Yeah that makes it a lot clearer thanks. Pretty cool set up BTW. I have had a built in desk PC build on my to do list for at LEAST 10 years now...ah well one of these days.
Based on your sketch and the scale/size of the upwards facing tube I take it to mean you want an upward facing tube that is the same diameter as the main reservoir tube? If so there is not a stock part for that. If you don't require the upward facing section to be the same diameter there are at least two parts that would work. The molded coupler has 2 side facing ports that would be on the top of the reservoir facing towards the desk top, and the end caps with side facing ports also have those ports.
Is your desk top material acrylic or glass? If it is glass, do you have the ability to cut/drill openings into it? Or do you lift the top to fill / top off the reservoir? I wouldn't mind making some custom machined aluminum fill port parts for a project like this if you you can make openings in the glass.
Another option would be to run the reservoir from the far left side to the far right side and have external fill and drain ports similar to the set up in the video I posted on that subject.