augustus: augustus.xml annotate

annotate augustus.xml @ 4:4de31938431b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e

author	iuc
date	Fri, 20 Oct 2017 03:48:57 -0400
parents	f5075dee9d6b
children	b3f5d0879dab

rev	line source
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	1 <tool id="augustus" name="Augustus" profile="16.04" version="@VERSION@">
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	2 <description>gene prediction for prokaryotic and eukaryotic genomes</description>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	3 <macros>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	4 <import>macros.xml</import>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	5 </macros>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	6 <expand macro="requirements"/>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	7 <command detect_errors="aggressive">
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	8 <![CDATA[
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	9 #if $model.augustus_mode == 'history'
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	10
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	11 ## Using an augustus model from history, we need to unzip it and let augustus find it
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	12
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	13 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	14
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	15 mkdir -p 'augustus_dir/species/' &&
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	16
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	17 tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /dev/null &&
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	18
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	19 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	20 #end if
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	21
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	22 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	23 ## script is used to extract the sequences into additional files
0 af307d3285c5 Uploaded bgruening parents: diff changeset	24
af307d3285c5 Uploaded bgruening parents: diff changeset	25 augustus
af307d3285c5 Uploaded bgruening parents: diff changeset	26 --strand=$strand
af307d3285c5 Uploaded bgruening parents: diff changeset	27 $noInFrameStop
af307d3285c5 Uploaded bgruening parents: diff changeset	28 $gff
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	29 --uniqueGeneId=true
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	30
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	31 #if 'protein' in str($outputs).split(','):
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	32 --protein=on
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	33 #else:
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	34 --protein=off
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	35 #end if
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	36
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	37 #if 'codingseq' in str($outputs).split(','):
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	38 --codingseq=on
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	39 #else:
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	40 --codingseq=off
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	41 #end if
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	42
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	43 #if 'introns' in str($outputs).split(','):
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	44 --introns=on
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	45 #else:
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	46 --introns=off
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	47 #end if
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	48
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	49 #if 'start' in str($outputs).split(','):
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	50 --start=on
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	51 #else:
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	52 --stop=off
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	53 #end if
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	54
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	55 #if 'stop' in str($outputs).split(','):
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	56 --stop=on
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	57 #else:
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	58 --stop=off
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	59 #end if
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	60
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	61 #if 'cds' in str($outputs).split(','):
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	62 --cds=on
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	63 #else:
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	64 --cds=off
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	65 #end if
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	66
0 af307d3285c5 Uploaded bgruening parents: diff changeset	67 $singlestrand
af307d3285c5 Uploaded bgruening parents: diff changeset	68 $input_genome
af307d3285c5 Uploaded bgruening parents: diff changeset	69 $utr
af307d3285c5 Uploaded bgruening parents: diff changeset	70 --genemodel=$genemodel
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	71
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	72
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	73 #if $model.augustus_mode == 'history'
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	74 --species=local
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	75 #else
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	76 --species=$model.organism
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	77 #end if
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	78
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	79 \| tee '$output'
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	80 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	81 \| python $__tool_directory__/extract_features.py
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	82 #if 'protein' in str($outputs).split(','):
0 af307d3285c5 Uploaded bgruening parents: diff changeset	83 --protein $protein_output
af307d3285c5 Uploaded bgruening parents: diff changeset	84 #end if
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	85 #if 'codingseq' in str($outputs).split(','):
0 af307d3285c5 Uploaded bgruening parents: diff changeset	86 --codingseq $codingseq_output
af307d3285c5 Uploaded bgruening parents: diff changeset	87 #end if
af307d3285c5 Uploaded bgruening parents: diff changeset	88 #end if
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	89 ]]>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	90 </command>
af307d3285c5 Uploaded bgruening parents: diff changeset	91 <inputs>
af307d3285c5 Uploaded bgruening parents: diff changeset	92 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	93 <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	94 label="Don't report transcripts with in-frame stop codons"
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	95 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	96 help="Otherwise, intron-spanning stop codons could occur." />
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	97 <param name="singlestrand" type="boolean" argument="--singlestrand"
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	98 label="Predict genes independently on each strand"
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	99 help="This allows overlapping genes on opposite strands."
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	100 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	101
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	102 <param name="utr" type="boolean" argument="--UTR"
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	103 label="Predict the untranslated regions in addition to the coding sequence"
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	104 truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	105 help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	106
0 af307d3285c5 Uploaded bgruening parents: diff changeset	107
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	108 <conditional name="model">
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	109 <param name="augustus_mode" type="select" label="Trainingset">
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	110 <option value="builtin">Run Augustus with a predefined trainingset</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	111 <option value="history">Run Augustus with a custom trainingset</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	112 </param>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	113 <when value="history">
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	114 <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	115 </when>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	116 <when value="builtin">
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	117 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	118 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	119 <option value="human">Homo sapiens</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	120 <option value="fly">Drosophila melanogaster</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	121 <option value="arabidopsis">Arabidopsis thaliana</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	122 <option value="brugia ">Brugia malayi</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	123 <option value="aedes">Aedes aegypti</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	124 <option value="tribolium2012">Tribolium castaneum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	125 <option value="schistosoma">Schistosoma mansoni</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	126 <option value="tetrahymena">Tetrahymena thermophila</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	127 <option value="galdieria">Galdieria sulphuraria</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	128 <option value="maize">Zea mays</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	129 <option value="toxoplasma">Toxoplasma gondii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	130 <option value="caenorhabditis ">Caenorhabditis elegans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	131 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	132 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	133 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	134 <option value="aspergillus_terreus">Aspergillus terreus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	135 <option value="botrytis_cinerea ">Botrytis cinerea</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	136 <option value="candida_albicans ">Candida albicans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	137 <option value="candida_guilliermondii ">Candida guilliermondii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	138 <option value="candida_tropicalis ">Candida tropicalis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	139 <option value="chaetomium_globosum">Chaetomium globosum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	140 <option value="coccidioides_immitis">Coccidioides immitis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	141 <option value="coprinus">Coprinus cinereus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	142 <option value="coprinus_cinereus">Coprinus cinereus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	143 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	144 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	145 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	146 <option value="cryptococcus">Cryptococcus neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	147 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	148 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	149 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	150 <option value="fusarium_graminearum ">Fusarium graminearum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	151 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	152 <option value="histoplasma">Histoplasma capsulatum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	153 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	154 <option value="laccaria_bicolor ">Laccaria bicolor</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	155 <option value="lamprey">Petromyzon marinus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	156 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	157 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	158 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	159 <option value="neurospora_crassa">Neurospora crassa</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	160 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	161 <option value="pichia_stipitis">Pichia stipitis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	162 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	163 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	164 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	165 <option value="saccharomyces">Saccharomyces cerevisiae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	166 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	167 <option value="trichinella">Trichinella spiralis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	168 <option value="ustilago_maydis">Ustilago maydis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	169 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	170 <option value="nasonia">Nasonia vitripennis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	171 <option value="tomato">Solanum lycopersicum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	172 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	173 <option value="amphimedon">Amphimedon queenslandica</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	174 <option value="pneumocystis">Pneumocystis jirovecii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	175 <option value="chicken">Gallus gallus domesticus (chicken)</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	176 <option value="cacao">Theobroma cacao (cacao)</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	177 <option value="heliconius_melpomene1">Heliconius melpomene</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	178 <option value="xenoturbella">Xenoturbella</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	179 <option value="E_coli_K12">E coli K12</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	180 <option value="c_elegans_trsk">c elegans trsk</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	181 <option value="camponotus_floridanus">Camponotus floridanus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	182 <option value="coyote_tobacco">Coyote tobacco</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	183 <option value="s_aureus">Staphylococcus aureus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	184 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	185 <option value="wheat">wheat</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	186 <option value="zebrafish">Danio rerio</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	187 <option value="anidulans">Aspergillus nidulans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	188 <option value="bombus_impatiens1">Bombus impatiens1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	189 <option value="bombus_terrestris2">Bombus terrestris2</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	190 <option value="botrytis_cinerea">Botrytis cinerea</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	191 <option value="brugia_malayi">Brugia malayi</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	192 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	193 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	194 <option value="culex_pipiens">Culex pipiens</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	195 <option value="elephant_shark">Callorhinchus milii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	196 <option value="honeybee1">Apis mellifera</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	197 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	198 <option value="pea_aphid">Acyrthosiphon pisum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	199 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	200 <option value="ustilago_maydis">Ustilago maydis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	201 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	202 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	203 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	204 <option value="adorsata">adorsata</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	205 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	206 <option value="maker2_athal1">maker2_athal1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	207 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	208 <option value="maker2_dmel1">maker2_dmel1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	209 <option value="maker2_spomb1">maker2_spomb1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	210 <option value="parasteatoda">parasteatoda</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	211 <option value="rice">rice</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	212 <option value="schistosoma2">schistosoma2</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	213 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	214 </param>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	215 </when>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	216 </conditional>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	217
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	218 <param name="strand" type="select" argument="--strand"
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	219 label="Predict genes on specific strands">
0 af307d3285c5 Uploaded bgruening parents: diff changeset	220 <option value="both">both</option>
af307d3285c5 Uploaded bgruening parents: diff changeset	221 <option value="forward">forward</option>
af307d3285c5 Uploaded bgruening parents: diff changeset	222 <option value="backward">backward</option>
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	223 </param>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	224
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	225 <param name="genemodel" label="Gene Model" type="select"
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	226 help="Gene Model to predict, for more information please refere to the help.">
0 af307d3285c5 Uploaded bgruening parents: diff changeset	227 <option value="complete">complete</option>
af307d3285c5 Uploaded bgruening parents: diff changeset	228 <option value="partial">partial</option>
af307d3285c5 Uploaded bgruening parents: diff changeset	229 <option value="intronless">intronless</option>
af307d3285c5 Uploaded bgruening parents: diff changeset	230 <option value="atleastone">atleastone</option>
af307d3285c5 Uploaded bgruening parents: diff changeset	231 <option value="exactlyone">exactlyone</option>
af307d3285c5 Uploaded bgruening parents: diff changeset	232 </param>
af307d3285c5 Uploaded bgruening parents: diff changeset	233
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	234 <param name="gff" type="boolean" label="GFF formated output"
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	235 help="Standard output is GTF."
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	236 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
0 af307d3285c5 Uploaded bgruening parents: diff changeset	237
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	238 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	239 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	240 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	241 <option value="introns">predicted intron sequences (--introns)</option>
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	242 <option value="start">predicted start codons (--start)</option>
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	243 <option value="stop">predicted stop codons (--stop)</option>
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	244 <option value="cds" selected="true">CDS region (--cds)</option>
e2b822d7408f Uploaded bgruening parents: 0 diff changeset	245 </param>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	246 </inputs>
af307d3285c5 Uploaded bgruening parents: diff changeset	247 <outputs>
af307d3285c5 Uploaded bgruening parents: diff changeset	248 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
af307d3285c5 Uploaded bgruening parents: diff changeset	249 <change_format>
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	250 <when input="gff" value="--gff3=on" format="gff3" />
0 af307d3285c5 Uploaded bgruening parents: diff changeset	251 </change_format>
af307d3285c5 Uploaded bgruening parents: diff changeset	252 </data>
af307d3285c5 Uploaded bgruening parents: diff changeset	253 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	254 <filter>'protein' in outputs</filter>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	255 </data>
af307d3285c5 Uploaded bgruening parents: diff changeset	256 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
1 e2b822d7408f Uploaded bgruening parents: 0 diff changeset	257 <filter>'codingseq' in outputs</filter>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	258 </data>
af307d3285c5 Uploaded bgruening parents: diff changeset	259 </outputs>
af307d3285c5 Uploaded bgruening parents: diff changeset	260 <tests>
af307d3285c5 Uploaded bgruening parents: diff changeset	261 <test>
af307d3285c5 Uploaded bgruening parents: diff changeset	262 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
af307d3285c5 Uploaded bgruening parents: diff changeset	263 <param name="organism" value="human" />
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	264 <param name="utr" value="True" />
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	265 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	266 </test>
af307d3285c5 Uploaded bgruening parents: diff changeset	267 <test>
af307d3285c5 Uploaded bgruening parents: diff changeset	268 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
af307d3285c5 Uploaded bgruening parents: diff changeset	269 <param name="organism" value="human" />
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	270 <param name="utr" value="True" />
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	271 <param name="gff" value="True" />
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	272 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	273 </test>
af307d3285c5 Uploaded bgruening parents: diff changeset	274 <test>
af307d3285c5 Uploaded bgruening parents: diff changeset	275 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
af307d3285c5 Uploaded bgruening parents: diff changeset	276 <param name="organism" value="human" />
3 f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	277 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac iuc parents: 2 diff changeset	278 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	279 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
af307d3285c5 Uploaded bgruening parents: diff changeset	280 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
af307d3285c5 Uploaded bgruening parents: diff changeset	281 </test>
af307d3285c5 Uploaded bgruening parents: diff changeset	282 </tests>
af307d3285c5 Uploaded bgruening parents: diff changeset	283 <help>
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	284 <![CDATA[
0 af307d3285c5 Uploaded bgruening parents: diff changeset	285
af307d3285c5 Uploaded bgruening parents: diff changeset	286 What it does
af307d3285c5 Uploaded bgruening parents: diff changeset	287
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	288 AUGUSTUS is a gene prediction program for prokaryotes and eukaryotes written by Mario Stanke and Oliver Keller.
0 af307d3285c5 Uploaded bgruening parents: diff changeset	289 It can be used as an ab initio program, which means it bases its prediction purely on the
af307d3285c5 Uploaded bgruening parents: diff changeset	290 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
af307d3285c5 Uploaded bgruening parents: diff changeset	291 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
af307d3285c5 Uploaded bgruening parents: diff changeset	292
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	293
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	294 Input
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	295
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	296 Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence.
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	297
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	298
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	299 Output
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	300
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	301 Augustus produces three output files: a FASTA file with predicted coding sequences, a FASTA file with predicted protein sequences and a gtf/GFF output file if selected.
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	302
0 af307d3285c5 Uploaded bgruening parents: diff changeset	303
af307d3285c5 Uploaded bgruening parents: diff changeset	304 Parameters
af307d3285c5 Uploaded bgruening parents: diff changeset	305
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	306 Gene Model:
0 af307d3285c5 Uploaded bgruening parents: diff changeset	307
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	308 partial: allow prediction of incomplete genes at the sequence boundaries (default)
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	309 intronless: only predict single-exon genes like in prokaryotes and some eukaryotes
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	310 complete: only predict complete genes
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	311 atleastone: predict at least one complete gene
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	312 exactlyone: predict exactly one complete gene
0 af307d3285c5 Uploaded bgruening parents: diff changeset	313
af307d3285c5 Uploaded bgruening parents: diff changeset	314
af307d3285c5 Uploaded bgruening parents: diff changeset	315
af307d3285c5 Uploaded bgruening parents: diff changeset	316 Example
af307d3285c5 Uploaded bgruening parents: diff changeset	317
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	318 Suppose you have the following DNA FASTA sequence:
0 af307d3285c5 Uploaded bgruening parents: diff changeset	319
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	320 >Seq1
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	321 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	322 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	323 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	324 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	325 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
0 af307d3285c5 Uploaded bgruening parents: diff changeset	326
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	327
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	328 Running this tool will produce this:
0 af307d3285c5 Uploaded bgruening parents: diff changeset	329
af307d3285c5 Uploaded bgruening parents: diff changeset	330 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1\|size1992969) -----
af307d3285c5 Uploaded bgruening parents: diff changeset	331 #
af307d3285c5 Uploaded bgruening parents: diff changeset	332 # Constraints/Hints:
af307d3285c5 Uploaded bgruening parents: diff changeset	333 # (none)
af307d3285c5 Uploaded bgruening parents: diff changeset	334 # Predicted genes for sequence number 1 on both strands
af307d3285c5 Uploaded bgruening parents: diff changeset	335 # start gene g1
af307d3285c5 Uploaded bgruening parents: diff changeset	336 scaffold1\|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6
af307d3285c5 Uploaded bgruening parents: diff changeset	337 scaffold1\|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1
af307d3285c5 Uploaded bgruening parents: diff changeset	338 scaffold1\|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	339 scaffold1\|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	340 scaffold1\|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	341 scaffold1\|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	342 scaffold1\|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	343 scaffold1\|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	344 scaffold1\|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	345 scaffold1\|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	346 scaffold1\|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	347 scaffold1\|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	348 scaffold1\|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	349 scaffold1\|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	350 scaffold1\|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded bgruening parents: diff changeset	351
af307d3285c5 Uploaded bgruening parents: diff changeset	352
2 a77a4e9921e0 Uploaded bgruening parents: 1 diff changeset	353 ]]>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	354 </help>
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 3 diff changeset	355 <expand macro="citations"/>
0 af307d3285c5 Uploaded bgruening parents: diff changeset	356 </tool>

Mercurial > repos > bgruening > augustus

annotate augustus.xml @ 4:4de31938431b draft