annotate NoiseFilterSGolay.xml @ 0:2b7b288f2d2a 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="NoiseFilterSGolay" name="NoiseFilterSGolay" version="2.1.0">
  <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description>
  <macros>
    <token name="@EXECUTABLE@">NoiseFilterSGolay</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>NoiseFilterSGolay

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_frame_length:
  -algorithm:frame_length $param_algorithm_frame_length
#end if
#if $param_algorithm_polynomial_order:
  -algorithm:polynomial_order $param_algorithm_polynomial_order
#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_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
    <param name="param_algorithm_polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help="(-polynomial_order) "/>
    <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 a Savitzky Golay filter. Requires uniform (equidistant) data.


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