The suggested configure_file is probably the easiest solution. However, it will not rerun the copy command to if you manually deleted the file from the build directory. To also handle this case, the following works for me:
add_custom_target(copy-test-makefile ALL DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/input.txt)
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/input.txt
COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/input.txt
${CMAKE_CURRENT_BINARY_DIR}/input.txt
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/input.txt)