view feature_finder_metabo.xml @ 2:cf0d72c7b482 draft

Update.

<tool id="openms_feature_finder_metabo" version="0.1.0" name="Feature Finder (Metabolites)">
  <description>
    Assembles metabolite features from singleton mass traces.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'FeatureFinderMetabo' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=$input1
out=$output
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="mzML Input" type="data" format="mzml" />
  </inputs>
  <outputs>
    <data format="featurexml" name="output" />
  </outputs>
  <help>
**What it does**

Mass traces alone would allow for further analyzes such as metabolite ID or statistical evaluation. However, in general, monoisotopic mass traces are accompanied with satellite C13 peaks and thus may render the analysis more difficult. FeatureFinderMetabo fulfills a further data reduction step by assembling compatible mass traces to metabolite features (that is, mass traces all stemming from one metabolite). To this end, multiple metabolite hypotheses are formulated and scored according to how well differences in RT and m/z or intensity ratios match to those of theoretical isotope patterns.

**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>