|
0
|
1 <tool id="openms_noise_filter" version="0.1.0" name="Noise Filter">
|
|
|
2 <description>
|
|
|
3 Utilize a filter to reduce the noise in an MS experiment.
|
|
|
4 </description>
|
|
2
|
5 <macros>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio" />
|
|
|
9 <expand macro="requires" />
|
|
0
|
10 <command interpreter="python">
|
|
|
11 #if $filter.type == "gaussian"
|
|
|
12 #set $filter_exec = "NoiseFilterGaussian"
|
|
|
13 #elif $filter.type == "sgolay"
|
|
|
14 #set $filter_exec = "NoiseFilterSGolay"
|
|
|
15 #end if
|
|
|
16 openms_wrapper.py --executable '$filter_exec' --config $config
|
|
|
17 </command>
|
|
|
18 <configfiles>
|
|
|
19 <configfile name="config">[simple_options]
|
|
|
20 in=${in}
|
|
|
21 out=${out}
|
|
|
22 </configfile>
|
|
|
23 </configfiles>
|
|
|
24 <inputs>
|
|
|
25 <param format="mzml" name="in" type="data" label="Input mzML"/>
|
|
|
26 <conditional name="filter">
|
|
|
27 <param type="select" name="type" label="Filter Type">
|
|
|
28 <option value="gaussian">Gaussian</option>
|
|
|
29 <option value="sgolay">Savitzky Golay</option>
|
|
|
30 </param>
|
|
|
31 </conditional>
|
|
|
32 </inputs>
|
|
|
33 <outputs>
|
|
|
34 <data format="mzml" name="out" />
|
|
|
35 </outputs>
|
|
|
36 <help>
|
|
|
37 **What it does**
|
|
|
38
|
|
|
39 TODO: Document
|
|
|
40
|
|
|
41 http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterSGolay.html
|
|
|
42 http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterGaussian.html
|
|
|
43
|
|
|
44 **Citation**
|
|
|
45
|
|
|
46 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.``
|
|
|
47
|
|
|
48 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
|
|
|
49 </help>
|
|
|
50 </tool>
|
