<tool id="snpSift_int" name="SnpSift Intervals" version="3.4">
    <description>Filter variants using intervals</description>
    <!-- 
        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
    -->
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <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="Variant input file in VCF format"/>
        <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>
    <expand macro="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).

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

    </help>
</tool>