<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>