diff snpSift_int.xml @ 0:c07c403fc470

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_int.xml	Thu Jan 17 16:31:12 2013 -0500
@@ -0,0 +1,31 @@
+<tool id="snpSift_int" name="SnpSift Intervals" version="3.1">
+	<description>Filter variants using intervals </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="package" version="3.1">snpEff</requirement>
+	</requirements>
+	<command>
+		cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
+	</command>
+	<inputs>
+		<param format="vcf" name="input" type="data" label="VCF input"/>
+		<param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
+	</inputs>
+	<outputs>
+		<data format="vcf" name="output" />
+	</outputs>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
+	<help>
+
+You can filter using intervals (BED file)
+
+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
+
+	</help>
+</tool>