<tool id="snpSift_int" name="SnpSift Intervals" version="3.2">
	<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="3.2">snpEff</requirement>
	</requirements>
	<command>
		java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $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)"/>
		<param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 
                       help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
	</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>
        <tests>

            <test>
                <param name="input" ftype="vcf" value="annotate_5.vcf"/>
                <param name="bedFile" ftype="bed" value="interval.bed"/>
                <param name="exclude" value="False"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="872687" />
                        <not_has_text text="1195966" />
                    </assert_contents>
                </output>
            </test>

            <test>
                <param name="input" ftype="vcf" value="annotate_5.vcf"/>
                <param name="bedFile" ftype="bed" value="interval.bed"/>
                <param name="exclude" value="True"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="1195966" />
                        <not_has_text text="872687" />
                    </assert_contents>
                </output>
            </test>

        </tests>

	<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>