annotate noise_filter.xml @ 6:42b843627623 draft default tip

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<tool id="openms_noise_filter" version="0.1.0" name="Noise Filter">
  <description>
    Utilize a filter to reduce the noise in an MS experiment.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    #if $filter.type == "gaussian"
    #set $filter_exec = "NoiseFilterGaussian"
    #elif $filter.type == "sgolay"
    #set $filter_exec = "NoiseFilterSGolay"
    #end if
    openms_wrapper.py --executable '$filter_exec' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=${in}
out=${out}
</configfile>
  </configfiles>
  <inputs>
    <param format="mzml" name="in" type="data" label="Input mzML"/>
    <conditional name="filter">
      <param type="select" name="type" label="Filter Type">
        <option value="gaussian">Gaussian</option>
        <option value="sgolay">Savitzky Golay</option>
      </param>
    </conditional>
  </inputs>
  <outputs>
    <data format="mzml" name="out" />
  </outputs>
  <help>
**What it does**

TODO: Document

http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterSGolay.html
http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterGaussian.html

**Citation**

For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
  </help>
</tool>