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comparison noise_filter.xml @ 0:ba86fd127f5a draft

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author galaxyp
date Wed, 19 Dec 2012 00:32:25 -0500
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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>
5 <requirements>
6 <requirement type="package">openms</requirement>
7 </requirements>
8 <command interpreter="python">
9 #if $filter.type == "gaussian"
10 #set $filter_exec = "NoiseFilterGaussian"
11 #elif $filter.type == "sgolay"
12 #set $filter_exec = "NoiseFilterSGolay"
13 #end if
14 openms_wrapper.py --executable '$filter_exec' --config $config
15 </command>
16 <configfiles>
17 <configfile name="config">[simple_options]
18 in=${in}
19 out=${out}
20 </configfile>
21 </configfiles>
22 <inputs>
23 <param format="mzml" name="in" type="data" label="Input mzML"/>
24 <conditional name="filter">
25 <param type="select" name="type" label="Filter Type">
26 <option value="gaussian">Gaussian</option>
27 <option value="sgolay">Savitzky Golay</option>
28 </param>
29 </conditional>
30 </inputs>
31 <outputs>
32 <data format="mzml" name="out" />
33 </outputs>
34 <help>
35 **What it does**
36
37 TODO: Document
38
39 http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterSGolay.html
40 http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterGaussian.html
41
42 **Citation**
43
44 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.``
45
46 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
47 </help>
48 </tool>