Hi rennif,
ftp file transfer will be FROM the FTP server for encryption purpose, and it will not automate the file transfer TO the FTP site post encryption.
As per my understanding, PGP Command Line does not currently provide any file transfer built in. You could write your own script to take an input file, encrypt it with PGP Command Line, and send it to the recipient.
OR,
For FTP automation you can use file transfer software like CuteFTP and write some VBScript.