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  ~ The MIT License (MIT)
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  ~ Copyright (c) 2007-2015 Broad Institute
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  ~ Permission is hereby granted, free of charge, to any person obtaining a copy
  ~ of this software and associated documentation files (the "Software"), to deal
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<!DOCTYPE cli_plugin SYSTEM "cli_plugin.dtd">
<cli_plugin api_version="alpha" plugin_version="0.1" name="snpEff"
            id="org.broad.igv.plugin.snpeff">
    <tool name="snpEff" defaultPath="snpEff.jar" visible="false"
          helpUrl="http://snpeff.sourceforge.net/SnpEff_manual.html" toolUrl="http://snpeff.sourceforge.net">

        <msg>java</msg>
        <msg>-jar</msg>
        <msg>-Xmx2g</msg>

        <command name="Effects" cmd="eff">
            <arg name="Config file path" type="TEXT" cmd_arg="-c" defaultValue="$toolDir/snpEff.config" visible="true"/>
            <arg name="No statistics" type="BOOL" cmd_arg="-noStats" defaultValue="false" visible="false"/>
            <arg name="Genome Version" type="TEXT" defaultValue="hg19"/>
            <arg name="Track" id="track" type="VARIANT_TRACK"/>
            <output name="Variants Track" defaultValue="Variants" type="VariantTrack">
                <parser source="stdout" format="vcf"/>
            </output>
        </command>

    </tool>
</cli_plugin>