Move __parse_cli() to __main__

- I felt __parse_cli() a bit confusing as it was dependent of docopt and there wasn't such things that couldn't be done outside of the function. The script is also more readable when these few arguments are parsed at the beginning of the scipt instead of calling a procedure like function, I think.
- stdin is now checked if it's pipe or not. If not pipe then print help message.
- Some cleanings