Mercurial > repos > peterjc > clinod

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded wrapper v0.0.1 (for clinod v1.3)
author peterjc
date Tue, 02 Aug 2011 06:51:52 -0400
parents
children 221d7dca03a5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.1">
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
3 <command>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
4 java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
5 ##I want the number of threads to be a Galaxy config option...
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
6 ##TODO - Make the -clean_sequece argument a parameter?
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
7 </command>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
8 <inputs>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
9 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
10 </inputs>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
11 <outputs>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
12 <data name="tabular_file" format="tabular" label="NoD results" />
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
13 </outputs>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
14 <requirements>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
15 <requirement type="binary">java</requirement>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
16 </requirements>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
17 <help>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
18
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
19 **What it does**
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
20
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
21 This calls the command line version of the NoD tool from the Barton Group for
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
22 prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
23 artificial neural network trained on a set of human NoLSs.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
24
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
25 The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
26 as a special nuclear localization sequence (NLS).
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
27
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
28 The input is a FASTA file of protein sequences, and the output is tabular with
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
29 four columns (multiple rows per protein):
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
30
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
31 * Sequence identifier
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
32 * Start of NoLS
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
33 * End of NoLS
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
34 * NoLS sequence
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
35
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
36 If a sequence has no predicted NoLS, then there is no line in the output file
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
37 for it.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
38
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
39 **References**
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
40
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
41 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
42 Characterization and prediction of protein nucleolar localization sequences.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
43 Nucleic Acids Research 38(21), 7388-7399, 2010.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
44 http://dx.doi.org/10.1093/nar/gkq653
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
45
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
46 M. S. Scott, P. V. Troshin and G. J. Barton.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
47 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
48 BMC Bioinformatics, in press, 2011.
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
49
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
50 http://www.compbio.dundee.ac.uk/www-nod/
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
51
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
52 </help>
b8be455c27d1 Uploaded wrapper v0.0.1 (for clinod v1.3)
peterjc
parents:
diff changeset
53 </tool>