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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
author bgruening
date Wed, 26 Jul 2017 10:14:05 -0400
parents d788d1abe238
children
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1:d788d1abe238 2:358f58401cd6
1 <tool id="aragorn_trna" name="tRNA and tmRNA" version="0.4"> 1 <tool id="aragorn_trna" name="tRNA and tmRNA" version="0.6">
2 <description>prediction (Aragorn)</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 <requirement type="package" version="2.7">python</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command><![CDATA[
8 <![CDATA[ 8 #if not $gff3_output:
9 aragorn 9 aragorn
10 $input 10 '$input'
11 -gc$genbank_gencode 11 -gc$genbank_gencode
12 $tmRNA 12 $tmRNA
13 $tRNA 13 $tRNA
14 $mtRNA 14 $mtRNA
15 $mam_mtRNA 15 $mam_mtRNA
16 $topology 16 $topology
17 -o $output 17 -o '$output'
18 $secondary_structure 18 $secondary_structure
19 $introns; 19 $introns
20 20 #end if
21 #if $gff3_output: 21
22 aragorn 22 #if $gff3_output:
23 $input 23 aragorn
24 -gc$genbank_gencode 24 '$input'
25 $tmRNA 25 -gc$genbank_gencode
26 $tRNA 26 $tmRNA
27 $mtRNA 27 $tRNA
28 $mam_mtRNA 28 $mtRNA
29 $topology 29 $mam_mtRNA
30 -fasta 30 $topology
31 $introns | python \$TRNAPRED_SCRIPT_PATH/aragorn_out_to_gff3.py > $gff3_output_file; 31 $introns
32 #end if 32 -w
33 ]]> 33 | python '$__tool_directory__/aragorn_out_to_gff3.py' $gff3_model > '$gff3_output_file'
34 #end if
35 ]]>
34 </command> 36 </command>
35 <inputs> 37 <inputs>
36 <param name="input" type="data" format="fasta" label="Genome Sequence"/> 38 <param name="input" type="data" format="fasta" label="Genome Sequence"/>
37 <param name="genbank_gencode" type="select" label="Genetic code"> 39 <param name="genbank_gencode" type="select" label="Genetic code">
38 <option value="1" select="True">1. Standard</option> 40 <option value="1" selected="true">1. Standard</option>
39 <option value="2">2. Vertebrate Mitochondrial</option> 41 <option value="2">2. Vertebrate Mitochondrial</option>
40 <option value="3">3. Yeast Mitochondrial</option> 42 <option value="3">3. Yeast Mitochondrial</option>
41 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> 43 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
42 <option value="5">5. Invertebrate Mitochondrial</option> 44 <option value="5">5. Invertebrate Mitochondrial</option>
43 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> 45 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
56 </param> 58 </param>
57 <param name="topology" type="select" label="Topology"> 59 <param name="topology" type="select" label="Topology">
58 <option value="-c">Assume that each sequence has a circular topology</option> 60 <option value="-c">Assume that each sequence has a circular topology</option>
59 <option value="-l">Assume that each sequence has a linear topology</option> 61 <option value="-l">Assume that each sequence has a linear topology</option>
60 </param> 62 </param>
61 <param name='tmRNA' type='boolean' label='Search for tmRNA genes (-m)' truevalue='-m' falsevalue='' checked="true" help='' /> 63 <param name='tmRNA' type='boolean' label='Search for tmRNA genes'
62 <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' /> 64 truevalue='-m' falsevalue='' checked="true" help='(-m)' />
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.' /> 65 <param name='tRNA' type='boolean' label='Search for tRNA genes'
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.' /> 66 truevalue='-t' falsevalue='' checked="true" help='(-t)' />
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).' /> 67 <param name='mtRNA' type='boolean' label='Search for Metazoan mitochondrial tRNA genes' truevalue='-mt' falsevalue='' checked="false"
66 <param name='secondary_structure' type='boolean' label='Print out secondary structure (-fasta,-fon)' truevalue='-fasta' falsevalue='-fon' checked="false" help='' /> 68 help='-i switch will be ignored. Composite Metazoan mitochondrial genetic code used. (-mt)' />
69 <param name='mam_mtRNA' type='boolean' label='Search for Mammalian mitochondrial tRNA genes'
70 truevalue='-mtmam' falsevalue='' checked="false" help='-i switch will be ignored. Mammalian mitochondrial genetic code used. (-mtmam)' />
71 <param name='introns' type='boolean' label='Search for tRNA genes with introns in anticodon loop'
72 truevalue='-i' falsevalue='' checked="false" help='With a maximum length of 3000 bases. (-i).' />
73 <param name='secondary_structure' type='boolean' label='Print out secondary structure'
74 truevalue='-fasta' falsevalue='-fon' checked="false" help='(-fasta,-fon)' />
67 <param name="gff3_output" type='boolean' label='Convert output to GFF3' truevalue='True' falsevalue='' checked="false" help='' /> 75 <param name="gff3_output" type='boolean' label='Convert output to GFF3' truevalue='True' falsevalue='' checked="false" help='' />
76 <param name="gff3_model" type='boolean' label='Full gene model for GFF3 data' truevalue='--full' checked='false' help='' />
68 </inputs> 77 </inputs>
69 <outputs> 78 <outputs>
70 <data name="output" format="fasta"> 79 <data name="output" format="fasta">
71 <change_format> 80 <change_format>
72 <when input="secondary_structure" value="true" format="text"/> 81 <when input="secondary_structure" value="-fasta" format="txt"/>
73 </change_format> 82 </change_format>
74 </data> 83 </data>
75 <data format="gff3" name="gff3_output_file" > 84 <data format="gff3" name="gff3_output_file" >
76 <filter>gff3_output</filter> 85 <filter>gff3_output</filter>
77 </data> 86 </data>
79 <tests> 88 <tests>
80 <test> 89 <test>
81 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" /> 90 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
82 <param name="genbank_gencode" value="1" /> 91 <param name="genbank_gencode" value="1" />
83 <param name="topology" value="-c" /> 92 <param name="topology" value="-c" />
84 <param name="tmRNA" value="-m" /> 93 <param name="tmRNA" value="True" />
85 <param name="tRNA" value="-t" /> 94 <param name="tRNA" value="True" />
86 <param name="mtRNA" value="" /> 95 <param name="mtRNA" value="False" />
87 <param name="mam_mtRNA" value="" /> 96 <param name="mam_mtRNA" value="False" />
88 <param name="introns" value="" /> 97 <param name="introns" value="False" />
89 <param name="secondary_structure" value="-fon" /> 98 <param name="secondary_structure" value="-fon" />
99 <param name="gff3_output" value="false" />
100 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.fasta" ftype="fasta" />
101 </test>
102
103 <test>
104 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
105 <param name="genbank_gencode" value="1" />
106 <param name="topology" value="-c" />
107 <param name="tmRNA" value="True" />
108 <param name="tRNA" value="True" />
109 <param name="mtRNA" value="False" />
110 <param name="mam_mtRNA" value="False" />
111 <param name="introns" value="False" />
112 <param name="secondary_structure" value="-fasta" />
113 <param name="gff3_output" value="false" />
114 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.txt" ftype="txt" lines_diff="2" />
115 </test>
116 <test>
117 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
118 <param name="genbank_gencode" value="1" />
119 <param name="topology" value="-c" />
120 <param name="tmRNA" value="True" />
121 <param name="tRNA" value="True" />
122 <param name="mtRNA" value="False" />
123 <param name="mam_mtRNA" value="False" />
124 <param name="introns" value="False" />
90 <param name="gff3_output" value="True" /> 125 <param name="gff3_output" value="True" />
91 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.fasta" ftype="fasta" /> 126 <output name="gff3_output_file" file="aragorn_tansl-table-1_tmRNA_tRNA.gff3" ftype="gff3" />
92 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.gff3" ftype="gff3" /> 127 </test>
128 <test>
129 <param name="input" value="genome_with_introns.fa" ftype="fasta" />
130 <param name="genbank_gencode" value="11" />
131 <param name="topology" value="-c" />
132 <param name="tmRNA" value="True" />
133 <param name="tRNA" value="True" />
134 <param name="mtRNA" value="False" />
135 <param name="mam_mtRNA" value="False" />
136 <param name="introns" value="True" />
137 <param name="gff3_output" value="True" />
138 <param name="gff3_model" value="True" />
139 <output name="gff3_output_file" file="aragorn_tansl-table-11_introns.gff3" ftype="gff3" />
93 </test> 140 </test>
94 </tests> 141 </tests>
95 <help> 142 <help>
96 <![CDATA[ 143 <![CDATA[
97 144
99 146
100 Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences. 147 Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences.
101 148
102 .. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ 149 .. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
103 150
104 ----- 151 **Input**
152
153 As input a genome sequence FASTA file is needed. Select the right genetic code and the topology for your organism and choose what you want to have analyzed.
154
155 By default, ARAGORN assumes that each sequence has a circular topology (search wraps around ends), that both strands should be searched, that the progress of the search is not reported, both tRNA and tmRNA genes are detected, and tRNA genes containing C‐loop introns are not detected.
156
157 **Output**
158
159 The output of Aragorn reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.
160
161 Optionally, your output can be converted to GFF3.
105 162
106 **Example** 163 **Example**
107 164
108 Suppose you have the following nucleotide sequences:: 165 Suppose you have the following nucleotide sequences::
109 166
187 244
188 Number of tRNA genes = 86 245 Number of tRNA genes = 86
189 tRNA GC range = 50.0% to 85.1% 246 tRNA GC range = 50.0% to 85.1%
190 Number of tmRNA genes = 1 247 Number of tmRNA genes = 1
191 248
192 -------
193
194 **References**
195
196 Dean Laslett and Bjorn Canback
197
198 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
199
200 doi:10.1093/nar/gkh152
201 249
202 ]]> 250 ]]>
203 </help> 251 </help>
252 <citations>
253 <citation type="doi">10.1093/nar/gkh152</citation>
254 </citations>
204 </tool> 255 </tool>