|
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>
|
|
|
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>
|
