@helenmai FS-UAE is the best Amiga emulator for Ubuntu. It's worth checking the documentation for FS-UAE:
The setup script will also install the FS-UAE Launcher which may be useful.
https://fs-uae.net/launcher
https://openretro.org/fs-uae-launcher
I have managed to launch SWOS 96-97 in FS-UAE from floppies using a shell script. I installed FS-UAE on my Linux Mint machine from the Software Center, not the RetroPie setup script so my method may require modification but I would be happy to share.
If you are unfamiliar with the Amiga hardware/emulation, then I would recommend using Amiberry on a Raspberry Pi. I found the process to be a far more straightforward.