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comparison tools/clinod/clinod.xml @ 2:d1aebb0acee7 draft

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Uploaded v0.0.5, automated installation
author peterjc
date Thu, 30 May 2013 13:26:33 -0400
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1:221d7dca03a5 2:d1aebb0acee7
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>