annotate MRMTransitionGroupPicker.xml @ 5:7dca11634139 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.3.0">
  <description>Picks peaks in SRM/MRM chromatograms.</description>
  <macros>
    <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MRMTransitionGroupPicker

#if $param_in:
  -in $param_in
#end if
#if $param_tr:
  -tr $param_tr
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_stop_after_feature:
  -algorithm:stop_after_feature $param_algorithm_stop_after_feature
#end if
#if $param_algorithm_stop_after_intensity_ratio:
  -algorithm:stop_after_intensity_ratio $param_algorithm_stop_after_intensity_ratio
#end if
#if $param_algorithm_PeakPickerMRM_sgolay_frame_length:
  -algorithm:PeakPickerMRM:sgolay_frame_length $param_algorithm_PeakPickerMRM_sgolay_frame_length
#end if
#if $param_algorithm_PeakPickerMRM_sgolay_polynomial_order:
  -algorithm:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_PeakPickerMRM_sgolay_polynomial_order
#end if
#if $param_algorithm_PeakPickerMRM_gauss_width:
  -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width
#end if
#if $param_algorithm_PeakPickerMRM_use_gauss:
  -algorithm:PeakPickerMRM:use_gauss
  #if " " in str($param_algorithm_PeakPickerMRM_use_gauss):
    "$param_algorithm_PeakPickerMRM_use_gauss"
  #else
    $param_algorithm_PeakPickerMRM_use_gauss
  #end if
#end if
#if $param_algorithm_PeakPickerMRM_peak_width:
  -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width
#end if
#if $param_algorithm_PeakPickerMRM_signal_to_noise:
  -algorithm:PeakPickerMRM:signal_to_noise $param_algorithm_PeakPickerMRM_signal_to_noise
#end if
#if $param_algorithm_PeakPickerMRM_sn_win_len:
  -algorithm:PeakPickerMRM:sn_win_len $param_algorithm_PeakPickerMRM_sn_win_len
#end if
#if $param_algorithm_PeakPickerMRM_sn_bin_count:
  -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count
#end if
#if $param_algorithm_PeakPickerMRM_write_sn_log_messages:
  -algorithm:PeakPickerMRM:write_sn_log_messages
  #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages):
    "$param_algorithm_PeakPickerMRM_write_sn_log_messages"
  #else
    $param_algorithm_PeakPickerMRM_write_sn_log_messages
  #end if
#end if
#if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks:
  -algorithm:PeakPickerMRM:remove_overlapping_peaks
#end if
#if $param_algorithm_PeakPickerMRM_method:
  -algorithm:PeakPickerMRM:method
  #if " " in str($param_algorithm_PeakPickerMRM_method):
    "$param_algorithm_PeakPickerMRM_method"
  #else
    $param_algorithm_PeakPickerMRM_method
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_min_peak_width:
  -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width
#end if
    #if $adv_opts.param_algorithm_background_subtraction:
  -algorithm:background_subtraction
  #if " " in str($adv_opts.param_algorithm_background_subtraction):
    "$adv_opts.param_algorithm_background_subtraction"
  #else
    $adv_opts.param_algorithm_background_subtraction
  #end if
#end if
    #if $adv_opts.param_algorithm_recalculate_peaks:
  -algorithm:recalculate_peaks
#end if
    #if $adv_opts.param_algorithm_use_precursors:
  -algorithm:use_precursors
#end if
    #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
  -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z
#end if
    #if $adv_opts.param_algorithm_minimal_quality:
  -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
#end if
    #if $adv_opts.param_algorithm_resample_boundary:
  -algorithm:resample_boundary $adv_opts.param_algorithm_resample_boundary
#end if
    #if $adv_opts.param_algorithm_compute_peak_quality:
  -algorithm:compute_peak_quality
#end if
#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,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
    <param name="param_algorithm_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_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>
    <param name="param_algorithm_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
    <param name="param_algorithm_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
    <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
    <param name="param_algorithm_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
      <option value="false">false</option>
      <option value="true" selected="true">true</option>
    </param>
    <param name="param_algorithm_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
    <param name="param_algorithm_PeakPickerMRM_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 (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
    <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
    <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
    <param name="param_algorithm_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help="(-write_sn_log_messages) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_algorithm_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
    <param name="param_algorithm_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" 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="(-method) ">
      <option value="legacy">legacy</option>
      <option value="corrected" selected="true">corrected</option>
      <option value="crawdad">crawdad</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_algorithm_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_algorithm_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
        <option value="none" selected="true">none</option>
        <option value="smoothed">smoothed</option>
        <option value="original">original</option>
      </param>
      <param name="param_algorithm_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
      <param name="param_algorithm_use_precursors" display="radio" type="boolean" truevalue="-algorithm:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
      <param name="param_algorithm_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="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
      <param name="param_algorithm_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_algorithm_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="(-resample_boundary) "/>
      <param name="param_algorithm_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Picks peaks in SRM/MRM chromatograms.


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