--- a/snpEff.xml	Mon Mar 23 05:17:19 2015 -0400
+++ b/snpEff.xml	Mon Apr 16 08:56:29 2018 -0400
@@ -1,9 +1,15 @@
-<tool id="snpEff" name="SnpEff" version="4.0">
-	<description>predicts SNP effect from a genomic VCF file</description>
+<tool id="snpEff" name="SnpEff" version="2.0.0">
+	<description>Predicts SNP effect from a genomic VCF file</description>
 	<requirements>
-		<requirement type="package" version="4.0">snpEff</requirement>
+		<requirement type="package" version="4.3.1">snpEff</requirement>
 	</requirements> 	
 
+        <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+        <stdio>
+            <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+            <exit_code range="1:" level="fatal" />
+        </stdio>
+
 	<!-- 
 	    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)
@@ -21,43 +27,56 @@
 		<data format="txt" name="log" label="Log file"/>
 	</outputs>
 
-	<help>
-
+    <tests>
+        <test>
+            <param name="vcf" value="snpeff_input.vcf"/>
+            <param name="genome" value="snpeff_in.fasta"/>
+            <param name="gff" value="snpeff_in.gff3"/>
+            <output name="output" file="snpeff_output.vcf" compare="diff" lines_diff="4"/>
+        </test>
+    </tests>
 
-
-
+    <help><![CDATA[
 
 .. class:: infomark
 
-**Program encapsulated in Galaxy by Southgreen**
+**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.
+
+.. class:: infomark
+
+**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
 
 .. class:: infomark
 
-**SnpEff version 4.0**
+**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
 
------
+---------------------------------------------------
 
-==============
- Please cite:
-==============
+======
+SnpEff
+======
 
-"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.
+-----------
+Description
+-----------
 
------
+  | 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 visit the SnpEff website_.
 
-===========
- Overview:
-===========
-
-Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
+.. _website: http://snpeff.sourceforge.net/
 
------
-
-For further informations, please visite the SnpEff_ website.
+------------
+Dependencies
+------------
+SnpEff
+        SnpEff_ 4.3.1, Conda version
 
+.. _snpeff: https://anaconda.org/bioconda/snpeff
 
-.. _SnpEff: http://snpeff.sourceforge.net/
-        </help>
-
+    ]]></help>
+    <citations>
+       <citation type="doi">10.4161/fly.19695</citation>
+    </citations>
 </tool>