Yes provided you have Data Interoperability extension licensed on the server, and on your desktop (authoring) machine - which is hopefully Pro. The canonical way is to embed your fmw source in your ETL tool, run it and publish the history item. The workflows are a little different depending on whether there is a portal present, but its the same as any web tool in either case. You must take care with parameters, they have to be supported by geoprocessing or cast to ones that are using Python snippets in a Model you wrap your ETL tool in. To be clear you don't have to use a Model, only when an input or output needs to be cast. Email bharold@esri.com if you need more tips.
