--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_download.xml	Wed Nov 27 09:11:32 2013 -0600
@@ -0,0 +1,34 @@
+<tool id="snpEff_download" name="SnpEff Download" version="3.4">
+    <description>Download a new database</description>
+    <requirements>
+        <requirement type="package" version="3.4">snpEff</requirement>
+    </requirements>
+    <command>
+    echo $genomeVersion > $snpeff_db; 
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile 
+    </command>
+    <inputs>
+        <param name="genomeVersion" type="select" label="Genome Version">
+            <options from_data_table="snpeff_databases"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="logfile" />
+        <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" />
+    </outputs>
+    <stdio>
+        <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal"   description="Error" />
+     </stdio>
+    <help>
+
+This tool downloads a SnpEff database into the users history for use by snpEff.
+
+For details about this tool, please go to http://snpEff.sourceforge.net
+
+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. PMID: 22728672 [PubMed - in process]
+
+    </help>
+</tool>
+