Mercurial > repos > bgruening > augustus
changeset 10:cb47e789ccaa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
| author | bgruening |
|---|---|
| date | Fri, 10 May 2019 08:25:57 -0400 |
| parents | 4611e8073293 |
| children | e519d7b4f9ac |
| files | augustus.xml extract_features.py macros.xml readme.rst test-data/annot.gff3 test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta test-data/human_augustus_protein_codingseq_introns_cds_main.gtf test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta test-data/human_augustus_utr-on.gff test-data/human_augustus_utr-on.gtf tool_dependencies.xml |
| diffstat | 11 files changed, 302 insertions(+), 303 deletions(-) [+] |
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--- a/augustus.xml Fri May 22 04:51:46 2015 -0400 +++ b/augustus.xml Fri May 10 08:25:57 2019 -0400 @@ -1,17 +1,24 @@ -<tool id="augustus" name="Augustus" version="3.1.0"> - <description>gene prediction for eukaryotic genomes</description> - <parallelism method="multi" split_inputs="input_genome" split_mode="to_size" split_size="10" merge_outputs="output,protein_output,codingseq_output"></parallelism> - <requirements> - <requirement type="package" version="3.1">augustus</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command> +<tool id="augustus" name="Augustus" profile="16.04" version="@VERSION@"> + <description>gene prediction for prokaryotic and eukaryotic genomes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"> <![CDATA[ + #if $model.augustus_mode == 'history' + + ## Using an augustus model from history, we need to unzip it and let augustus find it + + cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && + + mkdir -p 'augustus_dir/species/' && + + tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /dev/null && + + export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && + #end if + ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external ## script is used to extract the sequences into additional files @@ -61,9 +68,15 @@ $input_genome $utr --genemodel=$genemodel - --species=$organism + - | tee $output + #if $model.augustus_mode == 'history' + --species=local + #else + --species=$model.organism + #end if + + | tee '$output' #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','): | python $__tool_directory__/extract_features.py #if 'protein' in str($outputs).split(','): @@ -78,126 +91,139 @@ <inputs> <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> <param name="noInFrameStop" argument="--noInFrameStop" type="boolean" - label="Don't report transcripts with in-frame stop codons (--noInFrameStop)" + label="Don't report transcripts with in-frame stop codons" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" - help="Otherwise, intron-spanning stop codons could occur. (--noInFrameStop)" /> + help="Otherwise, intron-spanning stop codons could occur." /> <param name="singlestrand" type="boolean" argument="--singlestrand" label="Predict genes independently on each strand" - help="This allows overlapping genes on opposite strands. (--singlestrand)" + help="This allows overlapping genes on opposite strands." truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> <param name="utr" type="boolean" argument="--UTR" label="Predict the untranslated regions in addition to the coding sequence" truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" - help="This currently works only for human, galdieria, toxoplasma and caenorhabditis. (--UTR)" /> + help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." /> + - <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> - <option value="human">Homo sapiens</option> - <option value="fly">Drosophila melanogaster</option> - <option value="arabidopsis">Arabidopsis thaliana</option> - <option value="brugia ">Brugia malayi</option> - <option value="aedes">Aedes aegypti</option> - <option value="tribolium2012">Tribolium castaneum</option> - <option value="schistosoma">Schistosoma mansoni</option> - <option value="tetrahymena">Tetrahymena thermophila</option> - <option value="galdieria">Galdieria sulphuraria</option> - <option value="maize">Zea mays</option> - <option value="toxoplasma">Toxoplasma gondii</option> - <option value="caenorhabditis ">Caenorhabditis elegans</option> - <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> - <option value="aspergillus_nidulans ">Aspergillus nidulans</option> - <option value="aspergillus_oryzae ">Aspergillus oryzae</option> - <option value="aspergillus_terreus">Aspergillus terreus</option> - <option value="botrytis_cinerea ">Botrytis cinerea</option> - <option value="candida_albicans ">Candida albicans</option> - <option value="candida_guilliermondii ">Candida guilliermondii</option> - <option value="candida_tropicalis ">Candida tropicalis</option> - <option value="chaetomium_globosum">Chaetomium globosum</option> - <option value="coccidioides_immitis">Coccidioides immitis</option> - <option value="coprinus">Coprinus cinereus</option> - <option value="coprinus_cinereus">Coprinus cinereus</option> - <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> - <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option> - <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option> - <option value="cryptococcus">Cryptococcus neoformans</option> - <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> - <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> - <option value="eremothecium_gossypii">Eremothecium gossypii</option> - <option value="fusarium_graminearum ">Fusarium graminearum</option> - <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> - <option value="histoplasma">Histoplasma capsulatum</option> - <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> - <option value="laccaria_bicolor ">Laccaria bicolor</option> - <option value="lamprey">Petromyzon marinus</option> - <option value="leishmania_tarentolae">Leishmania tarentolae</option> - <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> - <option value="magnaporthe_grisea ">Magnaporthe grisea</option> - <option value="neurospora_crassa">Neurospora crassa</option> - <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> - <option value="pichia_stipitis">Pichia stipitis</option> - <option value="rhizopus_oryzae">Rhizopus oryzae</option> - <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option> - <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option> - <option value="saccharomyces">Saccharomyces cerevisiae</option> - <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> - <option value="trichinella">Trichinella spiralis</option> - <option value="ustilago_maydis">Ustilago maydis</option> - <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> - <option value="nasonia">Nasonia vitripennis</option> - <option value="tomato">Solanum lycopersicum</option> - <option value="chlamydomonas">Chlamydomonas reinhardtii</option> - <option value="amphimedon">Amphimedon queenslandica</option> - <option value="pneumocystis">Pneumocystis jirovecii</option> - <option value="chicken">Gallus gallus domesticus (chicken)</option> - <option value="cacao">Theobroma cacao (cacao)</option> - <option value="heliconius_melpomene1">Heliconius melpomene</option> - <option value="xenoturbella">Xenoturbella</option> - <option value="E_coli_K12">E coli K12</option> - <option value="c_elegans_trsk">c elegans trsk</option> - <option value="camponotus_floridanus">Camponotus floridanus</option> - <option value="coyote_tobacco">Coyote tobacco</option> - <option value="s_aureus">Staphylococcus aureus</option> - <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> - <option value="wheat">wheat</option> - <option value="zebrafish">Danio rerio</option> - <option value="anidulans">Aspergillus nidulans</option> - <option value="bombus_impatiens1">Bombus impatiens1</option> - <option value="bombus_terrestris2">Bombus terrestris2</option> - <option value="botrytis_cinerea">Botrytis cinerea</option> - <option value="brugia_malayi">Brugia malayi</option> - <option value="conidiobolus_coronatus">Conidiobolus coronatus</option> - <option value="cryptococcus_neoformans">Cryptococcus neoformans</option> - <option value="culex_pipiens">Culex pipiens</option> - <option value="elephant_shark">Callorhinchus milii</option> - <option value="honeybee1">Apis mellifera</option> - <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> - <option value="pea_aphid">Acyrthosiphon pisum</option> - <option value="rhodnius_prolixus">Rhodnius prolixus</option> - <option value="ustilago_maydis">Ustilago maydis</option> - <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option> - <option value="verticillium_longisporum1">Verticillium longisporum1</option> - <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> - <option value="adorsata">adorsata</option> - <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option> - <option value="maker2_athal1">maker2_athal1</option> - <option value="maker2_c_elegans1">maker2_c_elegans1</option> - <option value="maker2_dmel1">maker2_dmel1</option> - <option value="maker2_spomb1">maker2_spomb1</option> - <option value="parasteatoda">parasteatoda</option> - <option value="rice">rice</option> - <option value="schistosoma2">schistosoma2</option> - <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option> - </param> + <conditional name="model"> + <param name="augustus_mode" type="select" label="Trainingset"> + <option value="builtin">Run Augustus with a predefined trainingset</option> + <option value="history">Run Augustus with a custom trainingset</option> + </param> + <when value="history"> + <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/> + </when> + <when value="builtin"> + <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> + <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) --> + <option value="human">Homo sapiens</option> + <option value="fly">Drosophila melanogaster</option> + <option value="arabidopsis">Arabidopsis thaliana</option> + <option value="brugia ">Brugia malayi</option> + <option value="aedes">Aedes aegypti</option> + <option value="tribolium2012">Tribolium castaneum</option> + <option value="schistosoma">Schistosoma mansoni</option> + <option value="tetrahymena">Tetrahymena thermophila</option> + <option value="galdieria">Galdieria sulphuraria</option> + <option value="maize">Zea mays</option> + <option value="toxoplasma">Toxoplasma gondii</option> + <option value="caenorhabditis ">Caenorhabditis elegans</option> + <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> + <option value="aspergillus_nidulans ">Aspergillus nidulans</option> + <option value="aspergillus_oryzae ">Aspergillus oryzae</option> + <option value="aspergillus_terreus">Aspergillus terreus</option> + <option value="botrytis_cinerea ">Botrytis cinerea</option> + <option value="candida_albicans ">Candida albicans</option> + <option value="candida_guilliermondii ">Candida guilliermondii</option> + <option value="candida_tropicalis ">Candida tropicalis</option> + <option value="chaetomium_globosum">Chaetomium globosum</option> + <option value="coccidioides_immitis">Coccidioides immitis</option> + <option value="coprinus">Coprinus cinereus</option> + <option value="coprinus_cinereus">Coprinus cinereus</option> + <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> + <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option> + <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option> + <option value="cryptococcus">Cryptococcus neoformans</option> + <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> + <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> + <option value="eremothecium_gossypii">Eremothecium gossypii</option> + <option value="fusarium_graminearum ">Fusarium graminearum</option> + <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> + <option value="histoplasma">Histoplasma capsulatum</option> + <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> + <option value="laccaria_bicolor ">Laccaria bicolor</option> + <option value="lamprey">Petromyzon marinus</option> + <option value="leishmania_tarentolae">Leishmania tarentolae</option> + <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> + <option value="magnaporthe_grisea ">Magnaporthe grisea</option> + <option value="neurospora_crassa">Neurospora crassa</option> + <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> + <option value="pichia_stipitis">Pichia stipitis</option> + <option value="rhizopus_oryzae">Rhizopus oryzae</option> + <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option> + <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option> + <option value="saccharomyces">Saccharomyces cerevisiae</option> + <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> + <option value="trichinella">Trichinella spiralis</option> + <option value="ustilago_maydis">Ustilago maydis</option> + <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> + <option value="nasonia">Nasonia vitripennis</option> + <option value="tomato">Solanum lycopersicum</option> + <option value="chlamydomonas">Chlamydomonas reinhardtii</option> + <option value="amphimedon">Amphimedon queenslandica</option> + <option value="pneumocystis">Pneumocystis jirovecii</option> + <option value="chicken">Gallus gallus domesticus (chicken)</option> + <option value="cacao">Theobroma cacao (cacao)</option> + <option value="heliconius_melpomene1">Heliconius melpomene</option> + <option value="xenoturbella">Xenoturbella</option> + <option value="E_coli_K12">E coli K12</option> + <option value="c_elegans_trsk">c elegans trsk</option> + <option value="camponotus_floridanus">Camponotus floridanus</option> + <option value="coyote_tobacco">Coyote tobacco</option> + <option value="s_aureus">Staphylococcus aureus</option> + <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> + <option value="wheat">wheat</option> + <option value="zebrafish">Danio rerio</option> + <option value="anidulans">Aspergillus nidulans</option> + <option value="bombus_impatiens1">Bombus impatiens1</option> + <option value="bombus_terrestris2">Bombus terrestris2</option> + <option value="botrytis_cinerea">Botrytis cinerea</option> + <option value="brugia_malayi">Brugia malayi</option> + <option value="conidiobolus_coronatus">Conidiobolus coronatus</option> + <option value="cryptococcus_neoformans">Cryptococcus neoformans</option> + <option value="culex_pipiens">Culex pipiens</option> + <option value="elephant_shark">Callorhinchus milii</option> + <option value="honeybee1">Apis mellifera</option> + <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> + <option value="pea_aphid">Acyrthosiphon pisum</option> + <option value="rhodnius_prolixus">Rhodnius prolixus</option> + <option value="ustilago_maydis">Ustilago maydis</option> + <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option> + <option value="verticillium_longisporum1">Verticillium longisporum1</option> + <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> + <option value="adorsata">adorsata</option> + <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option> + <option value="maker2_athal1">maker2_athal1</option> + <option value="maker2_c_elegans1">maker2_c_elegans1</option> + <option value="maker2_dmel1">maker2_dmel1</option> + <option value="maker2_spomb1">maker2_spomb1</option> + <option value="parasteatoda">parasteatoda</option> + <option value="rice">rice</option> + <option value="schistosoma2">schistosoma2</option> + <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option> + </param> + </when> + </conditional> <param name="strand" type="select" argument="--strand" - label="Predict genes on specific strands" help="(--strand)"> + label="Predict genes on specific strands"> <option value="both">both</option> <option value="forward">forward</option> <option value="backward">backward</option> </param> <param name="genemodel" label="Gene Model" type="select" - help="Gene Model to predict, for more information please refere to the help. (--genemodel)"> + help="Gene Model to predict, for more information please refere to the help."> <option value="complete">complete</option> <option value="partial">partial</option> <option value="intronless">intronless</option> @@ -206,7 +232,7 @@ </param> <param name="gff" type="boolean" label="GFF formated output" - help="Standard output is GTF. (--gff3)" + help="Standard output is GTF." truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> @@ -216,10 +242,7 @@ <option value="start">predicted start codons (--start)</option> <option value="stop">predicted stop codons (--stop)</option> <option value="cds" selected="true">CDS region (--cds)</option> - - <validator type="no_options" message="Please select at least one output file." /> </param> - </inputs> <outputs> <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF"> @@ -262,37 +285,47 @@ **What it does** -AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. +AUGUSTUS is a gene prediction program for prokaryotes and eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. ------ + +**Input** + +Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence. + + +**Output** + +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. + **Parameters** -Gene Model:: +Gene Model: - partial : allow prediction of incomplete genes at the sequence boundaries (default) - intronless : only predict single-exon genes like in prokaryotes and some eukaryotes - complete : only predict complete genes - atleastone : predict at least one complete gene - exactlyone : predict exactly one complete gene +partial: allow prediction of incomplete genes at the sequence boundaries (default) +intronless: only predict single-exon genes like in prokaryotes and some eukaryotes +complete: only predict complete genes +atleastone: predict at least one complete gene +exactlyone: predict exactly one complete gene **Example** -Suppose you have the following DNA formatted sequences:: +Suppose you have the following DNA FASTA sequence: - >Seq1 - cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg - ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag - cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc - cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc - ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg +>Seq1 +cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg +ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag +cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc +cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc +ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg -Running this tool will produce this:: + +Running this tool will produce this: # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) ----- # @@ -319,7 +352,5 @@ ]]> </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btg1080</citation> - </citations> + <expand macro="citations"/> </tool>
--- a/extract_features.py Fri May 22 04:51:46 2015 -0400 +++ b/extract_features.py Fri May 10 08:25:57 2019 -0400 @@ -1,10 +1,10 @@ #!/usr/bin/env python -import os +import argparse import sys -import argparse import textwrap + def main( args ): """ Extract the protein and coding section from an augustus gff, gtf file @@ -45,6 +45,22 @@ if line.startswith('start gene'): gene_name = line[11:].strip() + if protein_seq: + if line.endswith(']'): + protein_seq += line[:-1] + po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) ) + protein_seq = '' + else: + protein_seq += line + + if coding_seq: + if line.endswith(']'): + coding_seq += line[:-1] + co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) ) + coding_seq = '' + else: + coding_seq += line + if args.protein and line.startswith('protein sequence = ['): if line.endswith(']'): protein_seq = line[20:-1] @@ -63,26 +79,12 @@ line = line[19:] coding_seq = line - if protein_seq: - if line.endswith(']'): - protein_seq += line[:-1] - po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) ) - protein_seq = '' - else: - protein_seq += line - - if coding_seq: - if line.endswith(']'): - coding_seq += line[:-1] - co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) ) - coding_seq = '' - else: - coding_seq += line if args.codingseq: co.close() if args.protein: po.close() + if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('-p', '--protein', help='Path to the protein file.') @@ -90,4 +92,3 @@ args = parser.parse_args() main( args ) -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 10 08:25:57 2019 -0400 @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">augustus</requirement> + <yield /> + </requirements> + </xml> + + <token name="@VERSION@">3.2.3</token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btg1080</citation> + <citation type="doi">10.1093/bioinformatics/btr010</citation> + <citation type="doi">10.1093/bioinformatics/btn013</citation> + </citations> + </xml> + +</macros>
--- a/readme.rst Fri May 22 04:51:46 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -Galaxy wrapper for Augustus -=========================== - -This wrapper is copyright 2012-2013 by Björn Grüning. - -This is a wrapper for the command line tool of Augustus_. - -.. _augustus: http://bioinf.uni-greifswald.de/augustus/ - -AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. - -Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011) -A novel hybrid gene prediction method employing protein multiple sequence alignments -Bioinformatics, doi: 10.1093/bioinformatics/btr010 - -Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008) -Using native and syntenically mapped cDNA alignments to improve de novo gene finding -Bioinformatics, doi: 10.1093/bioinformatics/btn013 - -Mario Stanke and Stephan Waack (2003) -Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. -Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225 - - -Installation -============ - -The recommended installation is by means of the toolshed_. -If you need to install it manually here is a short introduction. - -.. _toolshed: http://toolshed.g2.bx.psu.edu/view/bgruening/augustus - - -Install or downlaod augustus from:: - - http://bioinf.uni-greifswald.de/augustus/binaries/ - -and follow the installation instructions or copy the binaries into your $PATH. To install the wrapper copy the augustus folder in the galaxy tools folder and modify the tools_conf.xml file to make the tool available to Galaxy. - -For example:: - - <section name="Gene Prediction" id="gene_prediction"> - <tool file="gene_prediction/tools/augustus/augustus.xml" /> - </section> - - -Set the *AUGUSTUS_CONFIG_PATH* to /path_to_augustus/augustus/config with:: - - export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config - -or modify the wrapper and use the following additional commandline switch:: - - --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config - - -History -======= - -- v0.1: Initial public release -- v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson) -- v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files -- v0.3.1: added parallelism and changed the output parameters from boolean to a select box - -Licence (MIT) -============= - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot.gff3 Fri May 10 08:25:57 2019 -0400 @@ -0,0 +1,41 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0 +HS08198 maker mRNA 352 1848 2869 + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192 +HS08198 maker exon 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 421 582 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 812 894 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +### +HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0 +HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 +HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker five_prime_UTR 1813 1861 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 1862 1934 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +###
--- a/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta Fri May 22 04:51:46 2015 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta Fri May 10 08:25:57 2019 -0400 @@ -1,35 +1,33 @@ >HS04636.g1 atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca -tgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtcaa -aaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactg -ctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccact -tcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatca -catttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatta -tactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattcaa -atgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattcttt -gcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggt -ggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatc -agataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag -catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggga -acacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa -tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaattt -gacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggca -tccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattgc -tggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcca -cccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgcaa -acgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactct -atggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaacc -atggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaag -cacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggct -gtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgga -ctagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag +aaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaact +gctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccac +ttcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatc +acatttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatt +atactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattca +aatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctt +tgcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatgggg +tggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatat +cagataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctga +gcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggg +aacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggcta +atactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatt +tgacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggc +atccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattg +ctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcc +acccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgca +aacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactc +tatggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaac +catggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaa +gcacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggc +tgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgg +actagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag >HS08198.g2 -atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca -tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc -cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc -caccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcagg -tgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtg -gttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacgc -ccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccaga -tcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggca -agcatggcggcgtggtga +atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacg +ccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgagg +ccaccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcag +gtgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgt +ggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacg +cccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccag +atcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggc +aagcatggcggcgtggtga
--- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri May 22 04:51:46 2015 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri May 10 08:25:57 2019 -0400 @@ -1,6 +1,6 @@ -# This output was generated with AUGUSTUS (version 3.1.0). -# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de), -# Oliver Keller, Stefanie König and Lizzy Gerischer. +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
--- a/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta Fri May 22 04:51:46 2015 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta Fri May 10 08:25:57 2019 -0400 @@ -1,15 +1,13 @@ >HS04636.g1 -MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILML -ARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFK -GFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNE -IVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQI -IDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLIL -IGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLE -HGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYG -DIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCP -FTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL +MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTH +FKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDS +NEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY +QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRL +ILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSIL +LEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL +YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKG +CPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL >HS08198.g2 -MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICML -PPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVR -QLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIF -YFPKYGFCEAADQFHVLDGECTAGASMAAW +MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQ +VRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQ +IFYFPKYGFCEAADQFHVLDGECTAGASMAAW
--- a/test-data/human_augustus_utr-on.gff Fri May 22 04:51:46 2015 -0400 +++ b/test-data/human_augustus_utr-on.gff Fri May 10 08:25:57 2019 -0400 @@ -1,7 +1,7 @@ ##gff-version 3 -# This output was generated with AUGUSTUS (version 3.1.0). -# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de), -# Oliver Keller, Stefanie König and Lizzy Gerischer. +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
--- a/test-data/human_augustus_utr-on.gtf Fri May 22 04:51:46 2015 -0400 +++ b/test-data/human_augustus_utr-on.gtf Fri May 10 08:25:57 2019 -0400 @@ -1,6 +1,6 @@ -# This output was generated with AUGUSTUS (version 3.1.0). -# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de), -# Oliver Keller, Stefanie König and Lizzy Gerischer. +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
--- a/tool_dependencies.xml Fri May 22 04:51:46 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="augustus" version="3.1"> - <repository changeset_revision="820bf3789c44" name="package_augustus_3_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>