Use PKHeX https://projectpokemon.org/home/files/file/1-pkhex/
Get your save file from your cart, you need Custom Firmware or at least a way to run homebrew on your console (CFW is recommended). Check the tutorials for more details.
Once you got your save file you can import wondercards with PKHeX.
PKHeX works with original size save file (128 KB).
If you are using NO$GBA you have to manually change this line in *.ini file, then save in-game twice and restart the emulator.
SAV/SNA File Format == Raw
Follow the instructions linked by @theSLAYER
Simplocke.SAV