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annotate aragorn.xml @ 35:fa736576c7ed draft

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