Underneath the argument boxes, you can modify the tool behavior.
Use output window - if this box is checked, the tool will output processing information to the Atmel Studio output window, otherwise, the output will be suppressed.
Close on exit - if the box is checked the tool window, if any, will be automatically closed after completing all operations.
Prompt for arguments - used for toolchain automation. If the box is checked, the external tool will require user intervention to input additional processing parameters, otherwise, the tool will be silent.
Treat output as Unicode - internationalization option. Some tools have a capacity to output Unicode results for better interpretation. This option allows for correct output rendering if you are using such a tool.