Q: I'm trying to optionally include some code into my model. I was thinking this line would work, but it doesn't evaluate correctly. Could you please advise?

setglobal isUncertainty 1
...
$if %isUncertainty% == "1" $include ../uncertainty/input/coll10.gms

Try:

$SetGlobal isUncertainty
$if SetGlobal isUncertainty $Include sub.inc