As far as I know '-S' flag instructs the compiler to stop at the assembly step which makes the compilation a 2 step operation; 1st compile to assembly code, 2nd assembly to object file. I don't think generation of assembler code and compilation of a source file is possible in a single step operation. In that case you can use a prebuild step to generate your assembler files but be aware that they won't look like hand-written assembler. Consult your compiler documentation for the corresponding command to generate the assembler file. If I recall correctly, the command for avr-gcc should be something like:
gcc -S source.c -o source.S