--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/aragorn.xml	Wed Jan 11 05:57:32 2012 -0500
@@ -0,0 +1,124 @@
+<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>