trna_prediction: aragorn.xml annotate

annotate 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

rev	line source
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	1 <tool id="aragorn_trna" name="tRNA and tmRNA" version="0.6">
1 d788d1abe238 Uploaded bgruening parents: 0 diff changeset	2 <description>prediction (Aragorn)</description>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	3 <requirements>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	4 <requirement type="package" version="1.2.36">aragorn</requirement>
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	5 <requirement type="package" version="2.7">python</requirement>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	6 </requirements>
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	7 <command><![CDATA[
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	8 #if not $gff3_output:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	9 aragorn
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	10 '$input'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	11 -gc$genbank_gencode
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	12 $tmRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	13 $tRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	14 $mtRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	15 $mam_mtRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	16 $topology
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	17 -o '$output'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	18 $secondary_structure
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	19 $introns
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	20 #end if
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	21
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	22 #if $gff3_output:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	23 aragorn
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	24 '$input'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	25 -gc$genbank_gencode
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	26 $tmRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	27 $tRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	28 $mtRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	29 $mam_mtRNA
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	30 $topology
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	31 $introns
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	32 -w
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	33 \| python '$__tool_directory__/aragorn_out_to_gff3.py' $gff3_model > '$gff3_output_file'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	34 #end if
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	35 ]]>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	36 </command>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	37 <inputs>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	38 <param name="input" type="data" format="fasta" label="Genome Sequence"/>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	39 <param name="genbank_gencode" type="select" label="Genetic code">
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	40 <option value="1" selected="true">1. Standard</option>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	41 <option value="2">2. Vertebrate Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	42 <option value="3">3. Yeast Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	43 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	44 <option value="5">5. Invertebrate Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	45 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	46 <option value="9">9. Echinoderm Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	47 <option value="10">10. Euplotid Nuclear</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	48 <option value="11">11. Bacteria and Archaea</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	49 <option value="12">12. Alternative Yeast Nuclear</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	50 <option value="13">13. Ascidian Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	51 <option value="14">14. Flatworm Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	52 <option value="15">15. Blepharisma Macronuclear</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	53 <option value="16">16. Chlorophycean Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	54 <option value="21">21. Trematode Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	55 <option value="22">22. Scenedesmus obliquus mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	56 <option value="23">23. Thraustochytrium Mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	57 <option value="24">24. Pterobranchia mitochondrial</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	58 </param>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	59 <param name="topology" type="select" label="Topology">
d34f31cbc9dd Uploaded bgruening parents: diff changeset	60 <option value="-c">Assume that each sequence has a circular topology</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	61 <option value="-l">Assume that each sequence has a linear topology</option>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	62 </param>
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	63 <param name='tmRNA' type='boolean' label='Search for tmRNA genes'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	64 truevalue='-m' falsevalue='' checked="true" help='(-m)' />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	65 <param name='tRNA' type='boolean' label='Search for tRNA genes'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	66 truevalue='-t' falsevalue='' checked="true" help='(-t)' />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	67 <param name='mtRNA' type='boolean' label='Search for Metazoan mitochondrial tRNA genes' truevalue='-mt' falsevalue='' checked="false"
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	68 help='-i switch will be ignored. Composite Metazoan mitochondrial genetic code used. (-mt)' />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	69 <param name='mam_mtRNA' type='boolean' label='Search for Mammalian mitochondrial tRNA genes'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	70 truevalue='-mtmam' falsevalue='' checked="false" help='-i switch will be ignored. Mammalian mitochondrial genetic code used. (-mtmam)' />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	71 <param name='introns' type='boolean' label='Search for tRNA genes with introns in anticodon loop'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	72 truevalue='-i' falsevalue='' checked="false" help='With a maximum length of 3000 bases. (-i).' />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	73 <param name='secondary_structure' type='boolean' label='Print out secondary structure'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	74 truevalue='-fasta' falsevalue='-fon' checked="false" help='(-fasta,-fon)' />
1 d788d1abe238 Uploaded bgruening parents: 0 diff changeset	75 <param name="gff3_output" type='boolean' label='Convert output to GFF3' truevalue='True' falsevalue='' checked="false" help='' />
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	76 <param name="gff3_model" type='boolean' label='Full gene model for GFF3 data' truevalue='--full' checked='false' help='' />
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	77 </inputs>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	78 <outputs>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	79 <data name="output" format="fasta">
d34f31cbc9dd Uploaded bgruening parents: diff changeset	80 <change_format>
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	81 <when input="secondary_structure" value="-fasta" format="txt"/>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	82 </change_format>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	83 </data>
1 d788d1abe238 Uploaded bgruening parents: 0 diff changeset	84 <data format="gff3" name="gff3_output_file" >
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	85 <filter>gff3_output</filter>
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	86 </data>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	87 </outputs>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	88 <tests>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	89 <test>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	90 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
d34f31cbc9dd Uploaded bgruening parents: diff changeset	91 <param name="genbank_gencode" value="1" />
d34f31cbc9dd Uploaded bgruening parents: diff changeset	92 <param name="topology" value="-c" />
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	93 <param name="tmRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	94 <param name="tRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	95 <param name="mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	96 <param name="mam_mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	97 <param name="introns" value="False" />
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	98 <param name="secondary_structure" value="-fon" />
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	99 <param name="gff3_output" value="false" />
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	100 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.fasta" ftype="fasta" />
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	101 </test>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	102
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	103 <test>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	104 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	105 <param name="genbank_gencode" value="1" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	106 <param name="topology" value="-c" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	107 <param name="tmRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	108 <param name="tRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	109 <param name="mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	110 <param name="mam_mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	111 <param name="introns" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	112 <param name="secondary_structure" value="-fasta" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	113 <param name="gff3_output" value="false" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	114 <output name="output" file="aragorn_tansl-table-1_tmRNA_tRNA.txt" ftype="txt" lines_diff="2" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	115 </test>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	116 <test>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	117 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	118 <param name="genbank_gencode" value="1" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	119 <param name="topology" value="-c" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	120 <param name="tmRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	121 <param name="tRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	122 <param name="mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	123 <param name="mam_mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	124 <param name="introns" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	125 <param name="gff3_output" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	126 <output name="gff3_output_file" file="aragorn_tansl-table-1_tmRNA_tRNA.gff3" ftype="gff3" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	127 </test>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	128 <test>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	129 <param name="input" value="genome_with_introns.fa" ftype="fasta" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	130 <param name="genbank_gencode" value="11" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	131 <param name="topology" value="-c" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	132 <param name="tmRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	133 <param name="tRNA" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	134 <param name="mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	135 <param name="mam_mtRNA" value="False" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	136 <param name="introns" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	137 <param name="gff3_output" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	138 <param name="gff3_model" value="True" />
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	139 <output name="gff3_output_file" file="aragorn_tansl-table-11_introns.gff3" ftype="gff3" />
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	140 </test>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	141 </tests>
d34f31cbc9dd Uploaded bgruening parents: diff changeset	142 <help>
1 d788d1abe238 Uploaded bgruening parents: 0 diff changeset	143 <![CDATA[
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	144
d34f31cbc9dd Uploaded bgruening parents: diff changeset	145 What it does
d34f31cbc9dd Uploaded bgruening parents: diff changeset	146
d34f31cbc9dd Uploaded bgruening parents: diff changeset	147 Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences.
d34f31cbc9dd Uploaded bgruening parents: diff changeset	148
d34f31cbc9dd Uploaded bgruening parents: diff changeset	149 .. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
d34f31cbc9dd Uploaded bgruening parents: diff changeset	150
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	151 Input
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	152
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	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.
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	154
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	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.
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	156
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	157 Output
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	158
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	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.
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	160
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	161 Optionally, your output can be converted to GFF3.
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	162
d34f31cbc9dd Uploaded bgruening parents: diff changeset	163 Example
d34f31cbc9dd Uploaded bgruening parents: diff changeset	164
d34f31cbc9dd Uploaded bgruening parents: diff changeset	165 Suppose you have the following nucleotide sequences::
d34f31cbc9dd Uploaded bgruening parents: diff changeset	166
d34f31cbc9dd Uploaded bgruening parents: diff changeset	167 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
d34f31cbc9dd Uploaded bgruening parents: diff changeset	168 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
d34f31cbc9dd Uploaded bgruening parents: diff changeset	169 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
d34f31cbc9dd Uploaded bgruening parents: diff changeset	170 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
d34f31cbc9dd Uploaded bgruening parents: diff changeset	171 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
d34f31cbc9dd Uploaded bgruening parents: diff changeset	172 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
d34f31cbc9dd Uploaded bgruening parents: diff changeset	173 ....
d34f31cbc9dd Uploaded bgruening parents: diff changeset	174
d34f31cbc9dd Uploaded bgruening parents: diff changeset	175 Running this tool can produce a FASTA file with all detected RNAs or a more detailed text file like the following::
d34f31cbc9dd Uploaded bgruening parents: diff changeset	176
d34f31cbc9dd Uploaded bgruening parents: diff changeset	177 c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	178 c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	179 a
d34f31cbc9dd Uploaded bgruening parents: diff changeset	180 g-c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	181 g-c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	182 g-c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	183 c-g
d34f31cbc9dd Uploaded bgruening parents: diff changeset	184 g-c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	185 a-t
d34f31cbc9dd Uploaded bgruening parents: diff changeset	186 t-a ca
d34f31cbc9dd Uploaded bgruening parents: diff changeset	187 t tgacc a
d34f31cbc9dd Uploaded bgruening parents: diff changeset	188 ga a !!!!! g
d34f31cbc9dd Uploaded bgruening parents: diff changeset	189 t ctcg actgg c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	190 g !!!! c tt
d34f31cbc9dd Uploaded bgruening parents: diff changeset	191 g gagc t
d34f31cbc9dd Uploaded bgruening parents: diff changeset	192 aa g g
d34f31cbc9dd Uploaded bgruening parents: diff changeset	193 c-gag
d34f31cbc9dd Uploaded bgruening parents: diff changeset	194 t-a
d34f31cbc9dd Uploaded bgruening parents: diff changeset	195 t-a
d34f31cbc9dd Uploaded bgruening parents: diff changeset	196 c-g
d34f31cbc9dd Uploaded bgruening parents: diff changeset	197 g-c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	198 t c
d34f31cbc9dd Uploaded bgruening parents: diff changeset	199 t a
d34f31cbc9dd Uploaded bgruening parents: diff changeset	200 cac
d34f31cbc9dd Uploaded bgruening parents: diff changeset	201
d34f31cbc9dd Uploaded bgruening parents: diff changeset	202 tRNA-Val(cac)
d34f31cbc9dd Uploaded bgruening parents: diff changeset	203 74 bases, %GC = 58.1
d34f31cbc9dd Uploaded bgruening parents: diff changeset	204 Sequence [6669703,6669776]
d34f31cbc9dd Uploaded bgruening parents: diff changeset	205
d34f31cbc9dd Uploaded bgruening parents: diff changeset	206
d34f31cbc9dd Uploaded bgruening parents: diff changeset	207 tRNA Anticodon Frequency
1 d788d1abe238 Uploaded bgruening parents: 0 diff changeset	208 AAA Phe GAA Phe 1 CAA Leu 1 TAA Leu 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	209 AGA Ser GGA Ser 1 CGA Ser 2 TGA Ser 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	210 ACA Cys GCA Cys 2 CCA Trp 2 TCA seC
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	211 ATA Tyr GTA Tyr 1 CTA Pyl TTA Stop
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	212 AAG Leu GAG Leu 3 CAG Leu 1 TAG Leu 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	213 AGG Pro GGG Pro 2 CGG Pro 2 TGG Pro 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	214 ACG Arg 1 GCG Arg 2 CCG Arg 1 TCG Arg
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	215 ATG His GTG His 2 CTG Gln 2 TTG Gln 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	216 AAC Val GAC Val 3 CAC Val 2 TAC Val 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	217 AGC Ala GGC Ala 2 CGC Ala 3 TGC Ala 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	218 ACC Gly GCC Gly 5 CCC Gly 1 TCC Gly 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	219 ATC Asp GTC Asp 3 CTC Glu 2 TTC Glu 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	220 AAT Ile GAT Ile 3 CAT Met 6 TAT Ile
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	221 AGT Thr GGT Thr 2 CGT Thr 1 TGT Thr 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	222 ACT Ser GCT Ser 1 CCT Arg 1 TCT Arg 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	223 ATT Asn GTT Asn 3 CTT Lys 3 TTT Lys 2
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	224 Ambiguous: 1
d34f31cbc9dd Uploaded bgruening parents: diff changeset	225
d34f31cbc9dd Uploaded bgruening parents: diff changeset	226 tRNA Codon Frequency
1 d788d1abe238 Uploaded bgruening parents: 0 diff changeset	227 TTT Phe TTC Phe 1 TTG Leu 1 TTA Leu 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	228 TCT Ser TCC Ser 1 TCG Ser 2 TCA Ser 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	229 TGT Cys TGC Cys 2 TGG Trp 2 TGA seC
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	230 TAT Tyr TAC Tyr 1 TAG Pyl TAA Stop
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	231 CTT Leu CTC Leu 3 CTG Leu 1 CTA Leu 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	232 CCT Pro CCC Pro 2 CCG Pro 2 CCA Pro 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	233 CGT Arg 1 CGC Arg 2 CGG Arg 1 CGA Arg
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	234 CAT His CAC His 2 CAG Gln 2 CAA Gln 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	235 GTT Val GTC Val 3 GTG Val 2 GTA Val 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	236 GCT Ala GCC Ala 2 GCG Ala 3 GCA Ala 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	237 GGT Gly GGC Gly 5 GGG Gly 1 GGA Gly 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	238 GAT Asp GAC Asp 3 GAG Glu 2 GAA Glu 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	239 ATT Ile ATC Ile 3 ATG Met 6 ATA Ile
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	240 ACT Thr ACC Thr 2 ACG Thr 1 ACA Thr 2
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	241 AGT Ser AGC Ser 1 AGG Arg 1 AGA Arg 1
d788d1abe238 Uploaded bgruening parents: 0 diff changeset	242 AAT Asn AAC Asn 3 AAG Lys 3 AAA Lys 2
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	243 Ambiguous: 1
d34f31cbc9dd Uploaded bgruening parents: diff changeset	244
d34f31cbc9dd Uploaded bgruening parents: diff changeset	245 Number of tRNA genes = 86
d34f31cbc9dd Uploaded bgruening parents: diff changeset	246 tRNA GC range = 50.0% to 85.1%
d34f31cbc9dd Uploaded bgruening parents: diff changeset	247 Number of tmRNA genes = 1
d34f31cbc9dd Uploaded bgruening parents: diff changeset	248
d34f31cbc9dd Uploaded bgruening parents: diff changeset	249
1 d788d1abe238 Uploaded bgruening parents: 0 diff changeset	250 ]]>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	251 </help>
2 358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	252 <citations>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	253 <citation type="doi">10.1093/nar/gkh152</citation>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44 bgruening parents: 1 diff changeset	254 </citations>
0 d34f31cbc9dd Uploaded bgruening parents: diff changeset	255 </tool>

Mercurial > repos > bgruening > trna_prediction

annotate aragorn.xml @ 2:358f58401cd6 draft default tip