The most basic Nikto scan requires simply a host to target, since port 80 is assumed if none is specified. The host can either be an IP or a hostname of a machine, and is specified using the -h (-host) option. This will scan the IP 192.168.0.1 on TCP port 80:
perl nikto.pl -h 192.168.0.1
To check on a different port, specify the port number with the -p (-port) option. This will scan the IP 192.168.0.1 on TCP port 443:
perl nikto.pl -h 192.168.0.1 -p 443
Hosts, ports and protocols may also be specified by using a full URL syntax, and it will be scanned:
perl nikto.pl -h https://192.168.0.1:443/
There is no need to specify that port 443 may be SSL, as Nikto will first test regular HTTP and if that fails, HTTPS. If you are sure it is an SSL server, specifying -s (-ssl) will speed up the test.
perl nikto.pl -h 192.168.0.1 -p 443 -ssl