IS 6.5 provides native support for FTP over SSL. You can create FTPS port on IS 6.5, using Administrator. If upgrade is not an option then the services could be used to either send encrypted files over ftp or do the pgp encryption and transport using IS/TN. Also if your client is still concerned about security due to the intrinsic problems in the FTP protocol, I recommends using a VPN to protect FTP traffic. VPNs are interoperable (thanks to IPsec), and can be configured to provide protection for both the data and control streams.
#webMethods#Integration-Server-and-ESB#webmethods-Protocol-and-Transport