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

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<tool id="openms_feature_finder_isotope_wavelet" version="0.1.0" name="Feature Finder (Isotope Wavelet)">
  <description>
    The feature detection application for quantitation.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'FeatureFinderIsotopeWavelet' --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**

This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide.

The algorithm identifies pronounced regions of the data around so-called seeds. In the next step, we iteratively fit a model of the isotope profile and the retention time to these data points. Data points with a low probability under this model are removed from the feature region. The intensity of the feature is then given by the sum of the data points included in its regions.

Note:
that the wavelet transform is very slow on high-resolution spectra (i.e. FT, Orbitrap). We recommend to use a noise or intensity filter to remove spurious points first and to speed-up the feature detection process.

**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>