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Use these commands in your script:
...
setvar 0x8004 0x0 //0x0 is for the 1st pokemon in the party, 0x1 is for the 2nd pokemon...
callasm 0x8?????? //offset of the decrypt routine (replace the ? by a free space offset)
setvar 0x8005 0xF //0xf is the maximum duration of the virus (4 days I think...)
callasm 0x8?????? //offset of the give_pokerus routine
callasm 0x8?????? //offset of the encrypt routine
...
Now, you put the machine code of the routines at the offsets you choose: