Normally, for shell scripts, the way to do it is to pass args like you would for a normal shell command, like this:
./scriptnamehere arg1 arg2 arg3
etc.
Inside php, you get two vars for handling command line arguments, just like in C, $argc tells you how many args you got, and $argv[x] gives you the xth argument. The above command line would result in $argc=4 and $argv[0]=./scriptname, $argv[1]=arg1, $argv[2]=arg2 and $argv[3]=$arg3