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1 <tool id="aragorn_trna" name="tRNA and tmRNA" version="0.4">
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2 <description>prediction (Aragorn)</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.36">aragorn</requirement>
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5 <requirement type="set_environment">TRNAPRED_SCRIPT_PATH</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 aragorn
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10 $input
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11 -gc$genbank_gencode
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12 $tmRNA
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13 $tRNA
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14 $mtRNA
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15 $mam_mtRNA
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16 $topology
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17 -o $output
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18 $secondary_structure
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19 $introns;
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20
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21 #if $gff3_output:
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22 aragorn
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23 $input
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24 -gc$genbank_gencode
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25 $tmRNA
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26 $tRNA
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27 $mtRNA
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28 $mam_mtRNA
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29 $topology
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30 -fasta
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31 $introns | python \$TRNAPRED_SCRIPT_PATH/aragorn_out_to_gff3.py > $gff3_output_file;
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32 #end if
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param name="input" type="data" format="fasta" label="Genome Sequence"/>
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37 <param name="genbank_gencode" type="select" label="Genetic code">
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38 <option value="1" select="True">1. Standard</option>
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39 <option value="2">2. Vertebrate Mitochondrial</option>
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40 <option value="3">3. Yeast Mitochondrial</option>
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41 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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42 <option value="5">5. Invertebrate Mitochondrial</option>
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43 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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44 <option value="9">9. Echinoderm Mitochondrial</option>
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45 <option value="10">10. Euplotid Nuclear</option>
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46 <option value="11">11. Bacteria and Archaea</option>
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47 <option value="12">12. Alternative Yeast Nuclear</option>
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48 <option value="13">13. Ascidian Mitochondrial</option>
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49 <option value="14">14. Flatworm Mitochondrial</option>
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50 <option value="15">15. Blepharisma Macronuclear</option>
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51 <option value="16">16. Chlorophycean Mitochondrial</option>
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52 <option value="21">21. Trematode Mitochondrial</option>
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53 <option value="22">22. Scenedesmus obliquus mitochondrial</option>
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54 <option value="23">23. Thraustochytrium Mitochondrial</option>
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55 <option value="24">24. Pterobranchia mitochondrial</option>
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56 </param>
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57 <param name="topology" type="select" label="Topology">
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58 <option value="-c">Assume that each sequence has a circular topology</option>
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59 <option value="-l">Assume that each sequence has a linear topology</option>
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60 </param>
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61 <param name='tmRNA' type='boolean' label='Search for tmRNA genes (-m)' truevalue='-m' falsevalue='' checked="true" help='' />
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62 <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' />
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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.' />
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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.' />
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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).' />
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66 <param name='secondary_structure' type='boolean' label='Print out secondary structure (-fasta,-fon)' truevalue='-fasta' falsevalue='-fon' checked="false" help='' />
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67 <param name="gff3_output" type='boolean' label='Convert output to GFF3' truevalue='True' falsevalue='' checked="false" help='' />
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68 </inputs>
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69 <outputs>
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70 <data name="output" format="fasta">
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71 <change_format>
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72 <when input="secondary_structure" value="true" format="text"/>
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73 </change_format>
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74 </data>
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75 <data format="gff3" name="gff3_output_file" >
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76 <filter>gff3_output</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
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82 <param name="genbank_gencode" value="1" />
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83 <param name="topology" value="-c" />
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84 <param name="tmRNA" value="-m" />
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85 <param name="tRNA" value="-t" />
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86 <param name="mtRNA" value="" />
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87 <param name="mam_mtRNA" value="" />
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88 <param name="introns" value="" />
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89 <param name="secondary_structure" value="-fon" />
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90 <param name="gff3_output" value="True" />
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91 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.fasta" ftype="fasta" />
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92 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.gff3" ftype="gff3" />
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93 </test>
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94 </tests>
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95 <help>
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96 <![CDATA[
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97
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98 **What it does**
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99
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100 Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences.
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101
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102 .. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
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103
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104 -----
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105
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106 **Example**
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107
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108 Suppose you have the following nucleotide sequences::
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109
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110 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
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111 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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112 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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113 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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114 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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115 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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116 ....
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117
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118 Running this tool can produce a FASTA file with all detected RNAs or a more detailed text file like the following::
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119
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120 c
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121 c
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122 a
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123 g-c
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124 g-c
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125 g-c
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126 c-g
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127 g-c
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128 a-t
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129 t-a ca
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130 t tgacc a
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131 ga a !!!!! g
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132 t ctcg actgg c
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133 g !!!! c tt
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134 g gagc t
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135 aa g g
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136 c-gag
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137 t-a
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138 t-a
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139 c-g
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140 g-c
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141 t c
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142 t a
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143 cac
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144
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145 tRNA-Val(cac)
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146 74 bases, %GC = 58.1
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147 Sequence [6669703,6669776]
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148
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149
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150 tRNA Anticodon Frequency
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1
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151 AAA Phe GAA Phe 1 CAA Leu 1 TAA Leu 1
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152 AGA Ser GGA Ser 1 CGA Ser 2 TGA Ser 1
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153 ACA Cys GCA Cys 2 CCA Trp 2 TCA seC
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154 ATA Tyr GTA Tyr 1 CTA Pyl TTA Stop
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155 AAG Leu GAG Leu 3 CAG Leu 1 TAG Leu 2
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156 AGG Pro GGG Pro 2 CGG Pro 2 TGG Pro 2
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157 ACG Arg 1 GCG Arg 2 CCG Arg 1 TCG Arg
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158 ATG His GTG His 2 CTG Gln 2 TTG Gln 1
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159 AAC Val GAC Val 3 CAC Val 2 TAC Val 1
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160 AGC Ala GGC Ala 2 CGC Ala 3 TGC Ala 1
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161 ACC Gly GCC Gly 5 CCC Gly 1 TCC Gly 2
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162 ATC Asp GTC Asp 3 CTC Glu 2 TTC Glu 2
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163 AAT Ile GAT Ile 3 CAT Met 6 TAT Ile
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164 AGT Thr GGT Thr 2 CGT Thr 1 TGT Thr 2
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165 ACT Ser GCT Ser 1 CCT Arg 1 TCT Arg 1
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166 ATT Asn GTT Asn 3 CTT Lys 3 TTT Lys 2
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0
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167 Ambiguous: 1
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168
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169 tRNA Codon Frequency
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170 TTT Phe TTC Phe 1 TTG Leu 1 TTA Leu 1
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171 TCT Ser TCC Ser 1 TCG Ser 2 TCA Ser 1
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172 TGT Cys TGC Cys 2 TGG Trp 2 TGA seC
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173 TAT Tyr TAC Tyr 1 TAG Pyl TAA Stop
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174 CTT Leu CTC Leu 3 CTG Leu 1 CTA Leu 2
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175 CCT Pro CCC Pro 2 CCG Pro 2 CCA Pro 2
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176 CGT Arg 1 CGC Arg 2 CGG Arg 1 CGA Arg
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177 CAT His CAC His 2 CAG Gln 2 CAA Gln 1
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178 GTT Val GTC Val 3 GTG Val 2 GTA Val 1
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179 GCT Ala GCC Ala 2 GCG Ala 3 GCA Ala 1
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180 GGT Gly GGC Gly 5 GGG Gly 1 GGA Gly 2
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181 GAT Asp GAC Asp 3 GAG Glu 2 GAA Glu 2
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182 ATT Ile ATC Ile 3 ATG Met 6 ATA Ile
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183 ACT Thr ACC Thr 2 ACG Thr 1 ACA Thr 2
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184 AGT Ser AGC Ser 1 AGG Arg 1 AGA Arg 1
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185 AAT Asn AAC Asn 3 AAG Lys 3 AAA Lys 2
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186 Ambiguous: 1
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187
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188 Number of tRNA genes = 86
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189 tRNA GC range = 50.0% to 85.1%
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190 Number of tmRNA genes = 1
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191
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192 -------
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193
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194 **References**
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195
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196 Dean Laslett and Bjorn Canback
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197
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198 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
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199
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200 doi:10.1093/nar/gkh152
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201
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202 ]]>
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203 </help>
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204 </tool>
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