diff snpEff.xml @ 0:abde5b0387c8 draft

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+++ b/snpEff.xml	Mon Mar 23 05:17:19 2015 -0400
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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>
+