Mercurial > repos > bgruening > trna_prediction
diff aragorn.xml @ 1:d788d1abe238 draft
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 22 Jan 2015 13:15:51 -0500 |
| parents | d34f31cbc9dd |
| children | 358f58401cd6 |
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--- a/aragorn.xml Sat Jul 06 10:37:13 2013 -0400 +++ b/aragorn.xml Thu Jan 22 13:15:51 2015 -0500 @@ -1,11 +1,13 @@ -<tool id="aragorn_trna" name="tRNA and tmRNA" version="0.3"> - <description>prediction (Aragon)</description> +<tool id="aragorn_trna" name="tRNA and tmRNA" version="0.4"> + <description>prediction (Aragorn)</description> <requirements> <requirement type="package" version="1.2.36">aragorn</requirement> + <requirement type="set_environment">TRNAPRED_SCRIPT_PATH</requirement> </requirements> <command> - aragorn - $input +<![CDATA[ + aragorn + $input -gc$genbank_gencode $tmRNA $tRNA @@ -14,7 +16,21 @@ $topology -o $output $secondary_structure - $introns + $introns; + +#if $gff3_output: + aragorn + $input + -gc$genbank_gencode + $tmRNA + $tRNA + $mtRNA + $mam_mtRNA + $topology + -fasta + $introns | python \$TRNAPRED_SCRIPT_PATH/aragorn_out_to_gff3.py > $gff3_output_file; +#end if +]]> </command> <inputs> <param name="input" type="data" format="fasta" label="Genome Sequence"/> @@ -48,6 +64,7 @@ <param name='mam_mtRNA' type='boolean' label='Search for Mammalian mitochondrial tRNA genes (-mtmam)' truevalue='-mtmam' falsevalue='' checked="false" help='-i switch ignored. -tv switch set. Mammalian mitochondrial genetic code used.' /> <param name='introns' type='boolean' label='Search for tRNA genes with introns in anticodon loop ...' truevalue='-i' falsevalue='' checked="false" help='...with maximum length 3000 bases (-i).' /> <param name='secondary_structure' type='boolean' label='Print out secondary structure (-fasta,-fon)' truevalue='-fasta' falsevalue='-fon' checked="false" help='' /> + <param name="gff3_output" type='boolean' label='Convert output to GFF3' truevalue='True' falsevalue='' checked="false" help='' /> </inputs> <outputs> <data name="output" format="fasta"> @@ -55,6 +72,9 @@ <when input="secondary_structure" value="true" format="text"/> </change_format> </data> + <data format="gff3" name="gff3_output_file" > + <filter>gff3_output</filter> + </data> </outputs> <tests> <test> @@ -65,12 +85,15 @@ <param name="tRNA" value="-t" /> <param name="mtRNA" value="" /> <param name="mam_mtRNA" value="" /> - <param name="introns" value="" /> + <param name="introns" value="" /> <param name="secondary_structure" value="-fon" /> + <param name="gff3_output" value="True" /> <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.fasta" ftype="fasta" /> + <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.gff3" ftype="gff3" /> </test> </tests> <help> +<![CDATA[ **What it does** @@ -125,41 +148,41 @@ 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 + 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 + 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 @@ -174,7 +197,8 @@ 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 +doi:10.1093/nar/gkh152 +]]> </help> </tool>