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comparison peak_file_converter.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_peak_file_convert" version="0.1.0" name="Peak List File Converter">
2 <description>
3 Converts between different MS file formats.
4 </description>
5 <requirements>
6 <requirement type="package">openms</requirement>
7 </requirements>
8 <command interpreter="python">
9 openms_wrapper.py --executable 'FileConverter' --config $config
10 </command>
11 <configfiles>
12 <configfile name="config">[simple_options]
13 in=${in}
14 in_type=${in.ext}
15 out=${out}
16 out_type=${out_format}
17 </configfile>
18 </configfiles>
19 <inputs>
20 <param format="mzml,mgf,mzxml,ms2" name="in" type="data" label="Input mzML File"/>
21 <param type="select" name="out_format" label="Output Type">
22 <option value="mzml">mzML</option>
23 <option value="mzxml">mzXML</option>
24 <option value="mgf">MGF</option>
25 <option value="ms2">MS2</option>
26 </param>
27 </inputs>
28 <outputs>
29 <data format="mzml" name="out">
30 <change_format>
31 <when input="out_format" value="mzxml" format="mzxml" />
32 <when input="out_format" value="mgf" format="mgf" />
33 <when input="out_format" value="ms2" format="ms2" />
34 </change_format>
35 </data>
36 </outputs>
37 <help>
38 **What it does**
39
40 Extracts portions of the data from an mzML.
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>