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comparison OpenSwathWorkflow.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.0.0">
3 <description>Complete workflow to run OpenSWATH</description>
4 <macros>
5 <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>OpenSwathWorkflow
11
12 -in
13 #for token in $param_in:
14 $token
15 #end for
16 #if $param_tr:
17 -tr $param_tr
18 #end if
19 #if $param_tr_type:
20 -tr_type
21 #if " " in str($param_tr_type):
22 "$param_tr_type"
23 #else
24 $param_tr_type
25 #end if
26 #end if
27 #if $param_tr_irt:
28 -tr_irt $param_tr_irt
29 #end if
30 #if $param_out_features:
31 -out_features $param_out_features
32 #end if
33 #if $param_out_tsv:
34 -out_tsv "$param_out_tsv"
35 #end if
36 #if $param_out_chrom:
37 -out_chrom $param_out_chrom
38 #end if
39 #if $param_rt_extraction_window:
40 -rt_extraction_window $param_rt_extraction_window
41 #end if
42 #if $param_mz_extraction_window:
43 -mz_extraction_window $param_mz_extraction_window
44 #end if
45 #if $param_ppm:
46 -ppm
47 #end if
48 -threads \${GALAXY_SLOTS:-24}
49 #if $param_Scoring_stop_report_after_feature:
50 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
51 #end if
52 #if $param_Scoring_rt_normalization_factor:
53 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
54 #end if
55 #if $param_Scoring_TransitionGroupPicker_stop_after_feature:
56 -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature
57 #end if
58 #if $param_Scoring_TransitionGroupPicker_min_peak_width:
59 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
60 #end if
61 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
62 -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
63 #end if
64 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
65 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
66 #end if
67 #if $param_Scoring_TransitionGroupPicker_minimal_quality:
68 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
69 #end if
70 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
71 -Scoring:TransitionGroupPicker:compute_peak_quality "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
72 #end if
73 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
74 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
75 #end if
76 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
77 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
78 #end if
79 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width:
80 -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width
81 #end if
82 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss:
83 -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss"
84 #end if
85 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width:
86 -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width
87 #end if
88 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
89 -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
90 #end if
91 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
92 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
93 #end if
94 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
95 -Scoring:TransitionGroupPicker:PeakPickerMRM:method
96 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method):
97 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method"
98 #else
99 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
100 #end if
101 #end if
102 #if $param_Scoring_DIAScoring_dia_extraction_window:
103 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
104 #end if
105 #if $param_Scoring_DIAScoring_dia_centroided:
106 -Scoring:DIAScoring:dia_centroided
107 #end if
108 #if $param_Scoring_DIAScoring_dia_byseries_intensity_min:
109 -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min
110 #end if
111 #if $param_Scoring_DIAScoring_dia_byseries_ppm_diff:
112 -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff
113 #end if
114 #if $param_Scoring_DIAScoring_dia_nr_isotopes:
115 -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes
116 #end if
117 #if $param_Scoring_DIAScoring_dia_nr_charges:
118 -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges
119 #end if
120 #if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff:
121 -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff
122 #end if
123 #if $param_Scoring_EMGScoring_max_iteration:
124 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
125 #end if
126 #if $param_Scoring_EMGScoring_deltaRelError:
127 -Scoring:EMGScoring:deltaRelError $param_Scoring_EMGScoring_deltaRelError
128 #end if
129 #if $adv_opts.adv_opts_selector=='advanced':
130 #if $adv_opts.param_rt_norm:
131 -rt_norm $adv_opts.param_rt_norm
132 #end if
133 #if $adv_opts.param_swath_windows_file:
134 -swath_windows_file $adv_opts.param_swath_windows_file
135 #end if
136 #if $adv_opts.param_sort_swath_maps:
137 -sort_swath_maps
138 #end if
139 #if $adv_opts.param_use_ms1_traces:
140 -use_ms1_traces
141 #end if
142 #if $adv_opts.param_min_upper_edge_dist:
143 -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist
144 #end if
145 #if $adv_opts.param_extra_rt_extraction_window:
146 -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window
147 #end if
148 #if $adv_opts.param_min_rsq:
149 -min_rsq $adv_opts.param_min_rsq
150 #end if
151 #if $adv_opts.param_min_coverage:
152 -min_coverage $adv_opts.param_min_coverage
153 #end if
154 #if $adv_opts.param_split_file_input:
155 -split_file_input
156 #end if
157 #if $adv_opts.param_use_elution_model_score:
158 -use_elution_model_score
159 #end if
160 #if $adv_opts.param_readOptions:
161 -readOptions
162 #if " " in str($adv_opts.param_readOptions):
163 "$adv_opts.param_readOptions"
164 #else
165 $adv_opts.param_readOptions
166 #end if
167 #end if
168 #if $adv_opts.param_tempDirectory:
169 -tempDirectory "$adv_opts.param_tempDirectory"
170 #end if
171 #if $adv_opts.param_extraction_function:
172 -extraction_function
173 #if " " in str($adv_opts.param_extraction_function):
174 "$adv_opts.param_extraction_function"
175 #else
176 $adv_opts.param_extraction_function
177 #end if
178 #end if
179 #if $adv_opts.param_batchSize:
180 -batchSize $adv_opts.param_batchSize
181 #end if
182 #if $adv_opts.param_force:
183 -force
184 #end if
185 #if $adv_opts.param_Scoring_quantification_cutoff:
186 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
187 #end if
188 #if $adv_opts.param_Scoring_write_convex_hull:
189 -Scoring:write_convex_hull
190 #end if
191 #if $adv_opts.param_Scoring_Scores_use_shape_score:
192 -Scoring:Scores:use_shape_score
193 #end if
194 #if $adv_opts.param_Scoring_Scores_use_coelution_score:
195 -Scoring:Scores:use_coelution_score
196 #end if
197 #if $adv_opts.param_Scoring_Scores_use_rt_score:
198 -Scoring:Scores:use_rt_score
199 #end if
200 #if $adv_opts.param_Scoring_Scores_use_library_score:
201 -Scoring:Scores:use_library_score
202 #end if
203 #if $adv_opts.param_Scoring_Scores_use_intensity_score:
204 -Scoring:Scores:use_intensity_score
205 #end if
206 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
207 -Scoring:Scores:use_nr_peaks_score
208 #end if
209 #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
210 -Scoring:Scores:use_total_xic_score
211 #end if
212 #if $adv_opts.param_Scoring_Scores_use_sn_score:
213 -Scoring:Scores:use_sn_score
214 #end if
215 #if $adv_opts.param_Scoring_Scores_use_dia_scores:
216 -Scoring:Scores:use_dia_scores
217 #end if
218 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
219 -Scoring:Scores:use_ms1_correlation
220 #end if
221 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
222 -Scoring:Scores:use_ms1_fullscan
223 #end if
224 #end if
225 </command>
226 <inputs>
227 <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
228 <sanitizer>
229 <valid initial="string.printable">
230 <remove value="'"/>
231 <remove value="&quot;"/>
232 </valid>
233 </sanitizer>
234 </param>
235 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/>
236 <param name="param_tr_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) ">
237 <option value="traML">traML</option>
238 <option value="tsv">tsv</option>
239 <option value="csv">csv</option>
240 </param>
241 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
242 <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) ">
243 <sanitizer>
244 <valid initial="string.printable">
245 <remove value="'"/>
246 <remove value="&quot;"/>
247 </valid>
248 </sanitizer>
249 </param>
250 <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) "/>
251 <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) "/>
252 <param name="param_ppm" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
253 <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) "/>
254 <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)"/>
255 <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) "/>
256 <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) "/>
257 <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">
258 <sanitizer>
259 <valid initial="string.printable">
260 <remove value="'"/>
261 <remove value="&quot;"/>
262 </valid>
263 </sanitizer>
264 </param>
265 <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)"/>
266 <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) "/>
267 <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">
268 <sanitizer>
269 <valid initial="string.printable">
270 <remove value="'"/>
271 <remove value="&quot;"/>
272 </valid>
273 </sanitizer>
274 </param>
275 <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"/>
276 <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) "/>
277 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
278 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" type="text" size="30" value="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
279 <sanitizer>
280 <valid initial="string.printable">
281 <remove value="'"/>
282 <remove value="&quot;"/>
283 </valid>
284 </sanitizer>
285 </param>
286 <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"/>
287 <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"/>
288 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="true" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
289 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" type="select" optional="True" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
290 <option value="legacy">legacy</option>
291 <option value="corrected">corrected</option>
292 <option value="crawdad">crawdad</option>
293 </param>
294 <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) "/>
295 <param name="param_Scoring_DIAScoring_dia_centroided" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
296 <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) "/>
297 <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) "/>
298 <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) "/>
299 <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) "/>
300 <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) "/>
301 <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
302 <param name="param_Scoring_EMGScoring_deltaRelError" type="float" value="0.1" label="" help="(-deltaRelError) "/>
303 <expand macro="advanced_options">
304 <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"/>
305 <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
306 <param name="param_sort_swath_maps" 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) "/>
307 <param name="param_use_ms1_traces" 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) "/>
308 <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) "/>
309 <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)"/>
310 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
311 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
312 <param name="param_split_file_input" 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) "/>
313 <param name="param_use_elution_model_score" 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) "/>
314 <param name="param_readOptions" type="select" optional="True" 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">
315 <option value="normal">normal</option>
316 <option value="cache">cache</option>
317 </param>
318 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
319 <sanitizer>
320 <valid initial="string.printable">
321 <remove value="'"/>
322 <remove value="&quot;"/>
323 </valid>
324 </sanitizer>
325 </param>
326 <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
327 <option value="tophat">tophat</option>
328 <option value="bartlett">bartlett</option>
329 </param>
330 <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) "/>
331 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
332 <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) "/>
333 <param name="param_Scoring_write_convex_hull" 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) "/>
334 <param name="param_Scoring_Scores_use_shape_score" type="boolean" truevalue="-Scoring:Scores:use_shape_score" falsevalue="" checked="true" optional="True" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) "/>
335 <param name="param_Scoring_Scores_use_coelution_score" type="boolean" truevalue="-Scoring:Scores:use_coelution_score" falsevalue="" checked="true" optional="True" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) "/>
336 <param name="param_Scoring_Scores_use_rt_score" type="boolean" truevalue="-Scoring:Scores:use_rt_score" falsevalue="" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score) "/>
337 <param name="param_Scoring_Scores_use_library_score" type="boolean" truevalue="-Scoring:Scores:use_library_score" falsevalue="" checked="true" optional="True" label="Use the library score" help="(-use_library_score) "/>
338 <param name="param_Scoring_Scores_use_intensity_score" type="boolean" truevalue="-Scoring:Scores:use_intensity_score" falsevalue="" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score) "/>
339 <param name="param_Scoring_Scores_use_nr_peaks_score" type="boolean" truevalue="-Scoring:Scores:use_nr_peaks_score" falsevalue="" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score) "/>
340 <param name="param_Scoring_Scores_use_total_xic_score" type="boolean" truevalue="-Scoring:Scores:use_total_xic_score" falsevalue="" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score) "/>
341 <param name="param_Scoring_Scores_use_sn_score" type="boolean" truevalue="-Scoring:Scores:use_sn_score" falsevalue="" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score) "/>
342 <param name="param_Scoring_Scores_use_dia_scores" type="boolean" truevalue="-Scoring:Scores:use_dia_scores" falsevalue="" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "/>
343 <param name="param_Scoring_Scores_use_ms1_correlation" 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) "/>
344 <param name="param_Scoring_Scores_use_ms1_fullscan" 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) "/>
345 </expand>
346 </inputs>
347 <outputs>
348 <data name="param_out_features" format="featurexml"/>
349 <data name="param_out_chrom" format="mzml"/>
350 </outputs>
351 <help>**What it does**
352
353 Complete workflow to run OpenSWATH
354
355
356 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html</help>
357 <expand macro="references"/>
358 </tool>