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<?xml version='1.0' encoding='UTF-8'?>
<tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="1.12.0">
  <description>Picks peaks and finds features in an SRM experiment.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathAnalyzer

-in ${param_in}
-tr ${param_tr}
-rt_norm ${param_rt_norm}
-out ${param_out}
${param_no-strict}
-swath_files ${param_swath_files}
-min_upper_edge_dist ${param_min_upper_edge_dist}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:stop_report_after_feature ${param_stop_report_after_feature}
-algorithm:rt_extraction_window ${param_rt_extraction_window}
-algorithm:rt_normalization_factor ${param_rt_normalization_factor}
-algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature}
-algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio}
-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width}
-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss}
-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width}
-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len}
-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count}
${param_remove_overlapping_peaks}
-algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method}
-algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window}
${param_dia_centroided}
-algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min}
-algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff}
-algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes}
-algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges}
-algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff}
#if $adv_opts.adv_opts_selector=='advanced':
    -model:type ${adv_opts.param_type}
    ${adv_opts.param_symmetric_regression}
    -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff}
    ${adv_opts.param_write_convex_hull}
    -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra}
    -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling}
    -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width}
    -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction}
    -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks}
    -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z}
    -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality}
    -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality}
    -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step}
    -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box}
    -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration}
    -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean}
    -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance}
    ${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_elution_model_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" optional="False" label="input file containing the chromatograms." help="(-in)"/>
    <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/>
    <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)" help="(-rt_norm)"/>
    <param name="param_no-strict" type="boolean" truevalue="-no-strict true" falsevalue="-no-strict false" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped." help="(-no-strict)"/>
    <param name="param_swath_files" type="data" format="mzML" optional="True" size="20" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions. If present, SWATH specific scoring will be used." help="(-swath_files)"/>
    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist)"/>
    <param name="param_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_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). For this to work, the TraML input file needs to contain normalized RT values." help="(-rt_extraction_window)"/>
    <param name="param_rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (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_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio)"/>
    <param name="param_sgolay_frame_length" type="integer" value="15" 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="50.0" label="Gaussian width in seconds, estimated peak size." help="(-gauss_width)"/>
    <param name="param_use_gauss" type="text" size="20" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss)"/>
    <param name="param_peak_width" type="float" value="40.0" 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="1.0" 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_sn_win_len" type="float" value="1000.0" label="Signal to noise window length." help="(-sn_win_len)"/>
    <param name="param_sn_bin_count" type="integer" value="30" label="Signal to noise bin count." help="(-sn_bin_count)"/>
    <param name="param_remove_overlapping_peaks" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks true" falsevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks false" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks)"/>
    <param name="param_method" type="select" optional="True" value="legacy" 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="-algorithm:DIAScoring:dia_centroided true" falsevalue="-algorithm: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)"/>
    <expand macro="advanced_options">
      <param name="param_type" type="select" optional="True" value="linear" label="Type of model" help="(-type)">
        <option value="linear">linear</option>
        <option value="b_spline">b_spline</option>
        <option value="interpolated">interpolated</option>
      </param>
      <param name="param_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression true" falsevalue="-model:symmetric_regression false" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
      <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="-algorithm:write_convex_hull true" falsevalue="-algorithm: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_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra)"/>
      <param name="param_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling)"/>
      <param name="param_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)." help="(-min_peak_width)"/>
      <param name="param_background_subtraction" type="select" optional="True" value="none" label="Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that." help="(-background_subtraction)">
        <option value="none">none</option>
        <option value="smoothed">smoothed</option>
        <option value="original">original</option>
      </param>
      <param name="param_recalculate_peaks" type="text" size="20" value="false" 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="1.0" 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="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality)"/>
      <param name="param_compute_peak_quality" type="text" size="20" value="false" 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_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function." help="(-interpolation_step)"/>
      <param name="param_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data." help="(-tolerance_stdev_bounding_box)"/>
      <param name="param_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm." help="(-max_iteration)"/>
      <param name="param_mean" type="float" value="1.0" label="Centroid position of the model." help="(-mean)"/>
      <param name="param_variance" type="float" value="1.0" label="Variance of the model." help="(-variance)"/>
      <param name="param_use_shape_score" type="boolean" truevalue="-algorithm:Scores:use_shape_score true" falsevalue="-algorithm: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="-algorithm:Scores:use_coelution_score true" falsevalue="-algorithm: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="-algorithm:Scores:use_rt_score true" falsevalue="-algorithm: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="-algorithm:Scores:use_library_score true" falsevalue="-algorithm:Scores:use_library_score false" checked="true" optional="True" label="Use the library score" help="(-use_library_score)"/>
      <param name="param_use_elution_model_score" type="boolean" truevalue="-algorithm:Scores:use_elution_model_score true" falsevalue="-algorithm:Scores:use_elution_model_score false" checked="true" optional="True" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score)"/>
      <param name="param_use_intensity_score" type="boolean" truevalue="-algorithm:Scores:use_intensity_score true" falsevalue="-algorithm: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="-algorithm:Scores:use_nr_peaks_score true" falsevalue="-algorithm: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="-algorithm:Scores:use_total_xic_score true" falsevalue="-algorithm: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="-algorithm:Scores:use_sn_score true" falsevalue="-algorithm: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="-algorithm:Scores:use_dia_scores true" falsevalue="-algorithm: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="-algorithm:Scores:use_ms1_correlation true" falsevalue="-algorithm: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="-algorithm:Scores:use_ms1_fullscan true" falsevalue="-algorithm: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" label="output file" format="featureXML"/>
  </outputs>
  <help>**What it does**

Picks peaks and finds features in an SRM experiment.


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

@REFERENCES@
</help>
</tool>