You can use either webMethods Broker (formerly Enterprise, formerly ActiveWorks, formerly ActiveWeb, and probably formerly something else before that) with the I/O adapter or webMethods Integration Server, optionally with the EDI Adapter.
The I/O adapter with the Broker will pick up files from a directory automatically. It has all manner of parsing facilities for processing delimited records, fixed-length records and such.
The Integration Server (IS) can be used to process files in a variety of ways. Since it is an HTTP server and an FTP server, you can use either of those protocols to push the file to the server. Or you can drop the file in a directory and configure IS to pick it up from there. Depending on the complexity of the file and the processing you need to do, you may be able to use a combination of built-in services and your own custom Flow or Java services to process the file. You can also use the EDI adapter, which can be configured to process custom file formats.
Which approach you choose depends on a number of factors, including but not limited to: what you need to do with the data after you get it into one of the server environments; your comfort level with Broker and IS; connectivity options from the mainframe; interaction with external entities.