<!--
  ~ 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="GATK"
            id="org.broad.igv.plugin.gatk">
    <tool name="GATK" defaultPath="GenomeAnalysisTK.jar" visible="false"
          helpUrl="http://www.broadinstitute.org/gatk/gatkdocs/" toolUrl="http://www.broadinstitute.org/gatk/">

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

        <command name="Unified Genotyper" cmd="-T UnifiedGenotyper">
            <arg name="Reference Sequence" id="refseq" cmd_arg="-R" type="LONGTEXT" remembered="true"/>
            <arg name="Track" cmd_arg="-I" id="track" type="ALIGNMENT_TRACK"/>
            <arg name="Intervals" cmd_arg="-L" id="intervals" type="LOCUS" visible="false"/>
            <arg name="Output File" cmd_arg="-o" id="out" type="LONGTEXT" defaultValue="out.vcf"/>
            <output name="Variants Track" defaultValue="Variants">
                <parser source="$out" format="vcf"/>
            </output>
        </command>

    </tool>
</cli_plugin>