Ok. In Perl, the command line arguments are passed into the program as a pre-declared array, @ARGV.
So your filename.pl program might have something like this:

my ($file1,$file2,$col1fromfile1, $col2fromfile2) = @ARGV;
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Of course as with any user input, your program should check that the files can be opened and the 2 columns "make sense".

Write a simple program that gets 4 command line arguments and prints them. Let us know how it goes.