|
0
|
1 <tool id="openms_id_file_converter" version="0.1.0" name="ID File Converter">
|
|
|
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 'IDFileConverter' --config $config
|
|
|
12 </command>
|
|
|
13 <configfiles>
|
|
|
14 <configfile name="config">[simple_options]
|
|
|
15 in=${in}
|
|
|
16 in_type=${in.ext}
|
|
|
17 out=${out}
|
|
|
18 out_type=${output_type}
|
|
|
19 </configfile>
|
|
|
20 </configfiles>
|
|
|
21 <inputs>
|
|
|
22 <param format="pepxml,protxml,idxml" name="in" type="data" label="Input Identification File"/>
|
|
|
23 <param name="output_type" type="select" label="Output Type">
|
|
|
24 <option value="idxml">idXML</option>
|
|
|
25 <option value="pepxml">pepXM</option>
|
|
|
26 <option value="mzid">mzIdentML</option>
|
|
|
27 <option value="fasta">FASTA</option>
|
|
|
28 </param>
|
|
|
29 </inputs>
|
|
|
30 <outputs>
|
|
|
31 <data format="idxml" name="out">
|
|
|
32 <change_format>
|
|
|
33 <when input="output_type" value="pepxml" format="pepxml" />
|
|
|
34 <when input="output_type" value="mzid" format="mzid" />
|
|
|
35 <when input="output_type" value="fasta" format="fasta" />
|
|
|
36 </change_format>
|
|
|
37 </data>
|
|
|
38 </outputs>
|
|
|
39 <help>
|
|
|
40 **What it does**
|
|
|
41
|
|
|
42 Shows basic information about the file, such as data ranges and file type.
|
|
|
43
|
|
|
44 **Citation**
|
|
|
45
|
|
|
46 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.``
|
|
|
47
|
|
|
48 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
|
|
|
49 </help>
|
|
|
50 </tool>
|
