Mercurial > repos > jjohnson > augustus_dep
changeset 0:807dc2efb781 draft
Uploaded
| author | jjohnson |
|---|---|
| date | Mon, 22 Oct 2012 13:25:19 -0400 |
| parents | |
| children | b7e800db2632 |
| files | augustus.xml readme.txt tool_conf.xml tool_dependencies.xml |
| diffstat | 4 files changed, 289 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augustus.xml Mon Oct 22 13:25:19 2012 -0400 @@ -0,0 +1,186 @@ +<tool id="augustus" name="Augustus" version="0.2"> + <description>gene prediction for eukaryotic genomes</description> + <requirements> + <requirement type="package" version="2.2.5">augustus</requirement> + </requirements> + <command>augustus + --strand=$strand + $noInFrameStop + $gff + $protein + $introns + $start + $stop + $cds + $codingseq + $singlestrand + $input_genome + --genemodel=$genemodel + --species=$organism + --outfile=$output + + #please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config + #or use the --AUGUSTUS_CONFIG_PATH=path switch + + </command> + <inputs> + <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> + <param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" /> + <param name="gff" type="boolean" label="GFF formated output, standard is GTF" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> + <param name="protein" type="boolean" label="Output predicted protein sequences" truevalue="--protein=on" falsevalue="--protein=off" checked="false" /> + <param name="introns" type="boolean" label="Output predicted intron sequences" truevalue="--introns=on" falsevalue="--introns=off" checked="false" /> + <param name="start" type="boolean" label="Output predicted start codons" truevalue="--start=on" falsevalue="--start=off" checked="false" /> + <param name="stop" type="boolean" label="Output predicted stop codons" truevalue="--stop=on" falsevalue="--stop=off" checked="false" /> + <param name="cds" type="boolean" label="Output CDS region" truevalue="--cds=on" falsevalue="--cds=off" checked="true" /> + <param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="false" /> + + <param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> + + <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="tribolium">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="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> + </param> + + <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand."> + <option value="both">both</option> + <option value="forward">forward</option> + <option value="backward">backward</option> + </param> + + <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" 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> + <option value="atleastone">atleastone</option> + <option value="exactlyone">exactlyone</option> + </param> + + </inputs> + <outputs> + <data format="gtf" name="output"> + <change_format> + <when input="gff" value="--gff3=on" format="gff" /> + </change_format> + </data> + </outputs> + <help> + +**What it does** + +AUGUSTUS is a gene prediction program for 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. + +----- + +**Parameters** + +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 + + + +**Example** + +Suppose you have the following DNA formatted sequences:: + + >Seq1 + cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg + ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag + cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc + cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc + ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg + +Running this tool will produce this:: + + # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) ----- + # + # Constraints/Hints: + # (none) + # Predicted genes for sequence number 1 on both strands + # start gene g1 + scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6 + scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1 + scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6"; + + +**References** + +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 + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.txt Mon Oct 22 13:25:19 2012 -0400 @@ -0,0 +1,78 @@ +Galaxy wrapper for Augustus +===================================== + +This wrapper is copyright 2012 by Björn Grüning. + +This is a wrapper for the command line tool of 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 +============ + +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 + + +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_conf.xml Mon Oct 22 13:25:19 2012 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<toolbox> + <section name="Gene Prediction" id="gene_prediction"> + <tool file="gene_prediction/tools/augustus/augustus.xml" /> + </section> +</toolbox>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Oct 22 13:25:19 2012 -0400 @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="augustus" version="2.5.5"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz</action> + <action type="shell_command">make</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable> + </action> + </actions> + </install> + <readme>http://augustus.gobics.de/binaries/README.TXT</readme> + </package> +</tool_dependency> +