Mercurial > repos > bgruening > trna_prediction
diff aragorn.xml @ 2:358f58401cd6 draft default tip
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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--- a/aragorn.xml Thu Jan 22 13:15:51 2015 -0500 +++ b/aragorn.xml Wed Jul 26 10:14:05 2017 -0400 @@ -1,41 +1,43 @@ -<tool id="aragorn_trna" name="tRNA and tmRNA" version="0.4"> +<tool id="aragorn_trna" name="tRNA and tmRNA" version="0.6"> <description>prediction (Aragorn)</description> <requirements> <requirement type="package" version="1.2.36">aragorn</requirement> - <requirement type="set_environment">TRNAPRED_SCRIPT_PATH</requirement> + <requirement type="package" version="2.7">python</requirement> </requirements> - <command> -<![CDATA[ - aragorn - $input - -gc$genbank_gencode - $tmRNA - $tRNA - $mtRNA - $mam_mtRNA - $topology - -o $output - $secondary_structure - $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><![CDATA[ + #if not $gff3_output: + aragorn + '$input' + -gc$genbank_gencode + $tmRNA + $tRNA + $mtRNA + $mam_mtRNA + $topology + -o '$output' + $secondary_structure + $introns + #end if + + #if $gff3_output: + aragorn + '$input' + -gc$genbank_gencode + $tmRNA + $tRNA + $mtRNA + $mam_mtRNA + $topology + $introns + -w + | python '$__tool_directory__/aragorn_out_to_gff3.py' $gff3_model > '$gff3_output_file' + #end if + ]]> </command> <inputs> <param name="input" type="data" format="fasta" label="Genome Sequence"/> <param name="genbank_gencode" type="select" label="Genetic code"> - <option value="1" select="True">1. Standard</option> + <option value="1" selected="true">1. Standard</option> <option value="2">2. Vertebrate Mitochondrial</option> <option value="3">3. Yeast Mitochondrial</option> <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> @@ -58,18 +60,25 @@ <option value="-c">Assume that each sequence has a circular topology</option> <option value="-l">Assume that each sequence has a linear topology</option> </param> - <param name='tmRNA' type='boolean' label='Search for tmRNA genes (-m)' truevalue='-m' falsevalue='' checked="true" help='' /> - <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' /> - <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.' /> - <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='tmRNA' type='boolean' label='Search for tmRNA genes' + truevalue='-m' falsevalue='' checked="true" help='(-m)' /> + <param name='tRNA' type='boolean' label='Search for tRNA genes' + truevalue='-t' falsevalue='' checked="true" help='(-t)' /> + <param name='mtRNA' type='boolean' label='Search for Metazoan mitochondrial tRNA genes' truevalue='-mt' falsevalue='' checked="false" + help='-i switch will be ignored. Composite Metazoan mitochondrial genetic code used. (-mt)' /> + <param name='mam_mtRNA' type='boolean' label='Search for Mammalian mitochondrial tRNA genes' + truevalue='-mtmam' falsevalue='' checked="false" help='-i switch will be ignored. Mammalian mitochondrial genetic code used. (-mtmam)' /> + <param name='introns' type='boolean' label='Search for tRNA genes with introns in anticodon loop' + truevalue='-i' falsevalue='' checked="false" help='With a maximum length of 3000 bases. (-i).' /> + <param name='secondary_structure' type='boolean' label='Print out secondary structure' + truevalue='-fasta' falsevalue='-fon' checked="false" help='(-fasta,-fon)' /> <param name="gff3_output" type='boolean' label='Convert output to GFF3' truevalue='True' falsevalue='' checked="false" help='' /> + <param name="gff3_model" type='boolean' label='Full gene model for GFF3 data' truevalue='--full' checked='false' help='' /> </inputs> <outputs> <data name="output" format="fasta"> <change_format> - <when input="secondary_structure" value="true" format="text"/> + <when input="secondary_structure" value="-fasta" format="txt"/> </change_format> </data> <data format="gff3" name="gff3_output_file" > @@ -81,15 +90,53 @@ <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" /> <param name="genbank_gencode" value="1" /> <param name="topology" value="-c" /> - <param name="tmRNA" value="-m" /> - <param name="tRNA" value="-t" /> - <param name="mtRNA" value="" /> - <param name="mam_mtRNA" value="" /> - <param name="introns" value="" /> + <param name="tmRNA" value="True" /> + <param name="tRNA" value="True" /> + <param name="mtRNA" value="False" /> + <param name="mam_mtRNA" value="False" /> + <param name="introns" value="False" /> <param name="secondary_structure" value="-fon" /> - <param name="gff3_output" value="True" /> + <param name="gff3_output" value="false" /> <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> + + <test> + <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" /> + <param name="genbank_gencode" value="1" /> + <param name="topology" value="-c" /> + <param name="tmRNA" value="True" /> + <param name="tRNA" value="True" /> + <param name="mtRNA" value="False" /> + <param name="mam_mtRNA" value="False" /> + <param name="introns" value="False" /> + <param name="secondary_structure" value="-fasta" /> + <param name="gff3_output" value="false" /> + <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.txt" ftype="txt" lines_diff="2" /> + </test> + <test> + <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" /> + <param name="genbank_gencode" value="1" /> + <param name="topology" value="-c" /> + <param name="tmRNA" value="True" /> + <param name="tRNA" value="True" /> + <param name="mtRNA" value="False" /> + <param name="mam_mtRNA" value="False" /> + <param name="introns" value="False" /> + <param name="gff3_output" value="True" /> + <output name="gff3_output_file" file="aragorn_tansl-table-1_tmRNA_tRNA.gff3" ftype="gff3" /> + </test> + <test> + <param name="input" value="genome_with_introns.fa" ftype="fasta" /> + <param name="genbank_gencode" value="11" /> + <param name="topology" value="-c" /> + <param name="tmRNA" value="True" /> + <param name="tRNA" value="True" /> + <param name="mtRNA" value="False" /> + <param name="mam_mtRNA" value="False" /> + <param name="introns" value="True" /> + <param name="gff3_output" value="True" /> + <param name="gff3_model" value="True" /> + <output name="gff3_output_file" file="aragorn_tansl-table-11_introns.gff3" ftype="gff3" /> </test> </tests> <help> @@ -101,7 +148,17 @@ .. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ ------ +**Input** + +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. + +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. + +**Output** + +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. + +Optionally, your output can be converted to GFF3. **Example** @@ -189,16 +246,10 @@ 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> + <citations> + <citation type="doi">10.1093/nar/gkh152</citation> + </citations> </tool>