diff snpSift_annotate.xml @ 0:388f178f9e13

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_annotate.xml	Thu Sep 13 22:33:33 2012 -0400
@@ -0,0 +1,31 @@
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="1.0">
+	<description>Annotate SNPs from dbSnp</description>
+	<!-- 
+	    You will need to change the path to wherever your installation is.
+		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
+	-->
+	<requirements>
+		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
+	</requirements>
+	<command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
+	<inputs>
+		<param format="vcf" name="input" type="data" label="VCF input"/>
+		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
+	</inputs>
+        <stdio>
+          <exit_code range="-1"  level="fatal"   description="Error: Cannot open file" />
+        </stdio>
+
+	<outputs>
+		<data format="vcf" name="output" />
+	</outputs>
+
+	<help>
+
+This is typically used to annotate IDs from dbSnp.
+
+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
+
+	</help>
+</tool>
+