annotate OpenSwathAnalyzer.xml @ 8:a2a6e9551046 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Targeted Experiments]-->
<tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.3.0">
  <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[OpenSwathAnalyzer

#if $param_in:
  -in $param_in
#end if
#if $param_tr:
  -tr $param_tr
#end if
#if $param_rt_norm:
  -rt_norm $param_rt_norm
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_no_strict:
  -no-strict
#end if
-swath_files
  #for token in $param_swath_files:
    $token
  #end for
#if $param_min_upper_edge_dist:
  -min_upper_edge_dist $param_min_upper_edge_dist
#end if
#if $param_algorithm_stop_report_after_feature:
  -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
#end if
#if $param_algorithm_rt_extraction_window:
  -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
#end if
#if $param_algorithm_rt_normalization_factor:
  -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
#end if
#if $param_algorithm_uis_threshold_sn:
  -algorithm:uis_threshold_sn $param_algorithm_uis_threshold_sn
#end if
#if $param_algorithm_uis_threshold_peak_area:
  -algorithm:uis_threshold_peak_area $param_algorithm_uis_threshold_peak_area
#end if
#if $param_algorithm_TransitionGroupPicker_stop_after_feature:
  -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
#end if
#if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
  -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss):
    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
  #else
    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
  #end if
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages):
    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages"
  #else
    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
  #end if
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
#end if
#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
  -algorithm:TransitionGroupPicker:PeakPickerMRM:method
  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
  #else
    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
  #end if
#end if
#if $param_algorithm_DIAScoring_dia_extraction_window:
  -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
#end if
#if $param_algorithm_DIAScoring_dia_centroided:
  -algorithm:DIAScoring:dia_centroided
#end if
#if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
  -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
#end if
#if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
  -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
#end if
#if $param_algorithm_DIAScoring_dia_nr_isotopes:
  -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
#end if
#if $param_algorithm_DIAScoring_dia_nr_charges:
  -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
#end if
#if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
  -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_model_type:
  -model:type
  #if " " in str($adv_opts.param_model_type):
    "$adv_opts.param_model_type"
  #else
    $adv_opts.param_model_type
  #end if
#end if
    #if $adv_opts.param_model_symmetric_regression:
  -model:symmetric_regression
#end if
    #if $adv_opts.param_algorithm_quantification_cutoff:
  -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
#end if
    #if $adv_opts.param_algorithm_write_convex_hull:
  -algorithm:write_convex_hull
#end if
    #if $adv_opts.param_algorithm_add_up_spectra:
  -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
#end if
    #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
  -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
  -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
#end if
    #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
  -algorithm:TransitionGroupPicker:background_subtraction
  #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
    "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
  #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_resample_boundary:
  -algorithm:TransitionGroupPicker:resample_boundary $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary
#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:
  -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
#end if
    #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
  -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
#end if
    #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
  -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
#end if
    #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
  -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
#end if
    #if $adv_opts.param_algorithm_Scores_use_shape_score:
  -algorithm:Scores:use_shape_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
    "$adv_opts.param_algorithm_Scores_use_shape_score"
  #else
    $adv_opts.param_algorithm_Scores_use_shape_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_coelution_score:
  -algorithm:Scores:use_coelution_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
    "$adv_opts.param_algorithm_Scores_use_coelution_score"
  #else
    $adv_opts.param_algorithm_Scores_use_coelution_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_rt_score:
  -algorithm:Scores:use_rt_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
    "$adv_opts.param_algorithm_Scores_use_rt_score"
  #else
    $adv_opts.param_algorithm_Scores_use_rt_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_library_score:
  -algorithm:Scores:use_library_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
    "$adv_opts.param_algorithm_Scores_use_library_score"
  #else
    $adv_opts.param_algorithm_Scores_use_library_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
  -algorithm:Scores:use_elution_model_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
    "$adv_opts.param_algorithm_Scores_use_elution_model_score"
  #else
    $adv_opts.param_algorithm_Scores_use_elution_model_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_intensity_score:
  -algorithm:Scores:use_intensity_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
    "$adv_opts.param_algorithm_Scores_use_intensity_score"
  #else
    $adv_opts.param_algorithm_Scores_use_intensity_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
  -algorithm:Scores:use_nr_peaks_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
    "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
  #else
    $adv_opts.param_algorithm_Scores_use_nr_peaks_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
  -algorithm:Scores:use_total_xic_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
    "$adv_opts.param_algorithm_Scores_use_total_xic_score"
  #else
    $adv_opts.param_algorithm_Scores_use_total_xic_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_sn_score:
  -algorithm:Scores:use_sn_score
  #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
    "$adv_opts.param_algorithm_Scores_use_sn_score"
  #else
    $adv_opts.param_algorithm_Scores_use_sn_score
  #end if
#end if
    #if $adv_opts.param_algorithm_Scores_use_dia_scores:
  -algorithm:Scores:use_dia_scores
  #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
    "$adv_opts.param_algorithm_Scores_use_dia_scores"
  #else
    $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:
  -algorithm:Scores:use_uis_scores
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/>
    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
    <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) "/>
    <param name="param_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/>
    <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be used">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/>
    <param name="param_algorithm_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) "/>
    <param name="param_algorithm_rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values"/>
    <param name="param_algorithm_rt_normalization_factor" type="float" value="1.0" 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)"/>
    <param name="param_algorithm_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) "/>
    <param name="param_algorithm_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) "/>
    <param name="param_algorithm_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) "/>
    <param name="param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" 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"/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
      <option value="false">false</option>
      <option value="true" selected="true">true</option>
    </param>
    <param name="param_algorithm_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"/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" 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"/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="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) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="(-method) ">
      <option value="legacy">legacy</option>
      <option value="corrected" selected="true">corrected</option>
      <option value="crawdad">crawdad</option>
    </param>
    <param name="param_algorithm_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/>
    <param name="param_algorithm_DIAScoring_dia_centroided" display="radio" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
    <param name="param_algorithm_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) "/>
    <param name="param_algorithm_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) "/>
    <param name="param_algorithm_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/>
    <param name="param_algorithm_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/>
    <param name="param_algorithm_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) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) ">
        <option value="linear" selected="true">linear</option>
        <option value="b_spline">b_spline</option>
        <option value="interpolated">interpolated</option>
        <option value="lowess">lowess</option>
      </param>
      <param name="param_model_symmetric_regression" display="radio" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
      <param name="param_algorithm_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) "/>
      <param name="param_algorithm_write_convex_hull" display="radio" type="boolean" truevalue="-algorithm: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) "/>
      <param name="param_algorithm_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra) "/>
      <param name="param_algorithm_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling) "/>
      <param name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
      <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_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>
      <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 name="param_algorithm_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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_algorithm_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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_algorithm_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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_algorithm_Scores_use_library_score" display="radio" type="select" optional="False" value="true" label="Use the library score" help="(-use_library_score) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_algorithm_Scores_use_elution_model_score" display="radio" type="select" optional="False" value="true" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_algorithm_Scores_use_intensity_score" display="radio" type="select" optional="False" value="true" label="Use the intensity score" help="(-use_intensity_score) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_algorithm_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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_algorithm_Scores_use_total_xic_score" display="radio" type="select" optional="False" value="true" label="Use the total XIC score" help="(-use_total_xic_score) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </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>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Picks peaks and finds features in an SWATH-MS or SRM experiment.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathAnalyzer.html</help>
</tool>