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comparison tools/protein_analysis/clinod.xml @ 1:221d7dca03a5 draft

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Uploaded v0.0.4, which adds a unit test
author peterjc
date Tue, 16 Apr 2013 13:01:54 -0400
parents b8be455c27d1
children
comparison
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0:b8be455c27d1 1:221d7dca03a5
1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.1"> 1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.4">
2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> 2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
3 <command> 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 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... 5 ##I want the number of threads to be a Galaxy config option...
6 ##TODO - Make the -clean_sequece argument a parameter? 6 ##TODO - Make the -clean_sequence argument a parameter?
7 </command> 7 </command>
8 <stdio>
9 <!-- Assume anything other than zero is an error -->
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 </stdio>
8 <inputs> 13 <inputs>
9 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 14 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
10 </inputs> 15 </inputs>
11 <outputs> 16 <outputs>
12 <data name="tabular_file" format="tabular" label="NoD results" /> 17 <data name="tabular_file" format="tabular" label="NoD results" />
13 </outputs> 18 </outputs>
14 <requirements> 19 <requirements>
15 <requirement type="binary">java</requirement> 20 <requirement type="binary">java</requirement>
16 </requirements> 21 </requirements>
22 <tests>
23 <test>
24 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
25 <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
26 </test>
27 </tests>
17 <help> 28 <help>
18 29
19 **What it does** 30 **What it does**
20 31
21 This calls the command line version of the NoD tool from the Barton Group for 32 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 33 prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an
23 artificial neural network trained on a set of human NoLSs. 34 artificial neural network trained on a set of human NoLSs.
26 as a special nuclear localization sequence (NLS). 37 as a special nuclear localization sequence (NLS).
27 38
28 The input is a FASTA file of protein sequences, and the output is tabular with 39 The input is a FASTA file of protein sequences, and the output is tabular with
29 four columns (multiple rows per protein): 40 four columns (multiple rows per protein):
30 41
31 * Sequence identifier 42 ====== ===================
32 * Start of NoLS 43 Column Description
33 * End of NoLS 44 ------ -------------------
34 * NoLS sequence 45 1 Sequence identifier
46 2 Start of NoLS
47 3 End of NoLS
48 4 NoLS sequence
49 ====== ===================
35 50
36 If a sequence has no predicted NoLS, then there is no line in the output file 51 If a sequence has no predicted NoLS, then there is no line in the output file
37 for it. 52 for it.
53
38 54
39 **References** 55 **References**
40 56
41 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton. 57 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. 58 Characterization and prediction of protein nucleolar localization sequences.
43 Nucleic Acids Research 38(21), 7388-7399, 2010. 59 Nucleic Acids Research 38(21), 7388-7399, 2010.
44 http://dx.doi.org/10.1093/nar/gkq653 60 http://dx.doi.org/10.1093/nar/gkq653
45 61
46 M. S. Scott, P. V. Troshin and G. J. Barton. 62 M. S. Scott, P. V. Troshin and G. J. Barton.
47 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. 63 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
48 BMC Bioinformatics, in press, 2011. 64 BMC Bioinformatics, 12:317, 2011.
65 http://dx.doi.org/10.1186/1471-2105-12-317
49 66
50 http://www.compbio.dundee.ac.uk/www-nod/ 67 http://www.compbio.dundee.ac.uk/www-nod/
51 68
52 </help> 69 </help>
53 </tool> 70 </tool>