|
0
|
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>
|
