<tool id="aragorn_trna" name="Aragon" version="0.1">
	<description>Prediction of tRNAs</description>
	<command>aragorn $input > $output</command>
	<inputs>
		<param name="input" type="data" format="fasta" label="Genome Sequence"/>
	</inputs>
	<outputs>
		<data name="output" format="tabular"/>
	</outputs>
	<tests>
		<test>
		</test>
	</tests>
	<help>

**What it does**

This tool predicts, tRNA (and tmRNA) detection in nucleotide sequences.
http://130.235.46.10/ARAGORN/
-----	

**Example**

Suppose you have the following DNA formatted sequences::

    >SQ   Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
    cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
    ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
    cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
    cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
    ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg

Running this tool will produce this::
    --snip--
    87.
    
                 c
                c
               a
             g-c
             g-c
             g-c
             c-g
             g-c
             a-t
             t-a     ca
            t   tgacc  a
     ga    a    !!!!!  g
    t  ctcg     actgg  c
    g  !!!!    c     tt
    g  gagc     t
     aa    g     g
            c-gag
            t-a
            t-a
            c-g
            g-c
           t   c
           t   a
            cac
 
 
 
    tRNA-Val(cac)
    74 bases, %GC = 58.1
    Sequence [6669703,6669776]
 



    tRNA Anticodon Frequency
    AAA Phe       GAA Phe  1    CAA Leu  1    TAA Leu  1    
    AGA Ser       GGA Ser  1    CGA Ser  2    TGA Ser  1    
    ACA Cys       GCA Cys  2    CCA Trp  2    TCA seC       
    ATA Tyr       GTA Tyr  1    CTA Pyl       TTA Stop      
    AAG Leu       GAG Leu  3    CAG Leu  1    TAG Leu  2    
    AGG Pro       GGG Pro  2    CGG Pro  2    TGG Pro  2    
    ACG Arg  1    GCG Arg  2    CCG Arg  1    TCG Arg       
    ATG His       GTG His  2    CTG Gln  2    TTG Gln  1    
    AAC Val       GAC Val  3    CAC Val  2    TAC Val  1    
    AGC Ala       GGC Ala  2    CGC Ala  3    TGC Ala  1    
    ACC Gly       GCC Gly  5    CCC Gly  1    TCC Gly  2    
    ATC Asp       GTC Asp  3    CTC Glu  2    TTC Glu  2    
    AAT Ile       GAT Ile  3    CAT Met  6    TAT Ile       
    AGT Thr       GGT Thr  2    CGT Thr  1    TGT Thr  2    
    ACT Ser       GCT Ser  1    CCT Arg  1    TCT Arg  1    
    ATT Asn       GTT Asn  3    CTT Lys  3    TTT Lys  2    
    Ambiguous: 1

    tRNA Codon Frequency
    TTT Phe       TTC Phe  1    TTG Leu  1    TTA Leu  1    
    TCT Ser       TCC Ser  1    TCG Ser  2    TCA Ser  1    
    TGT Cys       TGC Cys  2    TGG Trp  2    TGA seC       
    TAT Tyr       TAC Tyr  1    TAG Pyl       TAA Stop      
    CTT Leu       CTC Leu  3    CTG Leu  1    CTA Leu  2    
    CCT Pro       CCC Pro  2    CCG Pro  2    CCA Pro  2    
    CGT Arg  1    CGC Arg  2    CGG Arg  1    CGA Arg       
    CAT His       CAC His  2    CAG Gln  2    CAA Gln  1    
    GTT Val       GTC Val  3    GTG Val  2    GTA Val  1    
    GCT Ala       GCC Ala  2    GCG Ala  3    GCA Ala  1    
    GGT Gly       GGC Gly  5    GGG Gly  1    GGA Gly  2    
    GAT Asp       GAC Asp  3    GAG Glu  2    GAA Glu  2    
    ATT Ile       ATC Ile  3    ATG Met  6    ATA Ile       
    ACT Thr       ACC Thr  2    ACG Thr  1    ACA Thr  2    
    AGT Ser       AGC Ser  1    AGG Arg  1    AGA Arg  1    
    AAT Asn       AAC Asn  3    AAG Lys  3    AAA Lys  2    
    Ambiguous: 1

    Number of tRNA genes = 86
    tRNA GC range = 50.0% to 85.1%
    Number of tmRNA genes = 1

-------

**References**

Dean Laslett and Bjorn Canback
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
doi:10.1093/nar/gkh152 



	</help>
</tool>