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comparison aragorn.xml @ 1:d788d1abe238 draft

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author bgruening
date Thu, 22 Jan 2015 13:15:51 -0500
parents d34f31cbc9dd
children 358f58401cd6
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0:d34f31cbc9dd 1:d788d1abe238
1 <tool id="aragorn_trna" name="tRNA and tmRNA" version="0.3"> 1 <tool id="aragorn_trna" name="tRNA and tmRNA" version="0.4">
2 <description>prediction (Aragon)</description> 2 <description>prediction (Aragorn)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.36">aragorn</requirement> 4 <requirement type="package" version="1.2.36">aragorn</requirement>
5 <requirement type="set_environment">TRNAPRED_SCRIPT_PATH</requirement>
5 </requirements> 6 </requirements>
6 <command> 7 <command>
7 aragorn 8 <![CDATA[
8 $input 9 aragorn
10 $input
9 -gc$genbank_gencode 11 -gc$genbank_gencode
10 $tmRNA 12 $tmRNA
11 $tRNA 13 $tRNA
12 $mtRNA 14 $mtRNA
13 $mam_mtRNA 15 $mam_mtRNA
14 $topology 16 $topology
15 -o $output 17 -o $output
16 $secondary_structure 18 $secondary_structure
17 $introns 19 $introns;
20
21 #if $gff3_output:
22 aragorn
23 $input
24 -gc$genbank_gencode
25 $tmRNA
26 $tRNA
27 $mtRNA
28 $mam_mtRNA
29 $topology
30 -fasta
31 $introns | python \$TRNAPRED_SCRIPT_PATH/aragorn_out_to_gff3.py > $gff3_output_file;
32 #end if
33 ]]>
18 </command> 34 </command>
19 <inputs> 35 <inputs>
20 <param name="input" type="data" format="fasta" label="Genome Sequence"/> 36 <param name="input" type="data" format="fasta" label="Genome Sequence"/>
21 <param name="genbank_gencode" type="select" label="Genetic code"> 37 <param name="genbank_gencode" type="select" label="Genetic code">
22 <option value="1" select="True">1. Standard</option> 38 <option value="1" select="True">1. Standard</option>
46 <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' /> 62 <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' />
47 <param name='mtRNA' type='boolean' label='Search for Metazoan mitochondrial tRNA genes (-mt)' truevalue='-mt' falsevalue='' checked="false" help='-i switch ignored. Composite Metazoan mitochondrial genetic code used.' /> 63 <param name='mtRNA' type='boolean' label='Search for Metazoan mitochondrial tRNA genes (-mt)' truevalue='-mt' falsevalue='' checked="false" help='-i switch ignored. Composite Metazoan mitochondrial genetic code used.' />
48 <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.' /> 64 <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.' />
49 <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).' /> 65 <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).' />
50 <param name='secondary_structure' type='boolean' label='Print out secondary structure (-fasta,-fon)' truevalue='-fasta' falsevalue='-fon' checked="false" help='' /> 66 <param name='secondary_structure' type='boolean' label='Print out secondary structure (-fasta,-fon)' truevalue='-fasta' falsevalue='-fon' checked="false" help='' />
67 <param name="gff3_output" type='boolean' label='Convert output to GFF3' truevalue='True' falsevalue='' checked="false" help='' />
51 </inputs> 68 </inputs>
52 <outputs> 69 <outputs>
53 <data name="output" format="fasta"> 70 <data name="output" format="fasta">
54 <change_format> 71 <change_format>
55 <when input="secondary_structure" value="true" format="text"/> 72 <when input="secondary_structure" value="true" format="text"/>
56 </change_format> 73 </change_format>
74 </data>
75 <data format="gff3" name="gff3_output_file" >
76 <filter>gff3_output</filter>
57 </data> 77 </data>
58 </outputs> 78 </outputs>
59 <tests> 79 <tests>
60 <test> 80 <test>
61 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" /> 81 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
63 <param name="topology" value="-c" /> 83 <param name="topology" value="-c" />
64 <param name="tmRNA" value="-m" /> 84 <param name="tmRNA" value="-m" />
65 <param name="tRNA" value="-t" /> 85 <param name="tRNA" value="-t" />
66 <param name="mtRNA" value="" /> 86 <param name="mtRNA" value="" />
67 <param name="mam_mtRNA" value="" /> 87 <param name="mam_mtRNA" value="" />
68 <param name="introns" value="" /> 88 <param name="introns" value="" />
69 <param name="secondary_structure" value="-fon" /> 89 <param name="secondary_structure" value="-fon" />
90 <param name="gff3_output" value="True" />
70 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.fasta" ftype="fasta" /> 91 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.fasta" ftype="fasta" />
92 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.gff3" ftype="gff3" />
71 </test> 93 </test>
72 </tests> 94 </tests>
73 <help> 95 <help>
96 <![CDATA[
74 97
75 **What it does** 98 **What it does**
76 99
77 Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences. 100 Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences.
78 101
123 74 bases, %GC = 58.1 146 74 bases, %GC = 58.1
124 Sequence [6669703,6669776] 147 Sequence [6669703,6669776]
125 148
126 149
127 tRNA Anticodon Frequency 150 tRNA Anticodon Frequency
128 AAA Phe GAA Phe 1 CAA Leu 1 TAA Leu 1 151 AAA Phe GAA Phe 1 CAA Leu 1 TAA Leu 1
129 AGA Ser GGA Ser 1 CGA Ser 2 TGA Ser 1 152 AGA Ser GGA Ser 1 CGA Ser 2 TGA Ser 1
130 ACA Cys GCA Cys 2 CCA Trp 2 TCA seC 153 ACA Cys GCA Cys 2 CCA Trp 2 TCA seC
131 ATA Tyr GTA Tyr 1 CTA Pyl TTA Stop 154 ATA Tyr GTA Tyr 1 CTA Pyl TTA Stop
132 AAG Leu GAG Leu 3 CAG Leu 1 TAG Leu 2 155 AAG Leu GAG Leu 3 CAG Leu 1 TAG Leu 2
133 AGG Pro GGG Pro 2 CGG Pro 2 TGG Pro 2 156 AGG Pro GGG Pro 2 CGG Pro 2 TGG Pro 2
134 ACG Arg 1 GCG Arg 2 CCG Arg 1 TCG Arg 157 ACG Arg 1 GCG Arg 2 CCG Arg 1 TCG Arg
135 ATG His GTG His 2 CTG Gln 2 TTG Gln 1 158 ATG His GTG His 2 CTG Gln 2 TTG Gln 1
136 AAC Val GAC Val 3 CAC Val 2 TAC Val 1 159 AAC Val GAC Val 3 CAC Val 2 TAC Val 1
137 AGC Ala GGC Ala 2 CGC Ala 3 TGC Ala 1 160 AGC Ala GGC Ala 2 CGC Ala 3 TGC Ala 1
138 ACC Gly GCC Gly 5 CCC Gly 1 TCC Gly 2 161 ACC Gly GCC Gly 5 CCC Gly 1 TCC Gly 2
139 ATC Asp GTC Asp 3 CTC Glu 2 TTC Glu 2 162 ATC Asp GTC Asp 3 CTC Glu 2 TTC Glu 2
140 AAT Ile GAT Ile 3 CAT Met 6 TAT Ile 163 AAT Ile GAT Ile 3 CAT Met 6 TAT Ile
141 AGT Thr GGT Thr 2 CGT Thr 1 TGT Thr 2 164 AGT Thr GGT Thr 2 CGT Thr 1 TGT Thr 2
142 ACT Ser GCT Ser 1 CCT Arg 1 TCT Arg 1 165 ACT Ser GCT Ser 1 CCT Arg 1 TCT Arg 1
143 ATT Asn GTT Asn 3 CTT Lys 3 TTT Lys 2 166 ATT Asn GTT Asn 3 CTT Lys 3 TTT Lys 2
144 Ambiguous: 1 167 Ambiguous: 1
145 168
146 tRNA Codon Frequency 169 tRNA Codon Frequency
147 TTT Phe TTC Phe 1 TTG Leu 1 TTA Leu 1 170 TTT Phe TTC Phe 1 TTG Leu 1 TTA Leu 1
148 TCT Ser TCC Ser 1 TCG Ser 2 TCA Ser 1 171 TCT Ser TCC Ser 1 TCG Ser 2 TCA Ser 1
149 TGT Cys TGC Cys 2 TGG Trp 2 TGA seC 172 TGT Cys TGC Cys 2 TGG Trp 2 TGA seC
150 TAT Tyr TAC Tyr 1 TAG Pyl TAA Stop 173 TAT Tyr TAC Tyr 1 TAG Pyl TAA Stop
151 CTT Leu CTC Leu 3 CTG Leu 1 CTA Leu 2 174 CTT Leu CTC Leu 3 CTG Leu 1 CTA Leu 2
152 CCT Pro CCC Pro 2 CCG Pro 2 CCA Pro 2 175 CCT Pro CCC Pro 2 CCG Pro 2 CCA Pro 2
153 CGT Arg 1 CGC Arg 2 CGG Arg 1 CGA Arg 176 CGT Arg 1 CGC Arg 2 CGG Arg 1 CGA Arg
154 CAT His CAC His 2 CAG Gln 2 CAA Gln 1 177 CAT His CAC His 2 CAG Gln 2 CAA Gln 1
155 GTT Val GTC Val 3 GTG Val 2 GTA Val 1 178 GTT Val GTC Val 3 GTG Val 2 GTA Val 1
156 GCT Ala GCC Ala 2 GCG Ala 3 GCA Ala 1 179 GCT Ala GCC Ala 2 GCG Ala 3 GCA Ala 1
157 GGT Gly GGC Gly 5 GGG Gly 1 GGA Gly 2 180 GGT Gly GGC Gly 5 GGG Gly 1 GGA Gly 2
158 GAT Asp GAC Asp 3 GAG Glu 2 GAA Glu 2 181 GAT Asp GAC Asp 3 GAG Glu 2 GAA Glu 2
159 ATT Ile ATC Ile 3 ATG Met 6 ATA Ile 182 ATT Ile ATC Ile 3 ATG Met 6 ATA Ile
160 ACT Thr ACC Thr 2 ACG Thr 1 ACA Thr 2 183 ACT Thr ACC Thr 2 ACG Thr 1 ACA Thr 2
161 AGT Ser AGC Ser 1 AGG Arg 1 AGA Arg 1 184 AGT Ser AGC Ser 1 AGG Arg 1 AGA Arg 1
162 AAT Asn AAC Asn 3 AAG Lys 3 AAA Lys 2 185 AAT Asn AAC Asn 3 AAG Lys 3 AAA Lys 2
163 Ambiguous: 1 186 Ambiguous: 1
164 187
165 Number of tRNA genes = 86 188 Number of tRNA genes = 86
166 tRNA GC range = 50.0% to 85.1% 189 tRNA GC range = 50.0% to 85.1%
167 Number of tmRNA genes = 1 190 Number of tmRNA genes = 1
172 195
173 Dean Laslett and Bjorn Canback 196 Dean Laslett and Bjorn Canback
174 197
175 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16 198 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
176 199
177 doi:10.1093/nar/gkh152 200 doi:10.1093/nar/gkh152
178 201
202 ]]>
179 </help> 203 </help>
180 </tool> 204 </tool>