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comparison aragorn.xml @ 35:fa736576c7ed draft
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| author | jjkoehorst |
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| date | Mon, 04 Jul 2016 10:37:59 -0400 |
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| 34:f2cbf1230026 | 35:fa736576c7ed |
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| 1 <tool id="DAragorn" name="tRNA and tmRNA prediction" version="0.3"> | |
| 2 <description>SAPP - Aragorn tRNA and tmRNA prediction</description> | |
| 3 <requirements> | |
| 4 <container type="docker">jjkoehorst/sappdocker:ARAGORN</container> | |
| 5 </requirements> | |
| 6 <command interpreter="docker">java -jar /aragorn/aragorn-0.0.1-SNAPSHOT-jar-with-dependencies.jar | |
| 7 '-input' '$input' '-output' '$output' '-gc' $genbank_gencode | |
| 8 '$tmRNA' '$tRNA' '$topology' -format TURTLE | |
| 9 </command> | |
| 10 <inputs> | |
| 11 <param format="ttl" label="RDF Genome" name="input" type="data"/> | |
| 12 <param label="Genetic code" name="genbank_gencode" type="select"> | |
| 13 <option select="True" value="1">1. Standard</option> | |
| 14 <option value="2">2. Vertebrate Mitochondrial</option> | |
| 15 <option value="3">3. Yeast Mitochondrial</option> | |
| 16 <option value="4">4. Mold, Protozoan, and Coelenterate | |
| 17 Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
| 18 <option value="5">5. Invertebrate Mitochondrial</option> | |
| 19 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear | |
| 20 Code</option> | |
| 21 <option value="9">9. Echinoderm Mitochondrial</option> | |
| 22 <option value="10">10. Euplotid Nuclear</option> | |
| 23 <option value="11">11. Bacteria and Archaea</option> | |
| 24 <option value="12">12. Alternative Yeast Nuclear</option> | |
| 25 <option value="13">13. Ascidian Mitochondrial</option> | |
| 26 <option value="14">14. Flatworm Mitochondrial</option> | |
| 27 <option value="15">15. Blepharisma Macronuclear</option> | |
| 28 <option value="16">16. Chlorophycean Mitochondrial</option> | |
| 29 <option value="21">21. Trematode Mitochondrial</option> | |
| 30 <option value="22">22. Scenedesmus obliquus mitochondrial</option> | |
| 31 <option value="23">23. Thraustochytrium Mitochondrial</option> | |
| 32 <option value="24">24. Pterobranchia mitochondrial</option> | |
| 33 </param> | |
| 34 <param label="Topology" name="topology" type="select"> | |
| 35 <option value="-c">Assume that each sequence has a circular | |
| 36 topology</option> | |
| 37 <option value="-l">Assume that each sequence has a linear topology | |
| 38 </option> | |
| 39 </param> | |
| 40 <param checked="true" falsevalue="" help="" label="Search for tmRNA genes (-m)" name="tmRNA" truevalue="-m" type="boolean"/> | |
| 41 <param checked="true" falsevalue="" help="" label="Search for tRNA genes (-t)" name="tRNA" truevalue="-t" type="boolean"/> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data format="ttl" label="Aragorn: ${input.name}" name="output"/> | |
| 45 </outputs> | |
| 46 <citations> | |
| 47 <citation type="bibtex">@article{Laslett2004, | |
| 48 abstract = {A computer program, ARAGORN, identifies tRNA and tmRNA genes. The | |
| 49 program employs heuristic algorithms to predict tRNA secondary | |
| 50 structure, based on homology with recognized tRNA consensus sequences | |
| 51 and ability to form a base-paired cloverleaf. tmRNA genes are | |
| 52 identified using a modified version of the BRUCE program. ARAGORN | |
| 53 achieves a detection sensitivity of 99\% from a set of 1290 | |
| 54 eubacterial, eukaryotic and archaeal tRNA genes and detects all | |
| 55 complete tmRNA sequences in the tmRNA database, improving on the | |
| 56 performance of the BRUCE program. Recently discovered tmRNA genes in | |
| 57 the chloroplasts of two species from the 'green' algae lineage are | |
| 58 detected. The output of the program reports the proposed tRNA | |
| 59 secondary structure and, for tmRNA genes, the secondary structure of | |
| 60 the tRNA domain, the tmRNA gene sequence, the tag peptide and a list | |
| 61 of organisms with matching tmRNA peptide tags.}, | |
| 62 author = {Laslett, Dean and Canback, Bjorn}, | |
| 63 doi = {10.1093/nar/gkh152}, | |
| 64 file = {:Users/koeho006/Library/Application Support/Mendeley | |
| 65 Desktop/Downloaded/Laslett, Canback - 2004 - ARAGORN, a program to | |
| 66 detect tRNA genes and tmRNA genes in nucleotide sequences.pdf:pdf}, | |
| 67 isbn = {1362-4962 (Electronic)$\backslash$n1362-4962 (Linking)}, | |
| 68 issn = {03051048}, | |
| 69 journal = {Nucleic Acids Research}, | |
| 70 mendeley-groups = {VAPP Application note}, | |
| 71 pages = {11--16}, | |
| 72 pmid = {14704338}, | |
| 73 title = {{ARAGORN, a program to detect tRNA genes and tmRNA genes in | |
| 74 nucleotide sequences}}, | |
| 75 volume = {32}, | |
| 76 year = {2004} | |
| 77 } | |
| 78 </citation> | |
| 79 </citations> | |
| 80 </tool> |