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<?xml version='1.0' encoding='UTF-8'?>
<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="1.12.0">
  <description>Complete workflow to run OpenSWATH</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathWorkflow

-in ${param_in}
-tr ${param_tr}
-tr_type ${param_tr_type}
-tr_irt ${param_tr_irt}
-out_features ${param_out_features}
-out_tsv ${param_out_tsv}
-rt_extraction_window ${param_rt_extraction_window}
-mz_extraction_window ${param_mz_extraction_window}
${param_ppm}
-threads \${GALAXY_SLOTS:-24} 
-Scoring:rt_normalization_factor ${param_rt_normalization_factor}
-Scoring:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature}
-Scoring:TransitionGroupPicker:min_peak_width ${param_min_peak_width}
-Scoring:TransitionGroupPicker:recalculate_peaks ${param_recalculate_peaks}
-Scoring:TransitionGroupPicker:recalculate_peaks_max_z ${param_recalculate_peaks_max_z}
-Scoring:TransitionGroupPicker:minimal_quality ${param_minimal_quality}
-Scoring:TransitionGroupPicker:compute_peak_quality ${param_compute_peak_quality}
-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
-Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width}
-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss}
-Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width}
-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
${param_remove_overlapping_peaks}
-Scoring:TransitionGroupPicker:PeakPickerMRM:method ${param_method}
-Scoring:DIAScoring:dia_extraction_window ${param_dia_extraction_window}
${param_dia_centroided}
-Scoring:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min}
-Scoring:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff}
-Scoring:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes}
-Scoring:DIAScoring:dia_nr_charges ${param_dia_nr_charges}
-Scoring:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff}
-Scoring:EMGScoring:max_iteration ${param_max_iteration}
-Scoring:EMGScoring:deltaRelError ${param_deltaRelError}
#if $adv_opts.adv_opts_selector=='advanced':
    -rt_norm ${adv_opts.param_rt_norm}
    -swath_windows_file ${adv_opts.param_swath_windows_file}
    ${adv_opts.param_sort_swath_maps}
    ${adv_opts.param_use_ms1_traces}
    -out_chrom ${adv_opts.param_out_chrom}
    -min_upper_edge_dist ${adv_opts.param_min_upper_edge_dist}
    -extra_rt_extraction_window ${adv_opts.param_extra_rt_extraction_window}
    -min_rsq ${adv_opts.param_min_rsq}
    -min_coverage ${adv_opts.param_min_coverage}
    ${adv_opts.param_split_file_input}
    ${adv_opts.param_use_elution_model_score}
    -readOptions ${adv_opts.param_readOptions}
    -tempDirectory ${adv_opts.param_tempDirectory}
    -extraction_function ${adv_opts.param_extraction_function}
    -batchSize ${adv_opts.param_batchSize}
    -Scoring:quantification_cutoff ${adv_opts.param_quantification_cutoff}
    ${adv_opts.param_write_convex_hull}
    ${adv_opts.param_use_shape_score}
    ${adv_opts.param_use_coelution_score}
    ${adv_opts.param_use_rt_score}
    ${adv_opts.param_use_library_score}
    ${adv_opts.param_use_intensity_score}
    ${adv_opts.param_use_nr_peaks_score}
    ${adv_opts.param_use_total_xic_score}
    ${adv_opts.param_use_sn_score}
    ${adv_opts.param_use_dia_scores}
    ${adv_opts.param_use_ms1_correlation}
    ${adv_opts.param_use_ms1_fullscan}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML,mzXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
    <param name="param_tr" type="data" format="tabular" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr)"/>
    <param name="param_tr_type" type="select" optional="True" label="input file type -- default: determined from file extension or content#br#" 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="" optional="True" label="transition file ('TraML')" help="(-tr_irt)"/>
    <param name="param_out_tsv" type="text" size="20" label="TSV output file (mProphet compatible)" help="(-out_tsv)"/>
    <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" type="boolean" truevalue="-ppm true" falsevalue="-ppm false" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm)"/>
    <param name="param_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 (e.g. it goes from 0 to 100, set this value to 100)" help="(-rt_normalization_factor)"/>
    <param name="param_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_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_recalculate_peaks" type="text" size="20" value="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large." help="(-recalculate_peaks)"/>
    <param name="param_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. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)." help="(-recalculate_peaks_max_z)"/>
    <param name="param_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_compute_peak_quality" type="text" size="20" value="true" label="Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad." help="(-compute_peak_quality)"/>
    <param name="param_sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing.#br#This number has to be uneven. If it is not, 1 will be added." help="(-sgolay_frame_length)"/>
    <param name="param_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted." help="(-sgolay_polynomial_order)"/>
    <param name="param_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size." help="(-gauss_width)"/>
    <param name="param_use_gauss" type="text" size="20" value="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss)"/>
    <param name="param_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off." help="(-peak_width)"/>
    <param name="param_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 (e.g. 1.0) can lead to peaks whose flanks are not fully captured." help="(-signal_to_noise)"/>
    <param name="param_remove_overlapping_peaks" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks true" falsevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks false" checked="true" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks)"/>
    <param name="param_method" type="select" optional="True" 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">corrected</option>
      <option value="crawdad">crawdad</option>
    </param>
    <param name="param_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_dia_centroided" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided true" falsevalue="-Scoring:DIAScoring:dia_centroided false" checked="false" optional="True" label="Use centroded DIA data." help="(-dia_centroided)"/>
    <param name="param_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to consider." help="(-dia_byseries_intensity_min)"/>
    <param name="param_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to consider." help="(-dia_byseries_ppm_diff)"/>
    <param name="param_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to consider." help="(-dia_nr_isotopes)"/>
    <param name="param_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to consider." help="(-dia_nr_charges)"/>
    <param name="param_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_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm." help="(-max_iteration)"/>
    <param name="param_deltaRelError" type="float" value="0.1" label="" help="(-deltaRelError)"/>
    <expand macro="advanced_options">
      <param name="param_rt_norm" type="data" format="" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library). If set, tr_irt may be omitted." help="(-rt_norm)"/>
      <param name="param_swath_windows_file" type="data" format="data" label="Optional, tab separated file containing the SWATH windows: lower_offset upper_offset \newline 400 425 \newline ... Note that the first line is a header and will be skipped." help="(-swath_windows_file)"/>
      <param name="param_sort_swath_maps" type="boolean" truevalue="-sort_swath_maps true" falsevalue="-sort_swath_maps false" 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" type="boolean" truevalue="-use_ms1_traces true" falsevalue="-use_ms1_traces false" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces)"/>
      <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 (e.g. to visually inspect a larger area of the chromatogram)" help="(-extra_rt_extraction_window)"/>
      <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" type="boolean" truevalue="-split_file_input true" falsevalue="-split_file_input false" 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" type="boolean" truevalue="-use_elution_model_score true" falsevalue="-use_elution_model_score false" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score)"/>
      <param name="param_readOptions" type="select" optional="True" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first. If you choose cache, make sure to also set tempDirectory" help="(-readOptions)">
        <option value="normal">normal</option>
        <option value="cache">cache</option>
      </param>
      <param name="param_tempDirectory" type="text" size="20" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory)"/>
      <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function)">
        <option value="tophat">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_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_write_convex_hull" type="boolean" truevalue="-Scoring:write_convex_hull true" falsevalue="-Scoring:write_convex_hull false" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull)"/>
      <param name="param_use_shape_score" type="boolean" truevalue="-Scoring:Scores:use_shape_score true" falsevalue="-Scoring:Scores:use_shape_score false" checked="true" optional="True" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score)"/>
      <param name="param_use_coelution_score" type="boolean" truevalue="-Scoring:Scores:use_coelution_score true" falsevalue="-Scoring:Scores:use_coelution_score false" checked="true" optional="True" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score)"/>
      <param name="param_use_rt_score" type="boolean" truevalue="-Scoring:Scores:use_rt_score true" falsevalue="-Scoring:Scores:use_rt_score false" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score)"/>
      <param name="param_use_library_score" type="boolean" truevalue="-Scoring:Scores:use_library_score true" falsevalue="-Scoring:Scores:use_library_score false" checked="true" optional="True" label="Use the library score" help="(-use_library_score)"/>
      <param name="param_use_intensity_score" type="boolean" truevalue="-Scoring:Scores:use_intensity_score true" falsevalue="-Scoring:Scores:use_intensity_score false" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score)"/>
      <param name="param_use_nr_peaks_score" type="boolean" truevalue="-Scoring:Scores:use_nr_peaks_score true" falsevalue="-Scoring:Scores:use_nr_peaks_score false" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score)"/>
      <param name="param_use_total_xic_score" type="boolean" truevalue="-Scoring:Scores:use_total_xic_score true" falsevalue="-Scoring:Scores:use_total_xic_score false" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score)"/>
      <param name="param_use_sn_score" type="boolean" truevalue="-Scoring:Scores:use_sn_score true" falsevalue="-Scoring:Scores:use_sn_score false" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score)"/>
      <param name="param_use_dia_scores" type="boolean" truevalue="-Scoring:Scores:use_dia_scores true" falsevalue="-Scoring:Scores:use_dia_scores false" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores)"/>
      <param name="param_use_ms1_correlation" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation true" falsevalue="-Scoring:Scores:use_ms1_correlation false" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation)"/>
      <param name="param_use_ms1_fullscan" type="boolean" truevalue="-Scoring:Scores:use_ms1_fullscan true" falsevalue="-Scoring:Scores:use_ms1_fullscan false" 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)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out_features" label="output file" format="featureXML"/>
    <data name="param_out_chrom" label="Also output all computed chromatograms (chrom.mzML) output" format="mzML"/>
  </outputs>
  <help>**What it does**

Complete workflow to run OpenSWATH


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

@REFERENCES@
</help>
</tool>