Mercurial > repos > bjoern-gruening > augustus
diff augustus.xml @ 5:a4fab0c1ae1a
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author | bjoern-gruening |
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date | Sun, 09 Jun 2013 07:54:25 -0400 |
parents | 796814f16b12 |
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--- a/augustus.xml Tue Oct 30 06:29:50 2012 -0400 +++ b/augustus.xml Sun Jun 09 07:54:25 2013 -0400 @@ -1,40 +1,48 @@ -<tool id="augustus" name="Augustus" version="0.2"> - <description>gene prediction for eukaryotic genomes</description> +<tool id="augustus" name="Augustus" version="0.3"> + <description>gene prediction for eukaryotic genomes</description> <requirements> - <requirement type="package" version="2.6.1">augustus</requirement> + <requirement type="package" version="2.7">augustus</requirement> + <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement> </requirements> - <command>augustus - --strand=$strand - $noInFrameStop - $gff - $protein - $introns - $start - $stop - $cds - $codingseq - $singlestrand - $input_genome - --genemodel=$genemodel - --species=$organism - --outfile=$output + <command> + ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config + ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed + ## 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 - #please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config - #or use the --AUGUSTUS_CONFIG_PATH=path switch - + augustus + --strand=$strand + $noInFrameStop + $gff + $protein + $introns + $start + $stop + $cds + $codingseq + $singlestrand + $input_genome + $mea + $utr + --genemodel=$genemodel + --species=$organism + ##--outfile=$output + | tee $output + #if $protein or $codingseq: + | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py + #if $protein: + --protein $protein_output + #end if + #if $codingseq: + --codingseq $codingseq_output + #end if + #end if </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" /> + <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 (--noInFrameStop)" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" help="Otherwise, intron-spanning stop codons could occur" /> + <param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands (--singlestrand)" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> + <param name="mea" type="boolean" label="Using the maximum expected accuracy approach (--mea)" truevalue="--mea=1" falsevalue="" checked="false" help="MEA is an alternative decoding approach." /> + <param name="utr" type="boolean" label="Predict the untranslated regions in addition to the coding sequence (--UTR)" truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" 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> @@ -42,7 +50,7 @@ <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="tribolium2012">Tribolium castaneum</option> <option value="schistosoma">Schistosoma mansoni</option> <option value="tetrahymena">Tetrahymena thermophila</option> <option value="galdieria">Galdieria sulphuraria</option> @@ -88,10 +96,14 @@ <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="tomato">Solanum lycopersicum</option> <option value="chlamydomonas">Chlamydomonas reinhardtii</option> - <option value="amphimedon ">Amphimedon queenslandica</option> - <option value="pneumocystis ">Pneumocystis jirovecii</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> </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."> @@ -106,16 +118,64 @@ <option value="intronless">intronless</option> <option value="atleastone">atleastone</option> <option value="exactlyone">exactlyone</option> + <option value="bacterium">bacterium (beta version)</option> </param> - </inputs> - <outputs> + <param name="protein" type="boolean" label="Output predicted protein sequences (--protein)" truevalue="--protein=on" falsevalue="--protein=off" checked="true" /> + <param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file (codingseq)" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="true" /> + <param name="introns" type="boolean" label="Output predicted intron sequences (--introns)" truevalue="--introns=on" falsevalue="--introns=off" checked="false" /> + <param name="start" type="boolean" label="Output predicted start codons (--start)" truevalue="--start=on" falsevalue="--start=off" checked="false" /> + <param name="stop" type="boolean" label="Output predicted stop codons (--stop)" truevalue="--stop=on" falsevalue="--stop=off" checked="false" /> + <param name="cds" type="boolean" label="Output CDS region (--cds)" truevalue="--cds=on" falsevalue="--cds=off" checked="true" /> + <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> + + </inputs> + <outputs> <data format="gtf" name="output"> <change_format> <when input="gff" value="--gff3=on" format="gff" /> </change_format> </data> + <data format="fasta" name="protein_output"> + <filter>protein == True</filter> + </data> + <data format="fasta" name="codingseq_output"> + <filter>codingseq == True</filter> + </data> </outputs> + <tests> + <test> + <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> + <param name="organism" value="human" /> + <param name="utr" value="--UTR=on" /> + <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/> + </test> + <test> + <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> + <param name="organism" value="human" /> + <param name="utr" value="--UTR=on" /> + <param name="gff" value="--gff3=on" /> + <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/> + </test> + <test> + <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" /> + <param name="organism" value="arabidopsis" /> + <param name="singlestrand" value="--singlestrand=true" /> + <param name="mea" value="--mea=1" /> + <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/> + </test> + <test> + <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> + <param name="organism" value="human" /> + <param name="protein" value="--protein=on" /> + <param name="codingseq" value="--codingseq=on" /> + <param name="introns" value="--introns=on" /> + <param name="cds" value="--cds=on" /> + <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/> + <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" /> + <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" /> + </test> + </tests> <help> **What it does** @@ -125,7 +185,7 @@ 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** @@ -182,5 +242,5 @@ Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225 - </help> + </help> </tool>