annotate NoiseFilterGaussian.xml @ 0:b6baace535ae 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="NoiseFilterGaussian" name="NoiseFilterGaussian" version="2.1.0">
  <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
  <macros>
    <token name="@EXECUTABLE@">NoiseFilterGaussian</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>NoiseFilterGaussian

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_gaussian_width:
  -algorithm:gaussian_width $param_algorithm_gaussian_width
#end if
#if $param_algorithm_ppm_tolerance:
  -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance
#end if
#if $param_algorithm_use_ppm_tolerance:
  -algorithm:use_ppm_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_processOption:
  -processOption $adv_opts.param_processOption
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
    <param name="param_algorithm_gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help="(-gaussian_width) "/>
    <param name="param_algorithm_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian"/>
    <param name="param_algorithm_use_ppm_tolerance" display="radio" type="boolean" truevalue="-algorithm:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower"/>
    <expand macro="advanced_options">
      <param name="param_processOption" display="radio" type="select" optional="False" value="inmemory" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="(-processOption) ">
        <option value="inmemory" selected="true">inmemory</option>
        <option value="lowmemory">lowmemory</option>
      </param>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="mzml"/>
  </outputs>
  <help>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).


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