Mercurial > repos > galaxyp > openms_openswathrtnormalizer

comparison OpenSwathRTNormalizer.xml @ 3:13bfce690403 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 19:06:58 -0400
parents 580a0a6ab12f
children 672d03a9794b
comparison
equal deleted inserted replaced
2:20ac794a6fb5 3:13bfce690403
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.1.0"> 4 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.2.0">
5 <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description> 5 <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token> 7 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
185 #else 185 #else
186 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction 186 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
187 #end if 187 #end if
188 #end if 188 #end if
189 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: 189 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
190 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks" 190 -algorithm:TransitionGroupPicker:recalculate_peaks
191 #end if
192 #if $adv_opts.param_algorithm_TransitionGroupPicker_use_precursors:
193 -algorithm:TransitionGroupPicker:use_precursors
191 #end if 194 #end if
192 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: 195 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
193 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z 196 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
194 #end if 197 #end if
195 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality: 198 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
196 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality 199 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
197 #end if 200 #end if
198 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality: 201 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
199 -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality" 202 -algorithm:TransitionGroupPicker:compute_peak_quality
200 #end if 203 #end if
201 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step: 204 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
202 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step 205 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
203 #end if 206 #end if
204 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box: 207 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
293 $adv_opts.param_algorithm_Scores_use_dia_scores 296 $adv_opts.param_algorithm_Scores_use_dia_scores
294 #end if 297 #end if
295 #end if 298 #end if
296 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: 299 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
297 -algorithm:Scores:use_ms1_correlation 300 -algorithm:Scores:use_ms1_correlation
301 #end if
302 #if $adv_opts.param_algorithm_Scores_use_sonar_scores:
303 -algorithm:Scores:use_sonar_scores
298 #end if 304 #end if
299 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: 305 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
300 -algorithm:Scores:use_ms1_fullscan 306 -algorithm:Scores:use_ms1_fullscan
301 #end if 307 #end if
302 #if $adv_opts.param_algorithm_Scores_use_uis_scores: 308 #if $adv_opts.param_algorithm_Scores_use_uis_scores:
378 <param name="param_algorithm_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"> 384 <param name="param_algorithm_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">
379 <option value="none" selected="true">none</option> 385 <option value="none" selected="true">none</option>
380 <option value="smoothed">smoothed</option> 386 <option value="smoothed">smoothed</option>
381 <option value="original">original</option> 387 <option value="original">original</option>
382 </param> 388 </param>
383 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" 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"> 389 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:recalculate_peaks" falsevalue="" checked="false" optional="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"/>
384 <sanitizer> 390 <param name="param_algorithm_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
385 <valid initial="string.printable">
386 <remove value="'"/>
387 <remove value="&quot;"/>
388 </valid>
389 </sanitizer>
390 </param>
391 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" 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_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
392 <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> 392 <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
393 <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" 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 <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:compute_peak_quality" falsevalue="" checked="false" optional="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"/>
394 <sanitizer>
395 <valid initial="string.printable">
396 <remove value="'"/>
397 <remove value="&quot;"/>
398 </valid>
399 </sanitizer>
400 </param>
401 <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/> 394 <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>
402 <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/> 395 <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>
403 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/> 396 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
404 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/> 397 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
405 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/> 398 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
437 </param> 430 </param>
438 <param name="param_algorithm_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 <param name="param_algorithm_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) ">
439 <option value="true" selected="true">true</option> 432 <option value="true" selected="true">true</option>
440 <option value="false">false</option> 433 <option value="false">false</option>
441 </param> 434 </param>
442 <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "> 435 <param name="param_algorithm_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">
443 <option value="true" selected="true">true</option> 436 <option value="true" selected="true">true</option>
444 <option value="false">false</option> 437 <option value="false">false</option>
445 </param> 438 </param>
446 <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm: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_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
440 <param name="param_algorithm_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>
447 <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm: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) "/> 441 <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm: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) "/>
448 <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/> 442 <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
449 </expand> 443 </expand>
450 </inputs> 444 </inputs>
451 <outputs> 445 <outputs>