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comparison OpenSwathWorkflow.xml @ 0:380ced982ec7 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 12:53:40 -0500
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-1:000000000000 0:380ced982ec7
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: [Utilities]-->
4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.1.0">
5 <description>Complete workflow to run OpenSWATH</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathWorkflow
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 $param_tr_type:
23 -tr_type
24 #if " " in str($param_tr_type):
25 "$param_tr_type"
26 #else
27 $param_tr_type
28 #end if
29 #end if
30 #if $param_tr_irt:
31 -tr_irt $param_tr_irt
32 #end if
33 #if $param_out_features:
34 -out_features $param_out_features
35 #end if
36 #if $param_out_tsv:
37 -out_tsv "$param_out_tsv"
38 #end if
39 #if $param_out_chrom:
40 -out_chrom $param_out_chrom
41 #end if
42 #if $param_rt_extraction_window:
43 -rt_extraction_window $param_rt_extraction_window
44 #end if
45 #if $param_mz_extraction_window:
46 -mz_extraction_window $param_mz_extraction_window
47 #end if
48 #if $param_ppm:
49 -ppm
50 #end if
51 #if $param_Scoring_stop_report_after_feature:
52 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
53 #end if
54 #if $param_Scoring_rt_normalization_factor:
55 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
56 #end if
57 #if $param_Scoring_uis_threshold_sn:
58 -Scoring:uis_threshold_sn $param_Scoring_uis_threshold_sn
59 #end if
60 #if $param_Scoring_uis_threshold_peak_area:
61 -Scoring:uis_threshold_peak_area $param_Scoring_uis_threshold_peak_area
62 #end if
63 #if $param_Scoring_TransitionGroupPicker_stop_after_feature:
64 -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature
65 #end if
66 #if $param_Scoring_TransitionGroupPicker_min_peak_width:
67 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
68 #end if
69 #if $param_Scoring_TransitionGroupPicker_background_subtraction:
70 -Scoring:TransitionGroupPicker:background_subtraction $param_Scoring_TransitionGroupPicker_background_subtraction
71 #end if
72 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
73 -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
74 #end if
75 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
76 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
77 #end if
78 #if $param_Scoring_TransitionGroupPicker_minimal_quality:
79 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
80 #end if
81 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
82 -Scoring:TransitionGroupPicker:compute_peak_quality "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
83 #end if
84 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
85 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
86 #end if
87 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
88 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
89 #end if
90 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width:
91 -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width
92 #end if
93 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss:
94 -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss
95 #end if
96 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width:
97 -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width
98 #end if
99 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
100 -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
101 #end if
102 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
103 -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
104 #end if
105 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
106 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
107 #end if
108 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
109 -Scoring:TransitionGroupPicker:PeakPickerMRM:method $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
110 #end if
111 #if $param_Scoring_DIAScoring_dia_extraction_window:
112 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
113 #end if
114 #if $param_Scoring_DIAScoring_dia_centroided:
115 -Scoring:DIAScoring:dia_centroided
116 #end if
117 #if $param_Scoring_DIAScoring_dia_byseries_intensity_min:
118 -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min
119 #end if
120 #if $param_Scoring_DIAScoring_dia_byseries_ppm_diff:
121 -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff
122 #end if
123 #if $param_Scoring_DIAScoring_dia_nr_isotopes:
124 -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes
125 #end if
126 #if $param_Scoring_DIAScoring_dia_nr_charges:
127 -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges
128 #end if
129 #if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff:
130 -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff
131 #end if
132 #if $param_Scoring_EMGScoring_max_iteration:
133 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
134 #end if
135 #if $param_outlierDetection_outlierMethod:
136 -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod
137 #end if
138 #if $param_outlierDetection_useIterativeChauvenet:
139 -outlierDetection:useIterativeChauvenet
140 #end if
141 #if $param_outlierDetection_RANSACMaxIterations:
142 -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations
143 #end if
144 #if $param_outlierDetection_RANSACMaxPercentRTThreshold:
145 -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold
146 #end if
147 #if $param_outlierDetection_RANSACSamplingSize:
148 -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize
149 #end if
150 #if $param_outlierDetection_estimateBestPeptides:
151 -outlierDetection:estimateBestPeptides
152 #end if
153 #if $param_outlierDetection_InitialQualityCutoff:
154 -outlierDetection:InitialQualityCutoff $param_outlierDetection_InitialQualityCutoff
155 #end if
156 #if $param_outlierDetection_OverallQualityCutoff:
157 -outlierDetection:OverallQualityCutoff $param_outlierDetection_OverallQualityCutoff
158 #end if
159 #if $param_outlierDetection_NrRTBins:
160 -outlierDetection:NrRTBins $param_outlierDetection_NrRTBins
161 #end if
162 #if $param_outlierDetection_MinPeptidesPerBin:
163 -outlierDetection:MinPeptidesPerBin $param_outlierDetection_MinPeptidesPerBin
164 #end if
165 #if $param_outlierDetection_MinBinsFilled:
166 -outlierDetection:MinBinsFilled $param_outlierDetection_MinBinsFilled
167 #end if
168 #if $adv_opts.adv_opts_selector=='advanced':
169 #if $adv_opts.param_rt_norm:
170 -rt_norm $adv_opts.param_rt_norm
171 #end if
172 #if $adv_opts.param_swath_windows_file:
173 -swath_windows_file $adv_opts.param_swath_windows_file
174 #end if
175 #if $adv_opts.param_sort_swath_maps:
176 -sort_swath_maps
177 #end if
178 #if $adv_opts.param_use_ms1_traces:
179 -use_ms1_traces
180 #end if
181 #if $adv_opts.param_enable_uis_scoring:
182 -enable_uis_scoring
183 #end if
184 #if $adv_opts.param_min_upper_edge_dist:
185 -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist
186 #end if
187 #if $adv_opts.param_extra_rt_extraction_window:
188 -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window
189 #end if
190 #if $adv_opts.param_min_rsq:
191 -min_rsq $adv_opts.param_min_rsq
192 #end if
193 #if $adv_opts.param_min_coverage:
194 -min_coverage $adv_opts.param_min_coverage
195 #end if
196 #if $adv_opts.param_split_file_input:
197 -split_file_input
198 #end if
199 #if $adv_opts.param_use_elution_model_score:
200 -use_elution_model_score
201 #end if
202 #if $adv_opts.param_readOptions:
203 -readOptions $adv_opts.param_readOptions
204 #end if
205 #if $adv_opts.param_mz_correction_function:
206 -mz_correction_function $adv_opts.param_mz_correction_function
207 #end if
208 #if $adv_opts.param_tempDirectory:
209 -tempDirectory "$adv_opts.param_tempDirectory"
210 #end if
211 #if $adv_opts.param_extraction_function:
212 -extraction_function $adv_opts.param_extraction_function
213 #end if
214 #if $adv_opts.param_batchSize:
215 -batchSize $adv_opts.param_batchSize
216 #end if
217 #if $adv_opts.param_force:
218 -force
219 #end if
220 #if $adv_opts.param_Scoring_quantification_cutoff:
221 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
222 #end if
223 #if $adv_opts.param_Scoring_write_convex_hull:
224 -Scoring:write_convex_hull
225 #end if
226 #if $adv_opts.param_Scoring_Scores_use_shape_score:
227 -Scoring:Scores:use_shape_score $adv_opts.param_Scoring_Scores_use_shape_score
228 #end if
229 #if $adv_opts.param_Scoring_Scores_use_coelution_score:
230 -Scoring:Scores:use_coelution_score $adv_opts.param_Scoring_Scores_use_coelution_score
231 #end if
232 #if $adv_opts.param_Scoring_Scores_use_rt_score:
233 -Scoring:Scores:use_rt_score $adv_opts.param_Scoring_Scores_use_rt_score
234 #end if
235 #if $adv_opts.param_Scoring_Scores_use_library_score:
236 -Scoring:Scores:use_library_score $adv_opts.param_Scoring_Scores_use_library_score
237 #end if
238 #if $adv_opts.param_Scoring_Scores_use_intensity_score:
239 -Scoring:Scores:use_intensity_score $adv_opts.param_Scoring_Scores_use_intensity_score
240 #end if
241 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
242 -Scoring:Scores:use_nr_peaks_score $adv_opts.param_Scoring_Scores_use_nr_peaks_score
243 #end if
244 #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
245 -Scoring:Scores:use_total_xic_score $adv_opts.param_Scoring_Scores_use_total_xic_score
246 #end if
247 #if $adv_opts.param_Scoring_Scores_use_sn_score:
248 -Scoring:Scores:use_sn_score $adv_opts.param_Scoring_Scores_use_sn_score
249 #end if
250 #if $adv_opts.param_Scoring_Scores_use_dia_scores:
251 -Scoring:Scores:use_dia_scores $adv_opts.param_Scoring_Scores_use_dia_scores
252 #end if
253 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
254 -Scoring:Scores:use_ms1_correlation
255 #end if
256 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
257 -Scoring:Scores:use_ms1_fullscan
258 #end if
259 #if $adv_opts.param_Scoring_Scores_use_uis_scores:
260 -Scoring:Scores:use_uis_scores
261 #end if
262 #end if
263 </command>
264 <inputs>
265 <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
266 <sanitizer>
267 <valid initial="string.printable">
268 <remove value="'"/>
269 <remove value="&quot;"/>
270 </valid>
271 </sanitizer>
272 </param>
273 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/>
274 <param name="param_tr_type" display="radio" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) ">
275 <option value="traML">traML</option>
276 <option value="tsv">tsv</option>
277 <option value="csv">csv</option>
278 </param>
279 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
280 <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) ">
281 <sanitizer>
282 <valid initial="string.printable">
283 <remove value="'"/>
284 <remove value="&quot;"/>
285 </valid>
286 </sanitizer>
287 </param>
288 <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) "/>
289 <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) "/>
290 <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) "/>
291 <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) "/>
292 <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)"/>
293 <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) "/>
294 <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) "/>
295 <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) "/>
296 <param name="param_Scoring_TransitionGroupPicker_min_peak_width" type="float" value="14.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
297 <param name="param_Scoring_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">
298 <option value="none" selected="true">none</option>
299 <option value="smoothed">smoothed</option>
300 <option value="original">original</option>
301 </param>
302 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large">
303 <sanitizer>
304 <valid initial="string.printable">
305 <remove value="'"/>
306 <remove value="&quot;"/>
307 </valid>
308 </sanitizer>
309 </param>
310 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="0.75" 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)"/>
311 <param name="param_Scoring_TransitionGroupPicker_minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
312 <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="true" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">
313 <sanitizer>
314 <valid initial="string.printable">
315 <remove value="'"/>
316 <remove value="&quot;"/>
317 </valid>
318 </sanitizer>
319 </param>
320 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="11" 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"/>
321 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
322 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
323 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" falsevalue="" checked="false" optional="True" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "/>
324 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
325 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="0.1" 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"/>
326 <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) "/>
327 <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) ">
328 <option value="false">false</option>
329 <option value="true" selected="true">true</option>
330 </param>
331 <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) ">
332 <option value="legacy">legacy</option>
333 <option value="corrected" selected="true">corrected</option>
334 <option value="crawdad">crawdad</option>
335 </param>
336 <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) "/>
337 <param name="param_Scoring_DIAScoring_dia_centroided" display="radio" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
338 <param name="param_Scoring_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) "/>
339 <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) "/>
340 <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) "/>
341 <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) "/>
342 <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) "/>
343 <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
344 <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)">
345 <option value="iter_residual" selected="true">iter_residual</option>
346 <option value="iter_jackknife">iter_jackknife</option>
347 <option value="ransac">ransac</option>
348 <option value="none">none</option>
349 </param>
350 <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"/>
351 <param name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
352 <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"/>
353 <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) "/>
354 <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)"/>
355 <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)"/>
356 <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)"/>
357 <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)"/>
358 <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) "/>
359 <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
360 <expand macro="advanced_options">
361 <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"/>
362 <param name="param_swath_windows_file" type="data" format="text" 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"/>
363 <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) "/>
364 <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) "/>
365 <param name="param_enable_uis_scoring" display="radio" type="boolean" truevalue="-enable_uis_scoring" falsevalue="" checked="false" optional="True" label="Enable additional scoring of identification assays" help="(-enable_uis_scoring) "/>
366 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
367 <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/>
368 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
369 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
370 <param name="param_split_file_input" display="radio" type="boolean" truevalue="-split_file_input" falsevalue="" checked="false" optional="True" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help="(-split_file_input) "/>
371 <param name="param_use_elution_model_score" display="radio" type="boolean" truevalue="-use_elution_model_score" falsevalue="" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score) "/>
372 <param name="param_readOptions" display="radio" type="select" optional="False" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="(-readOptions) If you choose cache, make sure to also set tempDirectory">
373 <option value="normal" selected="true">normal</option>
374 <option value="cache">cache</option>
375 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
376 </param>
377 <param name="param_mz_correction_function" type="select" optional="False" value="none" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="(-mz_correction_function) ">
378 <option value="none" selected="true">none</option>
379 <option value="unweighted_regression">unweighted_regression</option>
380 <option value="weighted_regression">weighted_regression</option>
381 <option value="quadratic_regression">quadratic_regression</option>
382 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option>
383 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option>
384 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
385 </param>
386 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
387 <sanitizer>
388 <valid initial="string.printable">
389 <remove value="'"/>
390 <remove value="&quot;"/>
391 </valid>
392 </sanitizer>
393 </param>
394 <param name="param_extraction_function" display="radio" type="select" optional="False" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
395 <option value="tophat" selected="true">tophat</option>
396 <option value="bartlett">bartlett</option>
397 </param>
398 <param name="param_batchSize" type="integer" min="0" optional="True" value="0" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 500-1000)" help="(-batchSize) "/>
399 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
400 <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) "/>
401 <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) "/>
402 <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) ">
403 <option value="true" selected="true">true</option>
404 <option value="false">false</option>
405 </param>
406 <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) ">
407 <option value="true" selected="true">true</option>
408 <option value="false">false</option>
409 </param>
410 <param name="param_Scoring_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) ">
411 <option value="true" selected="true">true</option>
412 <option value="false">false</option>
413 </param>
414 <param name="param_Scoring_Scores_use_library_score" display="radio" type="select" optional="False" value="true" label="Use the library score" help="(-use_library_score) ">
415 <option value="true" selected="true">true</option>
416 <option value="false">false</option>
417 </param>
418 <param name="param_Scoring_Scores_use_intensity_score" display="radio" type="select" optional="False" value="true" label="Use the intensity score" help="(-use_intensity_score) ">
419 <option value="true" selected="true">true</option>
420 <option value="false">false</option>
421 </param>
422 <param name="param_Scoring_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) ">
423 <option value="true" selected="true">true</option>
424 <option value="false">false</option>
425 </param>
426 <param name="param_Scoring_Scores_use_total_xic_score" display="radio" type="select" optional="False" value="true" label="Use the total XIC score" help="(-use_total_xic_score) ">
427 <option value="true" selected="true">true</option>
428 <option value="false">false</option>
429 </param>
430 <param name="param_Scoring_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) ">
431 <option value="true" selected="true">true</option>
432 <option value="false">false</option>
433 </param>
434 <param name="param_Scoring_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) ">
435 <option value="true" selected="true">true</option>
436 <option value="false">false</option>
437 </param>
438 <param name="param_Scoring_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
439 <param name="param_Scoring_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-Scoring: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) "/>
440 <param name="param_Scoring_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
441 </expand>
442 </inputs>
443 <outputs>
444 <data name="param_out_features" format="featurexml"/>
445 <data name="param_out_chrom" format="mzml"/>
446 </outputs>
447 <help>Complete workflow to run OpenSWATH
448
449
450 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html</help>
451 </tool>