annotate PeakPickerIterative.xml @ 0:861c8e12c4ef draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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 CTD2Galaxy.-->
<!--Proposed Tool Section: [Signal processing and preprocessing]-->
<tool id="PeakPickerIterative" name="PeakPickerIterative" version="2.1.0">
  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">PeakPickerIterative</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PeakPickerIterative

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_signal_to_noise_:
  -algorithm:signal_to_noise_ $param_algorithm_signal_to_noise_
#end if
#if $param_algorithm_peak_width:
  -algorithm:peak_width $param_algorithm_peak_width
#end if
#if $param_algorithm_ms1_only:
  -algorithm:ms1_only
#end if
#if $param_algorithm_clear_meta_data:
  -algorithm:clear_meta_data
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_spacing_difference:
  -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
#end if
    #if $adv_opts.param_algorithm_sn_bin_count_:
  -algorithm:sn_bin_count_ $adv_opts.param_algorithm_sn_bin_count_
#end if
    #if $adv_opts.param_algorithm_nr_iterations_:
  -algorithm:nr_iterations_ $adv_opts.param_algorithm_nr_iterations_
#end if
    #if $adv_opts.param_algorithm_sn_win_len_:
  -algorithm:sn_win_len_ $adv_opts.param_algorithm_sn_win_len_
#end if
    #if $adv_opts.param_algorithm_check_width_internally:
  -algorithm:check_width_internally
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
    <param name="param_algorithm_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_algorithm_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)" help="(-peak_width) In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
    <param name="param_algorithm_ms1_only" display="radio" type="boolean" truevalue="-algorithm:ms1_only" falsevalue="" checked="false" optional="True" label="Only do MS1" help="(-ms1_only) "/>
    <param name="param_algorithm_clear_meta_data" display="radio" type="boolean" truevalue="-algorithm:clear_meta_data" falsevalue="" checked="false" optional="True" label="Delete meta data about peak width" help="(-clear_meta_data) "/>
    <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_spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="(-spacing_difference) 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"/>
      <param name="param_algorithm_sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help="(-sn_bin_count_) "/>
      <param name="param_algorithm_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_algorithm_sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help="(-sn_win_len_) "/>
      <param name="param_algorithm_check_width_internally" display="radio" type="boolean" truevalue="-algorithm:check_width_internally" falsevalue="" 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" format="mzml"/>
  </outputs>
  <help>Finds mass spectrometric peaks in profile mass spectra.


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