Mercurial > repos > dereeper > sniplay3
view snpEff/snpEff.xml @ 23:a1ab979f4551 draft
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author | dereeper |
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date | Mon, 23 Mar 2015 05:52:17 -0400 |
parents | 13cff72ec2d3 |
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<tool id="snpEff" name="SnpEff" version="4.0"> <description>predicts SNP effect from a genomic VCF file</description> <requirements> <requirement type="package" version="4.0">snpEff</requirement> </requirements> <!-- You will need to change the path to wherever your installation is. You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <command interpreter="bash">./snpEff-pipe.sh $vcf $genome $gff $output $statsFile $log</command> <inputs> <param format="vcf" name="vcf" type="data" label="VCF input file" help="Positions must be genomic positions"/> <param format="fasta" name="genome" type="data" label="Reference genome in Fasta" help=""/> <param format="gff3" name="gff" type="data" label="GFF annotation of the genome" help=""/> </inputs> <outputs> <data format="vcf" name="output" label="Annotated VCF" /> <data format="html" name="statsFile" label="HTML statistics output"/> <data format="txt" name="log" label="Log file"/> </outputs> <help> .. class:: infomark **Program encapsulated in Galaxy by Southgreen** .. class:: infomark **SnpEff version 4.0** ----- ============== Please cite: ============== "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", **Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.**, Fly (Austin). 2012 Apr-Jun;6(2):80-92. ----- =========== Overview: =========== Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). ----- For further informations, please visite the SnpEff_ website. .. _SnpEff: http://snpeff.sourceforge.net/ </help> </tool>