Mercurial > repos > galaxyp > openms
comparison peak_picker_hi_res.xml @ 0:ba86fd127f5a draft
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| author | galaxyp |
|---|---|
| date | Wed, 19 Dec 2012 00:32:25 -0500 |
| parents | |
| children | cf0d72c7b482 |
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| -1:000000000000 | 0:ba86fd127f5a |
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| 1 <tool id="openms_peak_picker_hi_res" version="0.1" name="Peak Peaker (Hi Res)"> | |
| 2 <description> | |
| 3 </description> | |
| 4 <requirements> | |
| 5 <requirement type="package">openms</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 openms_wrapper.py --executable 'PeakPickerHiRes' --config $config | |
| 9 </command> | |
| 10 <configfiles> | |
| 11 <configfile name="config">[simple_options] | |
| 12 in=${input} | |
| 13 out=${out} | |
| 14 algorithm!signal_to_noise=${signal_to_noise} | |
| 15 algorithm!ms1_only=${ms1_only} | |
| 16 </configfile> | |
| 17 </configfiles> | |
| 18 <inputs> | |
| 19 <param format="mzML" name="input" type="data" label="Input profile peak list"/> | |
| 20 <param type="float" name="signal_to_noise" value="1" label="Signal-to-noise ratio" help="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" /> | |
| 21 <param type="boolean" name="ms1_only" label="MS1 Only" help="If checked, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes." /> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="mzML" name="out" /> | |
| 25 </outputs> | |
| 26 <help> | |
| 27 **What it does** | |
| 28 | |
| 29 This peak-picking algorithm detects ion signals in raw data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak's m/z and intensity value is given by the maximum of the underlying peak spline. Please notice that this method is still experimental since it has not been tested thoroughly yet. | |
| 30 | |
| 31 The algorithm used by this tool is best suited for high-resolution MS data (FT-ICR-MS, Orbitrap). In high-resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. These properties faciliate a fast computation of picked peaks so that even large data sets can be processed very quickly. | |
| 32 | |
| 33 **Citation** | |
| 34 | |
| 35 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.`` | |
| 36 | |
| 37 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms | |
| 38 </help> | |
| 39 </tool> |