annotate genetic_elements/aragorn/aragorn.xml @ 24:9610ddbca991

.
author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 19:25:28 +0100
parents 27a2341f86cc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
1 <tool id="SAPP_aragorn_trna" name="tRNA and tmRNA" version="0.3">
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
2 <requirements>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
3 <requirement type='package' version="3.4">python</requirement>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
4 <requirement type='package' version="1.0">rdflib</requirement>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
5 <requirement type="package" version="1.2.36">aragorn</requirement>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
6 </requirements>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
7 <description>Aragon</description>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
8 <command interpreter="python3.4">aragorn.py '$input' '$output' '-gc$genbank_gencode' '$tmRNA' '$tRNA' '$topology' '-fon' '-sourcedb' 'SAPP'
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
9 </command>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
10 <inputs>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
11 <param name="input" type="data" format="rdf" label="RDF Genome"/>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
12
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
13 <param name="genbank_gencode" type="select" label="Genetic code">
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
14 <option value="1" select="True">1. Standard</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
15 <option value="2">2. Vertebrate Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
16 <option value="3">3. Yeast Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
17 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
18 <option value="5">5. Invertebrate Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
19 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
20 <option value="9">9. Echinoderm Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
21 <option value="10">10. Euplotid Nuclear</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
22 <option value="11">11. Bacteria and Archaea</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
23 <option value="12">12. Alternative Yeast Nuclear</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
24 <option value="13">13. Ascidian Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
25 <option value="14">14. Flatworm Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
26 <option value="15">15. Blepharisma Macronuclear</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
27 <option value="16">16. Chlorophycean Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
28 <option value="21">21. Trematode Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
29 <option value="22">22. Scenedesmus obliquus mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
30 <option value="23">23. Thraustochytrium Mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
31 <option value="24">24. Pterobranchia mitochondrial</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
32 </param>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
33 <param name="topology" type="select" label="Topology">
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
34 <option value="-c">Assume that each sequence has a circular topology</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
35 <option value="-l">Assume that each sequence has a linear topology</option>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
36 </param>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
37 <param name='tmRNA' type='boolean' label='Search for tmRNA genes (-m)' truevalue='-m' falsevalue='' checked="true" help='' />
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
38 <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' />
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
39 </inputs>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
40 <outputs>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
41 <data format="rdf" name="output" label="Aragorn: ${input.name}"></data>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
42 </outputs>
18
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
43 <tests>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
44 <test>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
45 <param name="input" value="test-data/NC_017117.fna"/>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
46 <output name="$output" file="NC_017117.rdf"/>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
47 <output name="$genbank_gencode" value="11"/>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
48 <output name="$tmRNA" value="-m"/>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
49 <output name="$tRNA" value="-t"/>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
50 <output name="$topology" value="-c"/>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
51 </test>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
52 </tests>
27a2341f86cc aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents: 17
diff changeset
53
17
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
54 <help>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
55
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
56 **What it does**
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
57
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
58 Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences.
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
59
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
60 .. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
61
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
62 -----
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
63
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
64 It requires an RDF genome file
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
65
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
66 </help>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
67 <citations>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
68 <citation type="bibtex">
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
69 @article{Laslett2004,
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
70 abstract = {A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99\% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
71 author = {Laslett, Dean and Canback, Bjorn},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
72 doi = {10.1093/nar/gkh152},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
73 file = {:Users/koeho006/Library/Application Support/Mendeley Desktop/Downloaded/Laslett, Canback - 2004 - ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.pdf:pdf},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
74 isbn = {1362-4962 (Electronic)$\backslash$n1362-4962 (Linking)},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
75 issn = {03051048},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
76 journal = {Nucleic Acids Research},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
77 mendeley-groups = {VAPP Application note},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
78 pages = {11--16},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
79 pmid = {14704338},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
80 title = {{ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences}},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
81 volume = {32},
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
82 year = {2004}
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
83 }
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
84 </citation>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
85 </citations>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
86
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
87 </tool>
2561c51e6605 aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
88