|
2
|
1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5">
|
|
|
2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="binary">java</requirement>
|
|
|
5 <requirement type="package" version="1.3">clinod</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command>
|
|
|
8 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
|
|
|
9 ##containing both clinod-1.3.jar and the batchman binary:
|
|
|
10 java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence
|
|
|
11 ##I want the number of threads to be a Galaxy config option...
|
|
|
12 ##TODO - Make the -clean_sequence argument a parameter?
|
|
|
13 </command>
|
|
|
14 <stdio>
|
|
|
15 <!-- Assume anything other than zero is an error -->
|
|
|
16 <exit_code range="1:" />
|
|
|
17 <exit_code range=":-1" />
|
|
|
18 </stdio>
|
|
|
19 <inputs>
|
|
|
20 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
|
|
|
21 </inputs>
|
|
|
22 <outputs>
|
|
|
23 <data name="tabular_file" format="tabular" label="NoD results" />
|
|
|
24 </outputs>
|
|
|
25 <tests>
|
|
|
26 <test>
|
|
|
27 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
|
|
|
28 <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
|
|
|
29 </test>
|
|
|
30 </tests>
|
|
|
31 <help>
|
|
|
32
|
|
|
33 **What it does**
|
|
|
34
|
|
|
35 This calls the command line version of the NoD tool from the Barton Group for
|
|
|
36 prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an
|
|
|
37 artificial neural network trained on a set of human NoLSs.
|
|
|
38
|
|
|
39 The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded
|
|
|
40 as a special nuclear localization sequence (NLS).
|
|
|
41
|
|
|
42 The input is a FASTA file of protein sequences, and the output is tabular with
|
|
|
43 four columns (multiple rows per protein):
|
|
|
44
|
|
|
45 ====== ===================
|
|
|
46 Column Description
|
|
|
47 ------ -------------------
|
|
|
48 1 Sequence identifier
|
|
|
49 2 Start of NoLS
|
|
|
50 3 End of NoLS
|
|
|
51 4 NoLS sequence
|
|
|
52 ====== ===================
|
|
|
53
|
|
|
54 If a sequence has no predicted NoLS, then there is no line in the output file
|
|
|
55 for it.
|
|
|
56
|
|
|
57 -----
|
|
|
58
|
|
|
59 **References**
|
|
|
60
|
|
|
61 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
|
|
|
62 Characterization and prediction of protein nucleolar localization sequences.
|
|
|
63 Nucleic Acids Research 38(21), 7388-7399, 2010.
|
|
|
64 http://dx.doi.org/10.1093/nar/gkq653
|
|
|
65
|
|
|
66 M. S. Scott, P. V. Troshin and G. J. Barton.
|
|
|
67 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
|
|
|
68 BMC Bioinformatics, 12:317, 2011.
|
|
|
69 http://dx.doi.org/10.1186/1471-2105-12-317
|
|
|
70
|
|
|
71 http://www.compbio.dundee.ac.uk/www-nod/
|
|
|
72
|
|
|
73 This wrapper is available to install into other Galaxy Instances via the Galaxy
|
|
|
74 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
|
|
|
75
|
|
|
76 </help>
|
|
|
77 </tool>
|
