annotate SpectraFilterWindowMower.xml @ 5:746db2c7b499 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: [Identification]-->
<tool id="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="2.3.0">
  <description>Applies thresholdfilter to peak spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">SpectraFilterWindowMower</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpectraFilterWindowMower

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_windowsize:
  -algorithm:windowsize $param_algorithm_windowsize
#end if
#if $param_algorithm_peakcount:
  -algorithm:peakcount $param_algorithm_peakcount
#end if
#if $param_algorithm_movetype:
  -algorithm:movetype
  #if " " in str($param_algorithm_movetype):
    "$param_algorithm_movetype"
  #else
    $param_algorithm_movetype
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#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_windowsize" type="float" value="50.0" label="The size of the sliding window along the m/z axis" help="(-windowsize) "/>
    <param name="param_algorithm_peakcount" type="integer" value="2" label="The number of peaks that should be kept" help="(-peakcount) "/>
    <param name="param_algorithm_movetype" display="radio" type="select" optional="False" value="slide" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="(-movetype) ">
      <option value="slide" selected="true">slide</option>
      <option value="jump">jump</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) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="mzml"/>
  </outputs>
  <help>Applies thresholdfilter to peak spectra.


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