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comparison decoy_database.xml @ 2:cf0d72c7b482 draft

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author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
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1 <tool id="openms_decoy_database" version="0.1.0" name="Decoy Database Creator">
2 <description>
3 Create decoy protein/peptide databases from normal ones.
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio" />
9 <expand macro="requires" />
10 <command interpreter="python">
11 openms_wrapper.py --executable 'DecoyDatabase' --config $config
12 </command>
13 <configfiles>
14 <configfile name="config">[simple_options]
15 in=${in}
16 out=${out}
17 decoy_string=${decoy_string}
18 decoy_string_position=${decoy_string_position}
19 append=${append}
20 shuffle=${shuffle}
21 </configfile>
22 </configfiles>
23 <inputs>
24 <param format="fasta" name="in" type="data" label="Input database"/>
25 <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
26 <param name="decoy_string_position" type="select" label="Decoy Position">
27 <option value="suffix" selected="true">Suffix</option>
28 <option value="prefix">Prefix</option>
29 </param>
30 <param type="boolean" name="append" label="Append to original database" checked="true" />
31 <param type="select" name="shuffle" label="Decoy type">
32 <option value="false" selected="true">Reverse</option>
33 <option value="true">Shuffle</option>
34 </param>
35 </inputs>
36 <outputs>
37 <data format="fasta" name="out" />
38 </outputs>
39 <stdio>
40 <exit_code range="1:" level="fatal" description="Error creating decoy database." />
41 </stdio>
42 <help>
43 **What it does**
44
45 Create decoy protein/peptide databases from normal ones.
46
47 **Citation**
48
49 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.``
50
51 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
52 </help>
53 </tool>