When your XML project requires to run an external tool different than a FO processor and which can be launched from the command line <oXygen/> offers you the option of integrating the tool by specifying just the command line for starting the executable file of the tool and its working directory. To integrate such a tool go to Options → Preferences+External Tools

If the external tool is applied on one of the files opened in <oXygen/> you should enable the option for saving all edited files automatically when an external tool is applied.

External tools can be launched from the External tools toolbar or from the submenu Tools → External tools. While the action is running its icon is a stop icon: . When the tool has finished running it will change the icon back to the original run icon: . Please note that even though you can stop the external tool by invoking the action again while it is running, that doesn't mean you can also stop the processes spawned by that external tool. This is especially a limiting factor when running a batch file as the batch will be stopped but without actually stopping the processes that the batch was running at the time.