view MRMTransitionGroupPicker.xml @ 3:ec62782f6c68 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="1.12.0">
  <macros>
    <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MRMTransitionGroupPicker

-in ${param_in}
-tr ${param_tr}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:stop_after_feature ${param_stop_after_feature}
-algorithm:stop_after_intensity_ratio ${param_stop_after_intensity_ratio}
-algorithm:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
-algorithm:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
-algorithm:PeakPickerMRM:gauss_width ${param_gauss_width}
-algorithm:PeakPickerMRM:use_gauss ${param_use_gauss}
-algorithm:PeakPickerMRM:peak_width ${param_peak_width}
-algorithm:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
-algorithm:PeakPickerMRM:sn_win_len ${param_sn_win_len}
-algorithm:PeakPickerMRM:sn_bin_count ${param_sn_bin_count}
${param_remove_overlapping_peaks}
-algorithm:PeakPickerMRM:method ${param_method}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:min_peak_width ${adv_opts.param_min_peak_width}
    -algorithm:background_subtraction ${adv_opts.param_background_subtraction}
    -algorithm:recalculate_peaks ${adv_opts.param_recalculate_peaks}
    -algorithm:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z}
    -algorithm:minimal_quality ${adv_opts.param_minimal_quality}
    -algorithm:compute_peak_quality ${adv_opts.param_compute_peak_quality}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="Input file" help="(-in)"/>
    <param name="param_tr" type="data" format="tabular" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr)"/>
    <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:PeakPickerMRM:remove_overlapping_peaks true" falsevalue="-algorithm: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>
    <expand macro="advanced_options">
      <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)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="output file" format="featureXML"/>
  </outputs>
  <help>**What it does**

None


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

@REFERENCES@
</help>
</tool>