<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>