|
0
|
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>
|
|
2
|
5 <macros>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio" />
|
|
|
9 <expand macro="requires" />
|
|
0
|
10 <command interpreter="python">
|
|
|
11 openms_wrapper.py --executable 'TextExporter' --config $config
|
|
|
12 </command>
|
|
|
13 <configfiles>
|
|
|
14 <configfile name="config">[simple_options]
|
|
|
15 in=${in}
|
|
|
16 out=${out}
|
|
4
|
17 $dump_type
|
|
|
18 id!first_dim_rt=$extra_rt
|
|
0
|
19 </configfile>
|
|
|
20 </configfiles>
|
|
|
21 <inputs>
|
|
|
22 <param format="idxml" name="in" type="data" label="Input Identification File"/>
|
|
|
23 <param name="dump_type" type="select" label="Export type">
|
|
4
|
24 <option value="">Run, peptide, and protein information</option>
|
|
|
25 <option value="id!proteins_only=true">Run and protein information only</option>
|
|
|
26 <option value="id!peptides_only=true">Peptide information only</option>
|
|
0
|
27 </param>
|
|
4
|
28 <param name="extra_rt" type="boolean" label="Include RT information (if present)" />
|
|
0
|
29 </inputs>
|
|
|
30 <outputs>
|
|
|
31 <data format="tabular" name="out">
|
|
|
32 </data>
|
|
|
33 </outputs>
|
|
|
34 <help>
|
|
|
35 **What it does**
|
|
|
36
|
|
|
37 Converts idXML files to tabular.
|
|
|
38
|
|
|
39 **Citation**
|
|
|
40
|
|
|
41 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.``
|
|
|
42
|
|
|
43 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
|
|
|
44 </help>
|
|
|
45 </tool>
|
