I would like to use the token service to generate a token for the user logged in on Windows, so I can use this token in my webapplication. How do I do this?

You can use the FME Server REST API to request a token, either directly or through the FMEServer javascript library. Some starting points:

• http://playground.fmeserver.com/javascript/authorization/request-a-token/
• https://docs.safe.com/fme/2016.1/html/FME_Server_Documentation/Content/ReferenceManual/service_token.htm

@david_r I know those pages, but I don't want to pass the user-id and password in the URL. That's a security issue. I also don't want the user to supply his username or password. I want to use Single-Sign-On to request a token, so the user doesn't have to enter his credentials anywhere.

We have FME Server configured for Single-Sign-On, so a user is automatically authenticated with his Windows credentials. The interface of FME server is not user friendly enough for non technical persons, so we want to integrate a webpage into our intranet where a user can run workspaces.