Manipulating files on a server behind firewall

Short version: Is it possible to pick up a file, convert it, and put it in another folder on a server that's behind a firewall without the use of an FTP?

I need to convert X12 EDI files into a Flat File format.  The file will be sent to a Samba share which I need to pick up with Celigo, convert into a flat file format, and then place elsewhere on our internal servers.

So far, I've tried using an agent but I can't figure out how to put it into a flow. According to the instructions I have to make a connection that is an On-Premise connection, but I don't have the option to change the mode from Cloud to On-premise. 

Any and all suggestions are appreciated.

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