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<tool id="openms_baseline_filter" version="0.1.0" name="Baseline Filter">
  <description>
    Executes the top-hat filter to remove the baseline of an MS experiment.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'BaselineFilter' --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"/>
  </inputs>
  <outputs>
    <data format="mzml" name="out" />
  </outputs>
  <help>
**What it does**

This nonlinear filter, known as the top-hat operator in morphological mathematics (see Soille, ''Morphological Image Analysis''), is independent of the underlying baseline shape. It is able to detect an over brightness even if the environment is not uniform. The principle is based on the subtraction of a signal from its opening (erosion followed by a dilation). The size the structuring element (here a flat line) being conditioned by the width of the lineament (in our case the maximum width of a mass spectrometric peak) to be detected.

http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_BaselineFilter.html
http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_example_signalprocessing.html#TOPP_example_signalprocessing_parameters

**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>