comparison OpenSwathAnalyzer.xml @ 3:ee58e9cf2d33 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

2:66b3eed59efd

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Targeted Experiments]-->
<tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.1.0">
  <description>Picks peaks and finds features in an SRM experiment.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
    <import>macros.xml</import>
  </macros>

  #else
    $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
  #end if
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
  -algorithm:TransitionGroupPicker:recalculate_peaks     "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
  -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
  -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
  -algorithm:TransitionGroupPicker:compute_peak_quality     "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
#end if
    #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
  -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
#end if
    #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:

    $adv_opts.param_algorithm_Scores_use_dia_scores
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
  -algorithm:Scores:use_ms1_correlation
#end if
    #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
  -algorithm:Scores:use_ms1_fullscan
#end if
    #if $adv_opts.param_algorithm_Scores_use_uis_scores:

      <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">
        <option value="none" selected="true">none</option>
        <option value="smoothed">smoothed</option>
        <option value="original">original</option>
      </param>
      <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">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <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)"/>
      <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) "/>
      <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">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <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) "/>
      <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) "/>
      <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
      <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
      <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>

      </param>
      <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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <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) "/>
      <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) "/>
      <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) "/>
    </expand>
  </inputs>
  <outputs>

3:ee58e9cf2d33

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Targeted Experiments]-->
<tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.2.0">
  <description>Picks peaks and finds features in an SRM experiment.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
    <import>macros.xml</import>
  </macros>

  #else
    $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
  #end if
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
  -algorithm:TransitionGroupPicker:recalculate_peaks
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_use_precursors:
  -algorithm:TransitionGroupPicker:use_precursors
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
  -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
  -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
  -algorithm:TransitionGroupPicker:compute_peak_quality
#end if
    #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
  -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
#end if
    #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:

    $adv_opts.param_algorithm_Scores_use_dia_scores
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
  -algorithm:Scores:use_ms1_correlation
#end if
    #if $adv_opts.param_algorithm_Scores_use_sonar_scores:
  -algorithm:Scores:use_sonar_scores
#end if
    #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
  -algorithm:Scores:use_ms1_fullscan
#end if
    #if $adv_opts.param_algorithm_Scores_use_uis_scores:

      <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">
        <option value="none" selected="true">none</option>
        <option value="smoothed">smoothed</option>
        <option value="original">original</option>
      </param>
      <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"/>
      <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) "/>
      <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)"/>
      <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) "/>
      <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"/>
      <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) "/>
      <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) "/>
      <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
      <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
      <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>

      </param>
      <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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <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">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <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) "/>
      <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) "/>
      <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) "/>
      <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) "/>
    </expand>
  </inputs>
  <outputs>