityCutoff
90 #end if
91 #if $param_RTNormalization_OverallQualityCutoff:
92 -RTNormalization:OverallQualityCutoff $param_RTNormalization_OverallQualityCutoff
93 #end if
94 #if $param_RTNormalization_NrRTBins:
95 -RTNormalization:NrRTBins $param_RTNormalization_NrRTBins
96 #end if
97 #if $param_RTNormalization_MinPeptidesPerBin:
98 -RTNormalization:MinPeptidesPerBin $param_RTNormalization_MinPeptidesPerBin
99 #end if
100 #if $param_RTNormalization_MinBinsFilled:
101 -RTNormalization:MinBinsFilled $param_RTNormalization_MinBinsFilled
102 #end if
103 #if $param_RTNormalization_lowess_span:
104 -RTNormalization:lowess:span $param_RTNormalization_lowess_span
105 #end if
106 #if $param_RTNormalization_b_spline_num_nodes:
107 -RTNormalization:b_spline:num_nodes $param_RTNormalization_b_spline_num_nodes
108 #end if
57 #if $param_Scoring_stop_report_after_feature: 109 #if $param_Scoring_stop_report_after_feature:
58 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature 110 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
59 #end if 111 #end if
60 #if $param_Scoring_rt_normalization_factor: 112 #if $param_Scoring_rt_normalization_factor:
61 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor 113 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
161 -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff 213 -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff
162 #end if 214 #end if
163 #if $param_Scoring_EMGScoring_max_iteration: 215 #if $param_Scoring_EMGScoring_max_iteration:
164 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration 216 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
165 #end if 217 #end if
166 #if $param_outlierDetection_outlierMethod:
167 -outlierDetection:outlierMethod
168 #if " " in str($param_outlierDetection_outlierMethod):
169 "$param_outlierDetection_outlierMethod"
170 #else
171 $param_outlierDetection_outlierMethod
172 #end if
173 #end if
174 #if $param_outlierDetection_useIterativeChauvenet:
175 -outlierDetection:useIterativeChauvenet
176 #end if
177 #if $param_outlierDetection_RANSACMaxIterations:
178 -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations
179 #end if
180 #if $param_outlierDetection_RANSACMaxPercentRTThreshold:
181 -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold
182 #end if
183 #if $param_outlierDetection_RANSACSamplingSize:
184 -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize
185 #end if
186 #if $param_outlierDetection_estimateBestPeptides:
187 -outlierDetection:estimateBestPeptides
188 #end if
189 #if $param_outlierDetection_InitialQualityCutoff:
190 -outlierDetection:InitialQualityCutoff $param_outlierDetection_InitialQualityCutoff
191 #end if
192 #if $param_outlierDetection_OverallQualityCutoff:
193 -outlierDetection:OverallQualityCutoff $param_outlierDetection_OverallQualityCutoff
194 #end if
195 #if $param_outlierDetection_NrRTBins:
196 -outlierDetection:NrRTBins $param_outlierDetection_NrRTBins
197 #end if
198 #if $param_outlierDetection_MinPeptidesPerBin:
199 -outlierDetection:MinPeptidesPerBin $param_outlierDetection_MinPeptidesPerBin
200 #end if
201 #if $param_outlierDetection_MinBinsFilled:
202 -outlierDetection:MinBinsFilled $param_outlierDetection_MinBinsFilled
203 #end if
204 #if $adv_opts.adv_opts_selector=='advanced': 218 #if $adv_opts.adv_opts_selector=='advanced':
205 #if $adv_opts.param_rt_norm: 219 #if $adv_opts.param_rt_norm:
206 -rt_norm $adv_opts.param_rt_norm 220 -rt_norm $adv_opts.param_rt_norm
207 #end if 221 #end if
208 #if $adv_opts.param_swath_windows_file: 222 #if $adv_opts.param_swath_windows_file:
294 #if $adv_opts.param_Scoring_write_convex_hull: 308 #if $adv_opts.param_Scoring_write_convex_hull:
295 -Scoring:write_convex_hull 309 -Scoring:write_convex_hull
296 #end if 310 #end if
297 #if $adv_opts.param_Scoring_TransitionGroupPicker_use_precursors: 311 #if $adv_opts.param_Scoring_TransitionGroupPicker_use_precursors:
298 -Scoring:TransitionGroupPicker:use_precursors 312 -Scoring:TransitionGroupPicker:use_precursors
313 #end if
314 #if $adv_opts.param_Scoring_TransitionGroupPicker_resample_boundary:
315 -Scoring:TransitionGroupPicker:resample_boundary $adv_opts.param_Scoring_TransitionGroupPicker_resample_boundary
299 #end if 316 #end if
300 #if $adv_opts.param_Scoring_Scores_use_shape_score: 317 #if $adv_opts.param_Scoring_Scores_use_shape_score:
301 -Scoring:Scores:use_shape_score 318 -Scoring:Scores:use_shape_score
302 #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score): 319 #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score):
303 "$adv_opts.param_Scoring_Scores_use_shape_score" 320 "$adv_opts.param_Scoring_Scores_use_shape_score"
401 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/> 418 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
402 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/> 419 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/>
403 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/> 420 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/>
404 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/> 421 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
405 <param name="param_sonar" display="radio" type="boolean" truevalue="-sonar" falsevalue="" checked="false" optional="True" label="data is scanning SWATH data" help="(-sonar) "/> 422 <param name="param_sonar" display="radio" type="boolean" truevalue="-sonar" falsevalue="" checked="false" optional="True" label="data is scanning SWATH data" help="(-sonar) "/>
423 <param name="param_RTNormalization_alignmentMethod" display="radio" type="select" optional="False" value="linear" label="How to perform the alignment to the normalized RT space using anchor points" help="(-alignmentMethod) 'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing">
424 <option value="linear" selected="true">linear</option>
425 <option value="interpolated">interpolated</option>
426 <option value="lowess">lowess</option>
427 <option value="b_spline">b_spline</option>
428 </param>
429 <param name="param_RTNormalization_outlierMethod" display="radio" type="select" optional="False" value="iter_residual" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="(-outlierMethod) Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
430 <option value="iter_residual" selected="true">iter_residual</option>
431 <option value="iter_jackknife">iter_jackknife</option>
432 <option value="ransac">ransac</option>
433 <option value="none">none</option>
434 </param>
435 <param name="param_RTNormalization_useIterativeChauvenet" display="radio" type="boolean" truevalue="-RTNormalization:useIterativeChauvenet" falsevalue="" checked="false" optional="True" label="Whether to use Chauvenet's criterion when using iterative methods" help="(-useIterativeChauvenet) This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
436 <param name="param_RTNormalization_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
437 <param name="param_RTNormalization_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="(-RANSACMaxPercentRTThreshold) Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
438 <param name="param_RTNormalization_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help="(-RANSACSamplingSize) "/>
439 <param name="param_RTNormalization_estimateBestPeptides" display="radio" type="boolean" truevalue="-RTNormalization: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)"/>
440 <param name="param_RTNormalization_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)"/>
441 <param name="param_RTNormalization_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)"/>
442 <param name="param_RTNormalization_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)"/>
443 <param name="param_RTNormalization_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/>
444 <param name="param_RTNormalization_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
445 <param name="param_RTNormalization_lowess_span" type="float" min="0.0" max="1.0" optional="True" value="0.666666666667" label="Span parameter for lowess" help="(-span) "/>
446 <param name="param_RTNormalization_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for b spline" help="(-num_nodes) "/>
406 <param name="param_Scoring_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) "/> 447 <param name="param_Scoring_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) "/>
407 <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" 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)"/> 448 <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" 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)"/>
408 <param name="param_Scoring_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) "/> 449 <param name="param_Scoring_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) "/>
409 <param name="param_Scoring_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) "/> 450 <param name="param_Scoring_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) "/>
410 <param name="param_Scoring_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) "/> 451 <param name="param_Scoring_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) "/>
433 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" falsevalue="" checked="false" optional="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) "/> 474 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" falsevalue="" checked="false" optional="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) "/>
434 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="select" optional="False" value="true" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "> 475 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="select" optional="False" value="true" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) ">
435 <option value="false">false</option> 476 <option value="false">false</option>
436 <option value="true" selected="true">true</option> 477 <option value="true" selected="true">true</option>
437 </param> 478 </param>
438 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) "> 479 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="(-method) ">
439 <option value="legacy">legacy</option> 480 <option value="legacy">legacy</option>
440 <option value="corrected" selected="true">corrected</option> 481 <option value="corrected" selected="true">corrected</option>
441 <option value="crawdad">crawdad</option> 482 <option value="crawdad">crawdad</option>
442 </param> 483 </param>
443 <param name="param_Scoring_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/> 484 <param name="param_Scoring_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/>
446 <param name="param_Scoring_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) "/> 487 <param name="param_Scoring_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) "/>
447 <param name="param_Scoring_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/> 488 <param name="param_Scoring_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/>
448 <param name="param_Scoring_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/> 489 <param name="param_Scoring_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/>
449 <param name="param_Scoring_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) "/> 490 <param name="param_Scoring_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) "/>
450 <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/> 491 <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
451 <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)">
452 <option value="iter_residual" selected="true">iter_residual</option>
453 <option value="iter_jackknife">iter_jackknife</option>
454 <option value="ransac">ransac</option>
455 <option value="none">none</option>
456 </param>
457 <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"/>
458 <param name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
459 <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"/>
460 <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) "/>
461 <param name="param_outlierDetection_estimateBestPeptides" display="radio" type="boolean" truevalue="-outlierDetection: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)"/>
462 <param name="param_outlierDetection_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)"/>
463 <param name="param_outlierDetection_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)"/>
464 <param name="param_outlierDetection_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)"/>
465 <param name="param_outlierDetection_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/>
466 <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
467 <expand macro="advanced_options"> 492 <expand macro="advanced_options">
468 <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) If set, tr_irt may be omitted"/> 493 <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) If set, tr_irt may be omitted"/>
469 <param name="param_swath_windows_file" type="data" format="txt" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/> 494 <param name="param_swath_windows_file" type="data" format="txt" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
470 <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/> 495 <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/>
471 <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/> 496 <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/>
515 <param name="param_Library_override_group_label_check" display="radio" type="boolean" truevalue="-Library:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/> 540 <param name="param_Library_override_group_label_check" display="radio" type="boolean" truevalue="-Library:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
516 <param name="param_Library_force_invalid_mods" display="radio" type="boolean" truevalue="-Library:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/> 541 <param name="param_Library_force_invalid_mods" display="radio" type="boolean" truevalue="-Library:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/>
517 <param name="param_Scoring_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) "/> 542 <param name="param_Scoring_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) "/>
518 <param name="param_Scoring_write_convex_hull" display="radio" type="boolean" truevalue="-Scoring: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) "/> 543 <param name="param_Scoring_write_convex_hull" display="radio" type="boolean" truevalue="-Scoring: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) "/>
519 <param name="param_Scoring_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/> 544 <param name="param_Scoring_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
545 <param name="param_Scoring_TransitionGroupPicker_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>
520 <param name="param_Scoring_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) "> 546 <param name="param_Scoring_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) ">
521 <option value="true" selected="true">true</option> 547 <option value="true" selected="true">true</option>
522 <option value="false">false</option> 548 <option value="false">false</option>
523 </param> 549 </param>
524 <param name="param_Scoring_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) "> 550 <param name="param_Scoring_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) ">