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1 <tool id="openms_feature_finder_isotope_wavelet" version="0.1.0" name="Feature Finder (Isotope Wavelet)">
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2 <description>
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3 The feature detection application for quantitation.
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio" />
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9 <expand macro="requires" />
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10 <command interpreter="python">
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11 openms_wrapper.py --executable 'FeatureFinderIsotopeWavelet' --config $config
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12 </command>
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13 <configfiles>
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14 <configfile name="config">[simple_options]
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15 in=$input1
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16 out=$output
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17 </configfile>
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18 </configfiles>
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19 <inputs>
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20 <param name="input1" label="mzML Input" type="data" format="mzml" />
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21 </inputs>
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22 <outputs>
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23 <data format="featurexml" name="output" />
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24 </outputs>
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25 <help>
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26 **What it does**
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27
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28 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.
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29
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30 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.
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31
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32 Note:
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33 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.
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34
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35 **Citation**
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36
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37 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.``
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38
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39 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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40 </help>
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41 </tool>
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