annotate OpenSwathRTNormalizer.xml @ 14:0eaf3d4219cf draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--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 and OpenSWATH]-->
<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <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>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in_cond.in &&
#if $in_cond.in_select == "no"
mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
#else
cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
#end if
mkdir tr &&
cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
mkdir out &&
#if $rt_norm:
  mkdir rt_norm &&
  cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
#if $in_cond.in_select == "no"
${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
#else
'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
#end if
-tr
'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
-out
'out/output.${gxy2omsext("trafoxml")}'
#if $rt_norm:
  -rt_norm
  'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("trafoxml")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <conditional name="in_cond">
      <param name="in_select" type="select" label="Run tool in batch mode for -in">
        <option value="no">No: process all datasets jointly</option>
        <option value="yes">Yes: process each dataset in an independent job</option>
      </param>
      <when value="no">
        <param argument="-in" type="data" format="mzml" multiple="true" label="Input files separated by blank" help=" select mzml data sets(s)"/>
      </when>
      <when value="yes">
        <param argument="-in" type="data" format="mzml" label="Input files separated by blank" help=" select mzml data sets(s)"/>
      </when>
    </conditional>
    <param argument="-tr" type="data" format="csv,traml" label="transition file with the RT peptides ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
    <param argument="-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=" select trafoxml data sets(s)"/>
    <param argument="-min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
    <param argument="-min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
    <param argument="-estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="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 (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
    <section name="RTNormalization" title="Parameters for the RTNormalization" help="RT normalization and outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="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>
        <expand macro="list_string_san" name="outlierMethod"/>
      </param>
      <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
      <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
      <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
      <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
    </section>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
      <param name="rt_extraction_window" argument="-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="For this to work, the TraML input file needs to contain normalized RT values"/>
      <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
      <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
      <param name="write_convex_hull" argument="-algorithm:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
        <option value="simple" selected="true">simple</option>
        <option value="resample">resample</option>
        <expand macro="list_string_san" name="spectrum_addition_method"/>
      </param>
      <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
      <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
      <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
      <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" label="Scoring model to use" help="">
        <option value="default" selected="true">default</option>
        <option value="single_transition">single_transition</option>
        <expand macro="list_string_san" name="scoring_model"/>
      </param>
      <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
      <param name="strict" argument="-algorithm:strict" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""/>
      <section name="TransitionGroupPicker" title="" help="" expanded="false">
        <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
        <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
        <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
          <option value="original" selected="true">original</option>
          <option value="smoothed">smoothed</option>
          <expand macro="list_string_san" name="peak_integration"/>
        </param>
        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
          <option value="none" selected="true">none</option>
          <option value="original">original</option>
          <option value="exact">exact</option>
          <expand macro="list_string_san" name="background_subtraction"/>
        </param>
        <param name="recalculate_peaks" argument="-algorithm:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
        <param name="use_precursors" argument="-algorithm:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
        <param name="use_consensus" argument="-algorithm:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
        <param name="recalculate_peaks_max_z" argument="-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="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
        <param name="minimal_quality" argument="-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=""/>
        <param name="resample_boundary" argument="-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=""/>
        <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
        <param name="compute_peak_shape_metrics" argument="-algorithm:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
        <param name="compute_total_mi" argument="-algorithm:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
          <option value="largest" selected="true">largest</option>
          <option value="widest">widest</option>
          <expand macro="list_string_san" name="boundary_selection_method"/>
        </param>
        <section name="PeakPickerMRM" title="" help="" expanded="false">
          <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
          <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
          <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
          <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
          <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
          <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
          <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/>
          <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/>
          <param name="write_sn_log_messages" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
          <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" 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="">
            <option value="legacy">legacy</option>
            <option value="corrected" selected="true">corrected</option>
            <option value="crawdad">crawdad</option>
            <expand macro="list_string_san" name="method"/>
          </param>
        </section>
        <section name="PeakIntegrator" title="" help="" expanded="false">
          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
            <option value="intensity_sum" selected="true">intensity_sum</option>
            <option value="simpson">simpson</option>
            <option value="trapezoid">trapezoid</option>
            <expand macro="list_string_san" name="integration_type"/>
          </param>
          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
            <option value="base_to_base" selected="true">base_to_base</option>
            <option value="vertical_division">vertical_division</option>
            <option value="vertical_division_min">vertical_division_min</option>
            <option value="vertical_division_max">vertical_division_max</option>
            <expand macro="list_string_san" name="baseline_type"/>
          </param>
          <param name="fit_EMG" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/>
        </section>
      </section>
      <section name="DIAScoring" title="" help="" expanded="false">
        <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
          <option value="Th" selected="true">Th</option>
          <option value="ppm">ppm</option>
          <expand macro="list_string_san" name="dia_extraction_unit"/>
        </param>
        <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
        <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
        <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
        <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
        <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" min="0" value="4" label="DIA number of charges to conside" help=""/>
        <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" min="0.0" 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=""/>
      </section>
      <section name="EMGScoring" title="" help="" expanded="false">
        <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
        <param name="tolerance_stdev_bounding_box" argument="-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=""/>
        <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
        <param name="init_mom" argument="-algorithm:EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Initialize parameters using method of moments estimators" help=""/>
        <section name="statistics" title="" help="" expanded="false">
          <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" value="1.0" label="Centroid position of the model" help=""/>
          <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" value="1.0" label="Variance of the model" help=""/>
        </section>
      </section>
      <section name="Scores" title="" help="" expanded="false">
        <param name="use_shape_score" argument="-algorithm:Scores:use_shape_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help=""/>
        <param name="use_coelution_score" argument="-algorithm:Scores:use_coelution_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help=""/>
        <param name="use_rt_score" argument="-algorithm:Scores:use_rt_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the retention time score (this score measure the difference in retention time)" help=""/>
        <param name="use_library_score" argument="-algorithm:Scores:use_library_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the library score" help=""/>
        <param name="use_elution_model_score" argument="-algorithm:Scores:use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help=""/>
        <param name="use_intensity_score" argument="-algorithm:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/>
        <param name="use_nr_peaks_score" argument="-algorithm:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/>
        <param name="use_total_xic_score" argument="-algorithm:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/>
        <param name="use_total_mi_score" argument="-algorithm:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/>
        <param name="use_sn_score" argument="-algorithm:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/>
        <param name="use_mi_score" argument="-algorithm:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/>
        <param name="use_dia_scores" argument="-algorithm:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/>
        <param name="use_ms1_correlation" argument="-algorithm:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/>
        <param name="use_sonar_scores" argument="-algorithm:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/>
        <param name="use_ion_mobility_scores" argument="-algorithm:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/>
        <param name="use_ms1_fullscan" argument="-algorithm:Scores:use_ms1_fullscan" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help=""/>
        <param name="use_ms1_mi" argument="-algorithm:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/>
        <param name="use_uis_scores" argument="-algorithm:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
        <param name="use_ionseries_scores" argument="-algorithm:Scores:use_ionseries_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level b/y ion-series scores for peptidoform identification" help=""/>
        <param name="use_ms2_isotope_scores" argument="-algorithm:Scores:use_ms2_isotope_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level isotope scores (pearson &amp; manhattan) across product transitions (based on ID if annotated or averagine)" help=""/>
      </section>
    </section>
    <section name="peptideEstimation" title="Parameters for the peptide estimation (use -estimateBestPeptides to enable)" help="" expanded="false">
      <param name="InitialQualityCutoff" argument="-peptideEstimation:InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
      <param name="OverallQualityCutoff" argument="-peptideEstimation:OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
      <param name="NrRTBins" argument="-peptideEstimation:NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="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="MinPeptidesPerBin" argument="-peptideEstimation:MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
      <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="trafoxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_OpenSwathRTNormalizer_test_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <conditional name="in_cond">
        <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
      </conditional>
      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
      <output name="out" value="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
      <param name="min_rsq" value="0.95"/>
      <param name="min_coverage" value="0.6"/>
      <param name="estimateBestPeptides" value="false"/>
      <section name="RTNormalization">
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
      </section>
      <section name="algorithm">
        <param name="stop_report_after_feature" value="-1"/>
        <param name="rt_extraction_window" value="-1.0"/>
        <param name="rt_normalization_factor" value="1.0"/>
        <param name="quantification_cutoff" value="0.0"/>
        <param name="write_convex_hull" value="false"/>
        <param name="spectrum_addition_method" value="simple"/>
        <param name="add_up_spectra" value="1"/>
        <param name="spacing_for_spectra_resampling" value="0.005"/>
        <param name="uis_threshold_sn" value="-1"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <param name="strict" value="true"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="stop_after_intensity_ratio" value="0.0001"/>
          <param name="min_peak_width" value="0.001"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="false"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="1.0"/>
          <param name="minimal_quality" value="-10000.0"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="false"/>
          <param name="compute_peak_shape_metrics" value="false"/>
          <param name="compute_total_mi" value="false"/>
          <param name="boundary_selection_method" value="largest"/>
          <section name="PeakPickerMRM">
            <param name="sgolay_frame_length" value="15"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="50.0"/>
            <param name="use_gauss" value="true"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="1.0"/>
            <param name="sn_win_len" value="1000.0"/>
            <param name="sn_bin_count" value="30"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="false"/>
            <param name="method" value="corrected"/>
          </section>
          <section name="PeakIntegrator">
            <param name="integration_type" value="intensity_sum"/>
            <param name="baseline_type" value="base_to_base"/>
            <param name="fit_EMG" value="false"/>
          </section>
        </section>
        <section name="DIAScoring">
          <param name="dia_extraction_window" value="0.05"/>
          <param name="dia_extraction_unit" value="Th"/>
          <param name="dia_centroided" value="false"/>
          <param name="dia_byseries_intensity_min" value="300.0"/>
          <param name="dia_byseries_ppm_diff" value="10.0"/>
          <param name="dia_nr_isotopes" value="4"/>
          <param name="dia_nr_charges" value="4"/>
          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
        </section>
        <section name="EMGScoring">
          <param name="interpolation_step" value="0.2"/>
          <param name="tolerance_stdev_bounding_box" value="3.0"/>
          <param name="max_iteration" value="500"/>
          <param name="init_mom" value="false"/>
          <section name="statistics">
            <param name="mean" value="1.0"/>
            <param name="variance" value="1.0"/>
          </section>
        </section>
        <section name="Scores">
          <param name="use_shape_score" value="true"/>
          <param name="use_coelution_score" value="true"/>
          <param name="use_rt_score" value="true"/>
          <param name="use_library_score" value="true"/>
          <param name="use_elution_model_score" value="true"/>
          <param name="use_intensity_score" value="true"/>
          <param name="use_nr_peaks_score" value="true"/>
          <param name="use_total_xic_score" value="true"/>
          <param name="use_total_mi_score" value="false"/>
          <param name="use_sn_score" value="true"/>
          <param name="use_mi_score" value="false"/>
          <param name="use_dia_scores" value="true"/>
          <param name="use_ms1_correlation" value="false"/>
          <param name="use_sonar_scores" value="false"/>
          <param name="use_ion_mobility_scores" value="false"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="false"/>
          <param name="use_uis_scores" value="false"/>
          <param name="use_ionseries_scores" value="true"/>
          <param name="use_ms2_isotope_scores" value="true"/>
        </section>
      </section>
      <section name="peptideEstimation">
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_OpenSwathRTNormalizer_test_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <conditional name="in_cond">
        <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
      </conditional>
      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
      <output name="out" value="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
      <param name="min_rsq" value="0.95"/>
      <param name="min_coverage" value="0.6"/>
      <param name="estimateBestPeptides" value="true"/>
      <section name="RTNormalization">
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
      </section>
      <section name="algorithm">
        <param name="stop_report_after_feature" value="-1"/>
        <param name="rt_extraction_window" value="-1.0"/>
        <param name="rt_normalization_factor" value="1.0"/>
        <param name="quantification_cutoff" value="0.0"/>
        <param name="write_convex_hull" value="false"/>
        <param name="spectrum_addition_method" value="simple"/>
        <param name="add_up_spectra" value="1"/>
        <param name="spacing_for_spectra_resampling" value="0.005"/>
        <param name="uis_threshold_sn" value="-1"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <param name="strict" value="true"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="stop_after_intensity_ratio" value="0.0001"/>
          <param name="min_peak_width" value="0.001"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="false"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="1.0"/>
          <param name="minimal_quality" value="-10000.0"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="false"/>
          <param name="compute_peak_shape_metrics" value="false"/>
          <param name="compute_total_mi" value="false"/>
          <param name="boundary_selection_method" value="largest"/>
          <section name="PeakPickerMRM">
            <param name="sgolay_frame_length" value="15"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="50.0"/>
            <param name="use_gauss" value="true"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="1.0"/>
            <param name="sn_win_len" value="1000.0"/>
            <param name="sn_bin_count" value="30"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="false"/>
            <param name="method" value="corrected"/>
          </section>
          <section name="PeakIntegrator">
            <param name="integration_type" value="intensity_sum"/>
            <param name="baseline_type" value="base_to_base"/>
            <param name="fit_EMG" value="false"/>
          </section>
        </section>
        <section name="DIAScoring">
          <param name="dia_extraction_window" value="0.05"/>
          <param name="dia_extraction_unit" value="Th"/>
          <param name="dia_centroided" value="false"/>
          <param name="dia_byseries_intensity_min" value="300.0"/>
          <param name="dia_byseries_ppm_diff" value="10.0"/>
          <param name="dia_nr_isotopes" value="4"/>
          <param name="dia_nr_charges" value="4"/>
          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
        </section>
        <section name="EMGScoring">
          <param name="interpolation_step" value="0.2"/>
          <param name="tolerance_stdev_bounding_box" value="3.0"/>
          <param name="max_iteration" value="500"/>
          <param name="init_mom" value="false"/>
          <section name="statistics">
            <param name="mean" value="1.0"/>
            <param name="variance" value="1.0"/>
          </section>
        </section>
        <section name="Scores">
          <param name="use_shape_score" value="true"/>
          <param name="use_coelution_score" value="true"/>
          <param name="use_rt_score" value="true"/>
          <param name="use_library_score" value="true"/>
          <param name="use_elution_model_score" value="true"/>
          <param name="use_intensity_score" value="true"/>
          <param name="use_nr_peaks_score" value="true"/>
          <param name="use_total_xic_score" value="true"/>
          <param name="use_total_mi_score" value="false"/>
          <param name="use_sn_score" value="true"/>
          <param name="use_mi_score" value="false"/>
          <param name="use_dia_scores" value="true"/>
          <param name="use_ms1_correlation" value="false"/>
          <param name="use_sonar_scores" value="false"/>
          <param name="use_ion_mobility_scores" value="false"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="false"/>
          <param name="use_uis_scores" value="false"/>
          <param name="use_ionseries_scores" value="true"/>
          <param name="use_ms2_isotope_scores" value="true"/>
        </section>
      </section>
      <section name="peptideEstimation">
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="3"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="3"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_OpenSwathRTNormalizer_test_4 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <conditional name="in_cond">
        <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
      </conditional>
      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
      <output name="out" value="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
      <param name="min_rsq" value="0.95"/>
      <param name="min_coverage" value="0.6"/>
      <param name="estimateBestPeptides" value="false"/>
      <section name="RTNormalization">
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
      </section>
      <section name="algorithm">
        <param name="stop_report_after_feature" value="-1"/>
        <param name="rt_extraction_window" value="-1.0"/>
        <param name="rt_normalization_factor" value="1.0"/>
        <param name="quantification_cutoff" value="0.0"/>
        <param name="write_convex_hull" value="false"/>
        <param name="spectrum_addition_method" value="simple"/>
        <param name="add_up_spectra" value="1"/>
        <param name="spacing_for_spectra_resampling" value="0.005"/>
        <param name="uis_threshold_sn" value="-1"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <param name="strict" value="true"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="stop_after_intensity_ratio" value="0.0001"/>
          <param name="min_peak_width" value="0.001"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="false"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="1.0"/>
          <param name="minimal_quality" value="-10000.0"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="false"/>
          <param name="compute_peak_shape_metrics" value="false"/>
          <param name="compute_total_mi" value="false"/>
          <param name="boundary_selection_method" value="largest"/>
          <section name="PeakPickerMRM">
            <param name="sgolay_frame_length" value="15"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="50.0"/>
            <param name="use_gauss" value="true"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="1.0"/>
            <param name="sn_win_len" value="1000.0"/>
            <param name="sn_bin_count" value="30"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="false"/>
            <param name="method" value="corrected"/>
          </section>
          <section name="PeakIntegrator">
            <param name="integration_type" value="intensity_sum"/>
            <param name="baseline_type" value="base_to_base"/>
            <param name="fit_EMG" value="false"/>
          </section>
        </section>
        <section name="DIAScoring">
          <param name="dia_extraction_window" value="0.05"/>
          <param name="dia_extraction_unit" value="Th"/>
          <param name="dia_centroided" value="false"/>
          <param name="dia_byseries_intensity_min" value="300.0"/>
          <param name="dia_byseries_ppm_diff" value="10.0"/>
          <param name="dia_nr_isotopes" value="4"/>
          <param name="dia_nr_charges" value="4"/>
          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
        </section>
        <section name="EMGScoring">
          <param name="interpolation_step" value="0.2"/>
          <param name="tolerance_stdev_bounding_box" value="3.0"/>
          <param name="max_iteration" value="500"/>
          <param name="init_mom" value="false"/>
          <section name="statistics">
            <param name="mean" value="1.0"/>
            <param name="variance" value="1.0"/>
          </section>
        </section>
        <section name="Scores">
          <param name="use_shape_score" value="true"/>
          <param name="use_coelution_score" value="true"/>
          <param name="use_rt_score" value="true"/>
          <param name="use_library_score" value="true"/>
          <param name="use_elution_model_score" value="true"/>
          <param name="use_intensity_score" value="true"/>
          <param name="use_nr_peaks_score" value="true"/>
          <param name="use_total_xic_score" value="true"/>
          <param name="use_total_mi_score" value="false"/>
          <param name="use_sn_score" value="true"/>
          <param name="use_mi_score" value="false"/>
          <param name="use_dia_scores" value="true"/>
          <param name="use_ms1_correlation" value="false"/>
          <param name="use_sonar_scores" value="false"/>
          <param name="use_ion_mobility_scores" value="false"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="false"/>
          <param name="use_uis_scores" value="false"/>
          <param name="use_ionseries_scores" value="true"/>
          <param name="use_ms2_isotope_scores" value="true"/>
        </section>
      </section>
      <section name="peptideEstimation">
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[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.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRTNormalizer.html]]></help>
  <expand macro="references"/>
</tool>