Here’s the piece that’s causing the confusion:
Co-operation through training and workshops to strengthen Irans ability to protect against, and respond to nuclear security threats, including sabotage
The newspaper in your link highlights: “...and respond to nuclear security threats” and implies that’s what we’ve agreed to do.
That’s just a sentence fragment though. When you look at the whole sentence it says “We will help Iran, using training and workshops, learn how to respond to nuclear security threats, including sabotage...”
While that’s bad enough, the out-of-context quote is simply not the meaning of the full sentence.
Where Trump is getting this is from Frank Gaffney who is a former Deputy Assistant Secretary of Defense for Nuclear Forces and Arms Control Policy in the Reagan Administration.
Gaffney and Robert Spencer hold very similar views re: the threat of islam and if Trump is listening to them, he is getting some very good advice.
Furthermore, if Trump is listening to them, he will be changing his view of Pamela Geller.