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comparison pepxml_protxml_merger.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_pepxml_protxml_merger" version="0.1.0" name="Merge idXML from PepXML and ProtXML">
2 <description>
3 </description>
4 <requirements>
5 <requirement type="package">openms</requirement>
6 </requirements>
7 <command interpreter="python">
8 openms_wrapper.py --executable 'IDMerger' --config $config
9 </command>
10 <configfiles>
11 <configfile name="config">[simple_options]
12 in="${pepxml} ${protxml}"
13 out=${out}
14 annotate_file_origin=${annotate_file_origin}
15 pepxml_protxml=true
16 </configfile>
17 </configfiles>
18 <inputs>
19 <param format="idxml" name="pepxml" type="data" label="idXML from PepXML"/>
20 <param format="idxml" name="protxml" type="data" label="idXML from ProtXML"/>
21 <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." />
22 </inputs>
23 <outputs>
24 <data format="idxml" name="out" />
25 </outputs>
26 <help>
27 **What it does**
28
29 Merge idXML files derived from a pepXML and corresponding protXML file.
30
31 **Citation**
32
33 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.``
34
35 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
36 </help>
37 </tool>