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planemo upload for repository https://github.com/refinery-platform/package_qualimap_2_2 commit eeb90d937d8ed1acb8b5dc4eae0d5a88a7a63951-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="qualimap" version="2.2">
        <install version="1.0">
            <actions_group>
                <actions>
                    <action type="download_by_url">https://depot.galaxyproject.org/software/qualimap/qualimap_2.2_src_all.zip</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
             <![CDATA[
                Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI)
                and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

                Supported types of experiments include:
                Whole-genome sequencing
                Whole-exome sequencing
                RNA-seq (speical mode available)
                ChIP-seq
                http://qualimap.bioinfo.cipf.es
            ]]>
        </readme>
    </package>
</tool_dependency>