Mercurial > repos > galaxyp > openms
comparison feature_finder_isotope_wavelet.xml @ 2:cf0d72c7b482 draft
Update.
| author | galaxyp |
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| date | Fri, 10 May 2013 17:31:05 -0400 |
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| 1:5c65f8116244 | 2:cf0d72c7b482 |
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| 1 <tool id="openms_feature_finder_isotope_wavelet" version="0.1.0" name="Feature Finder (Isotope Wavelet)"> | |
| 2 <description> | |
| 3 The feature detection application for quantitation. | |
| 4 </description> | |
| 5 <macros> | |
| 6 <import>macros.xml</import> | |
| 7 </macros> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="requires" /> | |
| 10 <command interpreter="python"> | |
| 11 openms_wrapper.py --executable 'FeatureFinderIsotopeWavelet' --config $config | |
| 12 </command> | |
| 13 <configfiles> | |
| 14 <configfile name="config">[simple_options] | |
| 15 in=$input1 | |
| 16 out=$output | |
| 17 </configfile> | |
| 18 </configfiles> | |
| 19 <inputs> | |
| 20 <param name="input1" label="mzML Input" type="data" format="mzml" /> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="featurexml" name="output" /> | |
| 24 </outputs> | |
| 25 <help> | |
| 26 **What it does** | |
| 27 | |
| 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. | |
| 29 | |
| 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. | |
| 31 | |
| 32 Note: | |
| 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. | |
| 34 | |
| 35 **Citation** | |
| 36 | |
| 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.`` | |
| 38 | |
| 39 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms | |
| 40 </help> | |
| 41 </tool> |