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comparison tools/protein_analysis/clinod.xml @ 0:b8be455c27d1

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Uploaded wrapper v0.0.1 (for clinod v1.3)
author peterjc
date Tue, 02 Aug 2011 06:51:52 -0400
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-1:000000000000 0:b8be455c27d1
1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.1">
2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
3 <command>
4 java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence
5 ##I want the number of threads to be a Galaxy config option...
6 ##TODO - Make the -clean_sequece argument a parameter?
7 </command>
8 <inputs>
9 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
10 </inputs>
11 <outputs>
12 <data name="tabular_file" format="tabular" label="NoD results" />
13 </outputs>
14 <requirements>
15 <requirement type="binary">java</requirement>
16 </requirements>
17 <help>
18
19 **What it does**
20
21 This calls the command line version of the NoD tool from the Barton Group for
22 prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an
23 artificial neural network trained on a set of human NoLSs.
24
25 The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded
26 as a special nuclear localization sequence (NLS).
27
28 The input is a FASTA file of protein sequences, and the output is tabular with
29 four columns (multiple rows per protein):
30
31 * Sequence identifier
32 * Start of NoLS
33 * End of NoLS
34 * NoLS sequence
35
36 If a sequence has no predicted NoLS, then there is no line in the output file
37 for it.
38
39 **References**
40
41 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
42 Characterization and prediction of protein nucleolar localization sequences.
43 Nucleic Acids Research 38(21), 7388-7399, 2010.
44 http://dx.doi.org/10.1093/nar/gkq653
45
46 M. S. Scott, P. V. Troshin and G. J. Barton.
47 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
48 BMC Bioinformatics, in press, 2011.
49
50 http://www.compbio.dundee.ac.uk/www-nod/
51
52 </help>
53 </tool>