If you can run a MapInfo script from the command line (and this page and this page tell me that you can) then you should be able to use the SystemCaller transformer in FME to do this.

Alternatively, you could use a shutdown script (see Navigator Window > Workspace Parameters > Advanced) to run such a command.

It depends on whether you need the workspace to finish before the script is executed. If you do, then use a shutdown script. If not, use a SystemCaller transformer.

Hope this helps

Mark

Thank you very much for your response. I'll give it a go and let you know how I get on.