<!--
  ~ 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="cufflinks"
            id="org.broad.igv.plugin.cufflinks">
    <tool name="cufflinks" defaultPath="cufflinks" visible="false">
        <command name="cufflinks" cmd="--quiet">
            <arg name="Output Dir" id="outdir" cmd_arg="-o" type="LONGTEXT" defaultValue="./"/>
            <arg name="Max Intron Length" cmd_arg="--max-intron-length" type="TEXT" defaultValue="300000"/>
            <arg name="Min Isoform Fraction" cmd_arg="--min-isoform-fraction" type="TEXT" defaultValue="0.00001"/>
            <arg name="Pre mRNA Fraction" cmd_arg="--pre-mrna-fraction" defaultValue="0.15" type="TEXT"/>
            <arg name="Perform Quartile Normalization" cmd_arg="--upper-quartile-norm" defaultValue="false" type="BOOL"/>
            <arg name="Use multi-read correct" cmd_arg="--multi-read-correct" defaultValue="false" type="BOOL"/>
            <arg name="Other arguments" cmd_arg="" type="LONGTEXT" defaultValue=""/>
            <arg name="Track" cmd_arg="" type="ALIGNMENT_TRACK"/>
            <output name="Transcripts Track" defaultValue="Transcripts">
                <parser source="$outdir/transcripts.gtf" decodingCodec="org.broad.igv.cli_plugin.CufflinksTranscriptDecoder"/>
            </output>
            <output name="Gene FPKM Track" type="DataSourceTrack" defaultValue="Gene FPKM">
                <parser source="$outdir/genes.fpkm_tracking" decodingCodec="org.broad.igv.data.cufflinks.FPKMTrackingSampleCodec"/>
            </output>
        </command>

    </tool>
</cli_plugin>