The current project I'm working on shows sample data from a spreadsheet column and asks the user which col headers to user.

Well, that wouldn't really make sense in an automated test, so I guess it's only for those people who run the tests manually in their console? In that case, you could provide some other way to pass that parameter in - just one example of many being an environment variable, and in your test script, only run that code when that environment variable is set. Another thing I like to do in my test scripts is use Test::More's diag and note appropriately, so that the output is not cluttered when running prove without -v.