<?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: [Utilities]-->
<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.1.0">
  <description>Complete workflow to run OpenSWATH</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathWorkflow

-in
  #for token in $param_in:
    $token
  #end for
#if $param_tr:
  -tr $param_tr
#end if
#if $param_tr_type:
  -tr_type
  #if " " in str($param_tr_type):
    "$param_tr_type"
  #else
    $param_tr_type
  #end if
#end if
#if $param_tr_irt:
  -tr_irt $param_tr_irt
#end if
#if $param_out_features:
  -out_features $param_out_features
#end if
#if $param_out_tsv:
  -out_tsv     "$param_out_tsv"
#end if
#if $param_out_chrom:
  -out_chrom $param_out_chrom
#end if
#if $param_rt_extraction_window:
  -rt_extraction_window $param_rt_extraction_window
#end if
#if $param_mz_extraction_window:
  -mz_extraction_window $param_mz_extraction_window
#end if
#if $param_ppm:
  -ppm
#end if
#if $param_Scoring_stop_report_after_feature:
  -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
#end if
#if $param_Scoring_rt_normalization_factor:
  -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
#end if
#if $param_Scoring_uis_threshold_sn:
  -Scoring:uis_threshold_sn $param_Scoring_uis_threshold_sn
#end if
#if $param_Scoring_uis_threshold_peak_area:
  -Scoring:uis_threshold_peak_area $param_Scoring_uis_threshold_peak_area
#end if
#if $param_Scoring_TransitionGroupPicker_stop_after_feature:
  -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature
#end if
#if $param_Scoring_TransitionGroupPicker_min_peak_width:
  -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
#end if
#if $param_Scoring_TransitionGroupPicker_background_subtraction:
  -Scoring:TransitionGroupPicker:background_subtraction $param_Scoring_TransitionGroupPicker_background_subtraction
#end if
#if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
  -Scoring:TransitionGroupPicker:recalculate_peaks     "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
#end if
#if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
  -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
#end if
#if $param_Scoring_TransitionGroupPicker_minimal_quality:
  -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
#end if
#if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
  -Scoring:TransitionGroupPicker:compute_peak_quality     "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
#end if
#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
  -Scoring:TransitionGroupPicker:PeakPickerMRM:method $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
#end if
#if $param_Scoring_DIAScoring_dia_extraction_window:
  -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
#end if
#if $param_Scoring_DIAScoring_dia_centroided:
  -Scoring:DIAScoring:dia_centroided
#end if
#if $param_Scoring_DIAScoring_dia_byseries_intensity_min:
  -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min
#end if
#if $param_Scoring_DIAScoring_dia_byseries_ppm_diff:
  -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff
#end if
#if $param_Scoring_DIAScoring_dia_nr_isotopes:
  -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes
#end if
#if $param_Scoring_DIAScoring_dia_nr_charges:
  -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges
#end if
#if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff:
  -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff
#end if
#if $param_Scoring_EMGScoring_max_iteration:
  -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
#end if
#if $param_outlierDetection_outlierMethod:
  -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod
#end if
#if $param_outlierDetection_useIterativeChauvenet:
  -outlierDetection:useIterativeChauvenet
#end if
#if $param_outlierDetection_RANSACMaxIterations:
  -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations
#end if
#if $param_outlierDetection_RANSACMaxPercentRTThreshold:
  -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold
#end if
#if $param_outlierDetection_RANSACSamplingSize:
  -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize
#end if
#if $param_outlierDetection_estimateBestPeptides:
  -outlierDetection:estimateBestPeptides
#end if
#if $param_outlierDetection_InitialQualityCutoff:
  -outlierDetection:InitialQualityCutoff $param_outlierDetection_InitialQualityCutoff
#end if
#if $param_outlierDetection_OverallQualityCutoff:
  -outlierDetection:OverallQualityCutoff $param_outlierDetection_OverallQualityCutoff
#end if
#if $param_outlierDetection_NrRTBins:
  -outlierDetection:NrRTBins $param_outlierDetection_NrRTBins
#end if
#if $param_outlierDetection_MinPeptidesPerBin:
  -outlierDetection:MinPeptidesPerBin $param_outlierDetection_MinPeptidesPerBin
#end if
#if $param_outlierDetection_MinBinsFilled:
  -outlierDetection:MinBinsFilled $param_outlierDetection_MinBinsFilled
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_rt_norm:
  -rt_norm $adv_opts.param_rt_norm
#end if
    #if $adv_opts.param_swath_windows_file:
  -swath_windows_file $adv_opts.param_swath_windows_file
#end if
    #if $adv_opts.param_sort_swath_maps:
  -sort_swath_maps
#end if
    #if $adv_opts.param_use_ms1_traces:
  -use_ms1_traces
#end if
    #if $adv_opts.param_enable_uis_scoring:
  -enable_uis_scoring
#end if
    #if $adv_opts.param_min_upper_edge_dist:
  -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist
#end if
    #if $adv_opts.param_extra_rt_extraction_window:
  -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window
#end if
    #if $adv_opts.param_min_rsq:
  -min_rsq $adv_opts.param_min_rsq
#end if
    #if $adv_opts.param_min_coverage:
  -min_coverage $adv_opts.param_min_coverage
#end if
    #if $adv_opts.param_split_file_input:
  -split_file_input
#end if
    #if $adv_opts.param_use_elution_model_score:
  -use_elution_model_score
#end if
    #if $adv_opts.param_readOptions:
  -readOptions $adv_opts.param_readOptions
#end if
    #if $adv_opts.param_mz_correction_function:
  -mz_correction_function $adv_opts.param_mz_correction_function
#end if
    #if $adv_opts.param_tempDirectory:
  -tempDirectory     "$adv_opts.param_tempDirectory"
#end if
    #if $adv_opts.param_extraction_function:
  -extraction_function $adv_opts.param_extraction_function
#end if
    #if $adv_opts.param_batchSize:
  -batchSize $adv_opts.param_batchSize
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_Scoring_quantification_cutoff:
  -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
#end if
    #if $adv_opts.param_Scoring_write_convex_hull:
  -Scoring:write_convex_hull
#end if
    #if $adv_opts.param_Scoring_Scores_use_shape_score:
  -Scoring:Scores:use_shape_score $adv_opts.param_Scoring_Scores_use_shape_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_coelution_score:
  -Scoring:Scores:use_coelution_score $adv_opts.param_Scoring_Scores_use_coelution_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_rt_score:
  -Scoring:Scores:use_rt_score $adv_opts.param_Scoring_Scores_use_rt_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_library_score:
  -Scoring:Scores:use_library_score $adv_opts.param_Scoring_Scores_use_library_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_intensity_score:
  -Scoring:Scores:use_intensity_score $adv_opts.param_Scoring_Scores_use_intensity_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
  -Scoring:Scores:use_nr_peaks_score $adv_opts.param_Scoring_Scores_use_nr_peaks_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
  -Scoring:Scores:use_total_xic_score $adv_opts.param_Scoring_Scores_use_total_xic_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_sn_score:
  -Scoring:Scores:use_sn_score $adv_opts.param_Scoring_Scores_use_sn_score
#end if
    #if $adv_opts.param_Scoring_Scores_use_dia_scores:
  -Scoring:Scores:use_dia_scores $adv_opts.param_Scoring_Scores_use_dia_scores
#end if
    #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
  -Scoring:Scores:use_ms1_correlation
#end if
    #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
  -Scoring:Scores:use_ms1_fullscan
#end if
    #if $adv_opts.param_Scoring_Scores_use_uis_scores:
  -Scoring:Scores:use_uis_scores
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/>
    <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) ">
      <option value="traML">traML</option>
      <option value="tsv">tsv</option>
      <option value="csv">csv</option>
    </param>
    <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
    <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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) "/>
    <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) "/>
    <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) "/>
    <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) "/>
    <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)"/>
    <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) "/>
    <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) "/>
    <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) "/>
    <param name="param_Scoring_TransitionGroupPicker_min_peak_width" type="float" value="14.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
    <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">
      <option value="none" selected="true">none</option>
      <option value="smoothed">smoothed</option>
      <option value="original">original</option>
    </param>
    <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">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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)"/>
    <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) "/>
    <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">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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"/>
    <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) "/>
    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
    <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) "/>
    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" falsevalue="" checked="false" optional="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) "/>
    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="select" optional="False" value="true" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) ">
      <option value="false">false</option>
      <option value="true" selected="true">true</option>
    </param>
    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
      <option value="legacy">legacy</option>
      <option value="corrected" selected="true">corrected</option>
      <option value="crawdad">crawdad</option>
    </param>
    <param name="param_Scoring_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/>
    <param name="param_Scoring_DIAScoring_dia_centroided" display="radio" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
    <param name="param_Scoring_DIAScoring_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to conside" help="(-dia_byseries_intensity_min) "/>
    <param name="param_Scoring_DIAScoring_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help="(-dia_byseries_ppm_diff) "/>
    <param name="param_Scoring_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/>
    <param name="param_Scoring_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/>
    <param name="param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff" type="float" min="0.0" optional="True" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help="(-peak_before_mono_max_ppm_diff) "/>
    <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
    <param name="param_outlierDetection_outlierMethod" display="radio" type="select" optional="False" value="iter_residual" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="(-outlierMethod) Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
      <option value="iter_residual" selected="true">iter_residual</option>
      <option value="iter_jackknife">iter_jackknife</option>
      <option value="ransac">ransac</option>
      <option value="none">none</option>
    </param>
    <param name="param_outlierDetection_useIterativeChauvenet" display="radio" type="boolean" truevalue="-outlierDetection:useIterativeChauvenet" falsevalue="" checked="false" optional="True" label="Whether to use Chauvenet's criterion when using iterative methods" help="(-useIterativeChauvenet) This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
    <param name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
    <param name="param_outlierDetection_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="(-RANSACMaxPercentRTThreshold) Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
    <param name="param_outlierDetection_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help="(-RANSACSamplingSize) "/>
    <param name="param_outlierDetection_estimateBestPeptides" display="radio" type="boolean" truevalue="-outlierDetection:estimateBestPeptides" falsevalue="" checked="false" optional="True" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization. Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (" help="(-estimateBestPeptides) e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
    <param name="param_outlierDetection_InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="(-InitialQualityCutoff) -2 to 2)"/>
    <param name="param_outlierDetection_OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="(-OverallQualityCutoff) 0 to 10)"/>
    <param name="param_outlierDetection_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="(-NrRTBins) This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
    <param name="param_outlierDetection_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/>
    <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
    <expand macro="advanced_options">
      <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) If set, tr_irt may be omitted"/>
      <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
      <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/>
      <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/>
      <param name="param_enable_uis_scoring" display="radio" type="boolean" truevalue="-enable_uis_scoring" falsevalue="" checked="false" optional="True" label="Enable additional scoring of identification assays" help="(-enable_uis_scoring) "/>
      <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
      <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/>
      <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
      <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
      <param name="param_split_file_input" display="radio" type="boolean" truevalue="-split_file_input" falsevalue="" checked="false" optional="True" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help="(-split_file_input) "/>
      <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) "/>
      <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">
        <option value="normal" selected="true">normal</option>
        <option value="cache">cache</option>
        <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
      </param>
      <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) ">
        <option value="none" selected="true">none</option>
        <option value="unweighted_regression">unweighted_regression</option>
        <option value="weighted_regression">weighted_regression</option>
        <option value="quadratic_regression">quadratic_regression</option>
        <option value="weighted_quadratic_regression">weighted_quadratic_regression</option>
        <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option>
        <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
      </param>
      <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_extraction_function" display="radio" type="select" optional="False" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
        <option value="tophat" selected="true">tophat</option>
        <option value="bartlett">bartlett</option>
      </param>
      <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) "/>
      <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_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) "/>
      <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) "/>
      <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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_Scoring_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_Scoring_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_Scoring_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_Scoring_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_Scoring_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_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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <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) ">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <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) "/>
      <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) "/>
      <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) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out_features" format="featurexml"/>
    <data name="param_out_chrom" format="mzml"/>
  </outputs>
  <help>Complete workflow to run OpenSWATH


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html</help>
</tool>