This Gist shows how to integrate Doxygen HTML doc generating into your CMake project. It assumes that a file called Doxyfile.cmake exists in the project, from which it generates the final Doxyfile (which means you can embed CMake variables such as directories in Doxyfile.cmake rather than hard-coding them)

doxygen.cmake

# Use -DBUILD_DOCUMENTATION=ON to enable Doxygen at build-time
option (BUILD_DOCUMENTATION
    "Use Doxygen to create the HTML based API documentation" OFF)

# Build Doxygen HTML docs
if (BUILD_DOCUMENTATION)
    FIND_PACKAGE(Doxygen)
    if (NOT DOXYGEN_FOUND)
        message (FATAL_ERROR
        "Doxygen not found on system, cannot build documentation")
    endif ()
    configure_file (
        ${CMAKE_SOURCE_DIR}/Doxyfile.cmake
        ${CMAKE_SOURCE_DIR}/build/Doxyfile)
    add_custom_target (doxygen ALL
        COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_SOURCE_DIR}/build/Doxyfile
        WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
        SOURCES ${CMAKE_SOURCE_DIR}/build/Doxyfile
        COMMENT "Generating Doxygen HTML documentation")
endif ()