From Obama´s speech at Cairo University:
"The fifth issue that we must address together is religious freedom. Islam has a proud tradition of tolerance. We see it in the history of Andalusia and Cordoba during the Inquisition...".
1. Cordoba is a city within a region - Andalusia -. It's like talking about the History of the USA and Washington D.C. We assume that with "Andalusia" he was referring to Al-Andalus (the part of Spain under Muslim dominion) although they aren't the same thing either.
2. Andalusia - and Cordoba - weren´t under Muslim dominion "during" the Inquisition. In fact Cordoba was captured in 1236 by king Fernando III during the Spanish Reconquista, and the Spanish Inquisition started in 1478. Just a difference of a couple of centuries.
3. Let´s say that there are different opinions about that "tradition of tolerance" in Al-Andalus.
4. Al-Andalus is known for being targeted by Muslim radicals and others not so radical. They want it to be Muslim, again.