Mercurial > repos > dereeper > sniplay3
diff snpEff/.svn/text-base/snpEff.xml.svn-base @ 20:13cff72ec2d3 draft
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author | dereeper |
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date | Mon, 23 Mar 2015 05:30:36 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff/.svn/text-base/snpEff.xml.svn-base Mon Mar 23 05:30:36 2015 -0400 @@ -0,0 +1,63 @@ +<tool id="snpEff" name="SnpEff" version="2.5"> + <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 2.5** + +----- + +============== + 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> +