You are in luck. What you want to do can be done very easily the built-in capabilities of Integration Server and Developer.
The Developer has a wizard to generate a Flow service that will receive an XML file and convert it to a document type. Click on the folder where you want the service to exist, hit Ctrl-N, choose “Receive An XML Document” and then follow the prompts to specify what source to use to describe the structure of the XML document to expect to receive (schema, DTD, etc.).
After processing the XML document using Flow, populate a response document type created from the schema (or sample XML) that describes what you want to return to the sender. Convert that doc type into an xml string using pub.xml:documentToXMLString and then map that to the “string” input of the pub.flow:setResponse service. When the service completes the string (xml doc) will be returned to the sender.
Since you are new to Integration Server, be sure to work through the Developer 4.6 tutorial available on Advantage (there’s not one for 6.x, but the 4.6 one is still very useful). Also, be sure to use try-catch sequences in your Flow so that you can handle exceptions properly.
Finally, take advantage of the existing documentation found in the Developer User’s Guide and the IS Built-In Services Guide. The built-in services I mentioned above are described in detail there. You will find these essential documents in the <wm_home>/Developer/doc folder.