rule copy_multiple_files:
    """
    Rule to copy all necessary file in a directory.
    """
    input:
        file_list = __copy_multiple_files__input
    output:
        directory = __copy_multiple_files__output,
        done = __copy_multiple_files__done
    shell:
        """
        for fl in {input.file_list}
        do
            cp $fl {output.directory}
        done
        touch {output.done}
        """
