view PeakPickerIterative.xml @ 3:ec62782f6c68 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="PeakPickerIterative" name="PeakPickerIterative" version="1.12.0">
  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">PeakPickerIterative</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PeakPickerIterative

-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:signal_to_noise_ ${param_signal_to_noise_}
-algorithm:peak_width ${param_peak_width}
${param_ms1_only}
${param_clear_meta_data}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:spacing_difference ${adv_opts.param_spacing_difference}
    -algorithm:sn_bin_count_ ${adv_opts.param_sn_bin_count_}
    -algorithm:nr_iterations_ ${adv_opts.param_nr_iterations_}
    -algorithm:sn_win_len_ ${adv_opts.param_sn_win_len_}
    ${adv_opts.param_check_width_internally}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/>
    <param name="param_signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help="(-signal_to_noise_)"/>
    <param name="param_peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing). In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value." help="(-peak_width)"/>
    <param name="param_ms1_only" type="boolean" truevalue="-algorithm:ms1_only true" falsevalue="-algorithm:ms1_only false" checked="false" optional="True" label="Only do MS1" help="(-ms1_only)"/>
    <param name="param_clear_meta_data" type="boolean" truevalue="-algorithm:clear_meta_data true" falsevalue="-algorithm:clear_meta_data false" checked="false" optional="True" label="Delete meta data about peak width" help="(-clear_meta_data)"/>
    <expand macro="advanced_options">
      <param name="param_spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue. The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak." help="(-spacing_difference)"/>
      <param name="param_sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation." help="(-sn_bin_count_)"/>
      <param name="param_nr_iterations_" type="integer" min="1" optional="True" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)." help="(-nr_iterations_)"/>
      <param name="param_sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation." help="(-sn_win_len_)"/>
      <param name="param_check_width_internally" type="boolean" truevalue="-algorithm:check_width_internally true" falsevalue="-algorithm:check_width_internally false" checked="false" optional="True" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help="(-check_width_internally)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="output file" format="mzML"/>
  </outputs>
  <help>**What it does**

Finds mass spectrometric peaks in profile mass spectra.


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

@REFERENCES@
</help>
</tool>