You can either change the values in your Doxyfile
or invoke doxygen with extra parameters as described in the manual in the paragraph Can I configure doxygen from the command line?:
Can I configure doxygen from the command line?
Not via command line options, but doxygen can read from stdin, so you
can pipe things through it. Here's an example how to override an
option in a configuration file from the command line (assuming a UNIX
like environment):
( cat Doxyfile ; echo "PROJECT_NUMBER=1.0" ) | doxygen -
For Windows the following would do the same:
( type Doxyfile & echo PROJECT_NUMBER=1.0 ) | doxygen.exe -
If multiple options with the same name are specified then doxygen will
use the last one. To append to an existing option you can use the +=
operator.