You could setup a Scripted Input to run a script every hour, perform whatever FTP you need, and index the results.
Scripted inputs are kicked off by Splunk on an interval, configured in inputs.conf. Now it'd be up to you to either write or find an appropriate script to kick off on the regular basis to get you want in this case.
Alternatively if you have access to the OS running the FTP server, you could put a Splunk forwarder on the FTP server and monitor the file that with built in monitor inputs.