<!--
  ~ Copyright (c) 2007-2012 The Broad Institute, Inc.
  ~ SOFTWARE COPYRIGHT NOTICE
  ~ This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
  ~
  ~ This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
  ~
  ~ This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
  ~ Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
  -->
<!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>