<?xml version="1.0"?>
<tool_dependency>
    <package name="tophat2" version="2.0.14">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-2.0.14.Linux_x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://tophat.cbcb.umd.edu/downloads/tophat-2.0.14.tar.gz</action>
                    <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                    <action type="make_install" />
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme />
    </package>
</tool_dependency>
<?xml version="1.0"?>
<tool_dependency>
    <package name="tophat" version="2.0.14">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-2.0.14.Linux_x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://tophat.cbcb.umd.edu/downloads/tophat-2.0.14.tar.gz</action>
                    <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                    <action type="make_install" />
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme />
    </package>
</tool_dependency>

Update package name for TopHat.
Update package name for TopHat.