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comparison idxml_to_tabular.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_idxml_to_tabular" version="0.1.0" name="Export idXML to Tabular">
2 <description>
3 Converts identification engine file formats.
4 </description>
5 <requirements>
6 <requirement type="package">openms</requirement>
7 </requirements>
8 <command interpreter="python">
9 openms_wrapper.py --executable 'TextExporter' --config $config
10 </command>
11 <configfiles>
12 <configfile name="config">[simple_options]
13 in=${in}
14 out=${out}
15 #if $dump_type == "protein"
16 proteins_only=true
17 #end if
18 #if $dump_type == "pepetide"
19 peptides_only=true
20 #end if
21 $extra_rt
22 </configfile>
23 </configfiles>
24 <inputs>
25 <param format="idxml" name="in" type="data" label="Input Identification File"/>
26 <param name="dump_type" type="select" label="Export type">
27 <option value="all">Run, peptide, and protein information</option>
28 <option value="protein">Run and protein information only</option>
29 <option value="peptide">Peptide information only</option>
30 </param>
31 <param name="extra_rt" type="boolean" truevalue="first_dim_rt=true" falsevalue="" label="Include RT information (if present)" />
32 </inputs>
33 <outputs>
34 <data format="tabular" name="out">
35 </data>
36 </outputs>
37 <help>
38 **What it does**
39
40 Converts idXML files to tabular.
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>