The IDE should be able to accept .S files (not .s - the difference is very important: .S will be preprocessed, .s won't).
Just create a new sketch, and create a new tab called whatever.S (obviously rename the whatever to whatever you want to call it.
Then in the main sketch .ino file put something like:
extern "C" void myAssemblyMain();
void setup() {
myAssemblyMain();
}
void loop() {
}
That will then call the function myAssemblyMain: in your assembly file and not much else.
(Note: I haven't tested this since I don't use the Arduino IDE).