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comparison OpenSwathWorkflow.xml @ 3:372279190f47 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author galaxyp
date Fri, 14 Jul 2017 19:07:41 -0400
parents 34479f097d1b
children aef076574eab
comparison
equal deleted inserted replaced
2:a46df1a24002 3:372279190f47
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.1.0"> 4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.2.0">
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>
32 #end if 32 #end if
33 #if $param_out_features: 33 #if $param_out_features:
34 -out_features $param_out_features 34 -out_features $param_out_features
35 #end if 35 #end if
36 #if $param_out_tsv: 36 #if $param_out_tsv:
37 -out_tsv "$param_out_tsv" 37 -out_tsv $param_out_tsv
38 #end if
39 #if $param_out_osw:
40 -out_osw $param_out_osw
38 #end if 41 #end if
39 #if $param_out_chrom: 42 #if $param_out_chrom:
40 -out_chrom $param_out_chrom 43 -out_chrom $param_out_chrom
41 #end if 44 #end if
42 #if $param_rt_extraction_window: 45 #if $param_rt_extraction_window:
45 #if $param_mz_extraction_window: 48 #if $param_mz_extraction_window:
46 -mz_extraction_window $param_mz_extraction_window 49 -mz_extraction_window $param_mz_extraction_window
47 #end if 50 #end if
48 #if $param_ppm: 51 #if $param_ppm:
49 -ppm 52 -ppm
53 #end if
54 #if $param_sonar:
55 -sonar
50 #end if 56 #end if
51 #if $param_Scoring_stop_report_after_feature: 57 #if $param_Scoring_stop_report_after_feature:
52 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature 58 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
53 #end if 59 #end if
54 #if $param_Scoring_rt_normalization_factor: 60 #if $param_Scoring_rt_normalization_factor:
73 #else 79 #else
74 $param_Scoring_TransitionGroupPicker_background_subtraction 80 $param_Scoring_TransitionGroupPicker_background_subtraction
75 #end if 81 #end if
76 #end if 82 #end if
77 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks: 83 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
78 -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks" 84 -Scoring:TransitionGroupPicker:recalculate_peaks
85 #if " " in str($param_Scoring_TransitionGroupPicker_recalculate_peaks):
86 "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
87 #else
88 $param_Scoring_TransitionGroupPicker_recalculate_peaks
89 #end if
79 #end if 90 #end if
80 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z: 91 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
81 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z 92 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
82 #end if 93 #end if
83 #if $param_Scoring_TransitionGroupPicker_minimal_quality: 94 #if $param_Scoring_TransitionGroupPicker_minimal_quality:
84 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality 95 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
85 #end if 96 #end if
86 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality: 97 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
87 -Scoring:TransitionGroupPicker:compute_peak_quality "$param_Scoring_TransitionGroupPicker_compute_peak_quality" 98 -Scoring:TransitionGroupPicker:compute_peak_quality
99 #if " " in str($param_Scoring_TransitionGroupPicker_compute_peak_quality):
100 "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
101 #else
102 $param_Scoring_TransitionGroupPicker_compute_peak_quality
103 #end if
88 #end if 104 #end if
89 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: 105 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
90 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length 106 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
91 #end if 107 #end if
92 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: 108 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
233 "$adv_opts.param_mz_correction_function" 249 "$adv_opts.param_mz_correction_function"
234 #else 250 #else
235 $adv_opts.param_mz_correction_function 251 $adv_opts.param_mz_correction_function
236 #end if 252 #end if
237 #end if 253 #end if
254 #if $adv_opts.param_irt_mz_extraction_window:
255 -irt_mz_extraction_window $adv_opts.param_irt_mz_extraction_window
256 #end if
257 #if $adv_opts.param_ppm_irtwindow:
258 -ppm_irtwindow
259 #end if
238 #if $adv_opts.param_tempDirectory: 260 #if $adv_opts.param_tempDirectory:
239 -tempDirectory "$adv_opts.param_tempDirectory" 261 -tempDirectory "$adv_opts.param_tempDirectory"
240 #end if 262 #end if
241 #if $adv_opts.param_extraction_function: 263 #if $adv_opts.param_extraction_function:
242 -extraction_function 264 -extraction_function
250 -batchSize $adv_opts.param_batchSize 272 -batchSize $adv_opts.param_batchSize
251 #end if 273 #end if
252 #if $adv_opts.param_force: 274 #if $adv_opts.param_force:
253 -force 275 -force
254 #end if 276 #end if
277 #if $adv_opts.param_Library_retentionTimeInterpretation:
278 -Library:retentionTimeInterpretation
279 #if " " in str($adv_opts.param_Library_retentionTimeInterpretation):
280 "$adv_opts.param_Library_retentionTimeInterpretation"
281 #else
282 $adv_opts.param_Library_retentionTimeInterpretation
283 #end if
284 #end if
285 #if $adv_opts.param_Library_override_group_label_check:
286 -Library:override_group_label_check
287 #end if
288 #if $adv_opts.param_Library_force_invalid_mods:
289 -Library:force_invalid_mods
290 #end if
255 #if $adv_opts.param_Scoring_quantification_cutoff: 291 #if $adv_opts.param_Scoring_quantification_cutoff:
256 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff 292 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
257 #end if 293 #end if
258 #if $adv_opts.param_Scoring_write_convex_hull: 294 #if $adv_opts.param_Scoring_write_convex_hull:
259 -Scoring:write_convex_hull 295 -Scoring:write_convex_hull
296 #end if
297 #if $adv_opts.param_Scoring_TransitionGroupPicker_use_precursors:
298 -Scoring:TransitionGroupPicker:use_precursors
260 #end if 299 #end if
261 #if $adv_opts.param_Scoring_Scores_use_shape_score: 300 #if $adv_opts.param_Scoring_Scores_use_shape_score:
262 -Scoring:Scores:use_shape_score 301 -Scoring:Scores:use_shape_score
263 #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score): 302 #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score):
264 "$adv_opts.param_Scoring_Scores_use_shape_score" 303 "$adv_opts.param_Scoring_Scores_use_shape_score"
331 #end if 370 #end if
332 #end if 371 #end if
333 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation: 372 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
334 -Scoring:Scores:use_ms1_correlation 373 -Scoring:Scores:use_ms1_correlation
335 #end if 374 #end if
375 #if $adv_opts.param_Scoring_Scores_use_sonar_scores:
376 -Scoring:Scores:use_sonar_scores
377 #end if
336 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan: 378 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
337 -Scoring:Scores:use_ms1_fullscan 379 -Scoring:Scores:use_ms1_fullscan
338 #end if 380 #end if
339 #if $adv_opts.param_Scoring_Scores_use_uis_scores: 381 #if $adv_opts.param_Scoring_Scores_use_uis_scores:
340 -Scoring:Scores:use_uis_scores 382 -Scoring:Scores:use_uis_scores
341 #end if 383 #end if
342 #end if 384 #end if
343 </command> 385 </command>
344 <inputs> 386 <inputs>
345 <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> 387 <param name="param_in" type="data" format="mzml,mzxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
346 <sanitizer> 388 <sanitizer>
347 <valid initial="string.printable"> 389 <valid initial="string.printable">
348 <remove value="'"/> 390 <remove value="'"/>
349 <remove value="&quot;"/> 391 <remove value="&quot;"/>
350 </valid> 392 </valid>
351 </sanitizer> 393 </sanitizer>
352 </param> 394 </param>
353 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/> 395 <param name="param_tr" type="data" format="traml,tabular,pqp" optional="False" label="transition file ('TraML','tsv','pqp')" help="(-tr) "/>
354 <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) "> 396 <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) ">
355 <option value="traML">traML</option> 397 <option value="traML">traML</option>
356 <option value="tsv">tsv</option> 398 <option value="tsv">tsv</option>
357 <option value="csv">csv</option> 399 <option value="pqp">pqp</option>
358 </param> 400 </param>
359 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/> 401 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
360 <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) ">
361 <sanitizer>
362 <valid initial="string.printable">
363 <remove value="'"/>
364 <remove value="&quot;"/>
365 </valid>
366 </sanitizer>
367 </param>
368 <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) "/> 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) "/>
369 <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) "/> 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) "/>
370 <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) "/> 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) "/>
405 <param name="param_sonar" display="radio" type="boolean" truevalue="-sonar" falsevalue="" checked="false" optional="True" label="data is scanning SWATH data" help="(-sonar) "/>
371 <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) "/> 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) "/>
372 <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)"/> 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)"/>
373 <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) "/> 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) "/>
374 <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) "/> 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) "/>
375 <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) "/> 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) "/>
377 <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"> 412 <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">
378 <option value="none" selected="true">none</option> 413 <option value="none" selected="true">none</option>
379 <option value="smoothed">smoothed</option> 414 <option value="smoothed">smoothed</option>
380 <option value="original">original</option> 415 <option value="original">original</option>
381 </param> 416 </param>
382 <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"> 417 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" display="radio" type="select" optional="False" 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">
383 <sanitizer> 418 <option value="true" selected="true">true</option>
384 <valid initial="string.printable"> 419 <option value="false">false</option>
385 <remove value="'"/>
386 <remove value="&quot;"/>
387 </valid>
388 </sanitizer>
389 </param> 420 </param>
390 <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)"/> 421 <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)"/>
391 <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) "/> 422 <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) "/>
392 <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"> 423 <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" display="radio" type="select" optional="False" 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">
393 <sanitizer> 424 <option value="true" selected="true">true</option>
394 <valid initial="string.printable"> 425 <option value="false">false</option>
395 <remove value="'"/>
396 <remove value="&quot;"/>
397 </valid>
398 </sanitizer>
399 </param> 426 </param>
400 <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"/> 427 <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"/>
401 <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) "/> 428 <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) "/>
402 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> 429 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
403 <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) "/> 430 <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) "/>
451 <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) "/> 478 <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) "/>
452 <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"> 479 <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">
453 <option value="normal" selected="true">normal</option> 480 <option value="normal" selected="true">normal</option>
454 <option value="cache">cache</option> 481 <option value="cache">cache</option>
455 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option> 482 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
483 <option value="workingInMemory">workingInMemory</option>
456 </param> 484 </param>
457 <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) "> 485 <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) ">
458 <option value="none" selected="true">none</option> 486 <option value="none" selected="true">none</option>
459 <option value="unweighted_regression">unweighted_regression</option> 487 <option value="unweighted_regression">unweighted_regression</option>
460 <option value="weighted_regression">weighted_regression</option> 488 <option value="weighted_regression">weighted_regression</option>
461 <option value="quadratic_regression">quadratic_regression</option> 489 <option value="quadratic_regression">quadratic_regression</option>
462 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option> 490 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option>
463 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option> 491 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option>
464 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option> 492 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
465 </param> 493 </param>
494 <param name="param_irt_mz_extraction_window" type="float" value="0.05" label="Extraction window used for iRT and m/z correction (in Thomson, use ppm use -ppm flag)" help="(-irt_mz_extraction_window) "/>
495 <param name="param_ppm_irtwindow" display="radio" type="boolean" truevalue="-ppm_irtwindow" falsevalue="" checked="false" optional="True" label="iRT m/z extraction_window is in ppm" help="(-ppm_irtwindow) "/>
466 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) "> 496 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
467 <sanitizer> 497 <sanitizer>
468 <valid initial="string.printable"> 498 <valid initial="string.printable">
469 <remove value="'"/> 499 <remove value="'"/>
470 <remove value="&quot;"/> 500 <remove value="&quot;"/>
475 <option value="tophat" selected="true">tophat</option> 505 <option value="tophat" selected="true">tophat</option>
476 <option value="bartlett">bartlett</option> 506 <option value="bartlett">bartlett</option>
477 </param> 507 </param>
478 <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) "/> 508 <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) "/>
479 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 509 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
510 <param name="param_Library_retentionTimeInterpretation" display="radio" type="select" optional="False" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) ">
511 <option value="iRT" selected="true">iRT</option>
512 <option value="seconds">seconds</option>
513 <option value="minutes">minutes</option>
514 </param>
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"/>
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) "/>
480 <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) "/> 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) "/>
481 <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) "/> 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) "/>
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) "/>
482 <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) "> 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) ">
483 <option value="true" selected="true">true</option> 521 <option value="true" selected="true">true</option>
484 <option value="false">false</option> 522 <option value="false">false</option>
485 </param> 523 </param>
486 <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) "> 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) ">
509 </param> 547 </param>
510 <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) "> 548 <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) ">
511 <option value="true" selected="true">true</option> 549 <option value="true" selected="true">true</option>
512 <option value="false">false</option> 550 <option value="false">false</option>
513 </param> 551 </param>
514 <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) "> 552 <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) If turned off, will not use fragment ion spectra for scoring">
515 <option value="true" selected="true">true</option> 553 <option value="true" selected="true">true</option>
516 <option value="false">false</option> 554 <option value="false">false</option>
517 </param> 555 </param>
518 <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) "/> 556 <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) "/>
557 <param name="param_Scoring_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>
519 <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) "/> 558 <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) "/>
520 <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) "/> 559 <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) "/>
521 </expand> 560 </expand>
522 </inputs> 561 </inputs>
523 <outputs> 562 <outputs>
524 <data name="param_out_features" format="featurexml"/> 563 <data name="param_out_features" format="featurexml"/>
564 <data name="param_out_tsv" format="tabular"/>
565 <data name="param_out_osw" format="osw"/>
525 <data name="param_out_chrom" format="mzml"/> 566 <data name="param_out_chrom" format="mzml"/>
526 </outputs> 567 </outputs>
527 <help>Complete workflow to run OpenSWATH 568 <help>Complete workflow to run OpenSWATH
528 569
529 570