how do you cut a tube?

Why cut the sonotube at an angle?  If I remember your project correctly you are putting a straight piece of sonotube into a wedge enclosure, right?  Just make the wedge, cut the opening the correct diameter and insert the tube.  Something like this:

You will have to cut an ellipse into the angled side.  Calculate the diameter of the ellipse by measuring the angle of the plane you are cutting into in relation to the desired angle of the cylinder (the Sonotube.)  This becomes the hypotenuse of the resulting triangle created by the intersection of the two shapes.  Then it is a simple geometry calculation to determine the length of the long side of the resulting right triangle (Z): the diameter of the sonotube is one side (X,) the depth of insertion is another (Y.)  The formula which you may remember from 8th grade geometry is the Pythagorean Theorem, Zsquared = Xsquared + Ysquared.  Here's a reference.  Once you know the length of the long side, this becomes the long axis of the ellipse.  The diameter of the Sonotube is the short axis of the ellipse.  The formula for calculating the diameter of the ellipse is PI X Square-Root of 2 X ((1/2 long axis)squared + (1/2 short axis)squared).   Here's a handy-dandy calculator for you.

Me, I hate Sonotubes and wouldn't build the enclosure that way at all.  There must be easier ways to skin that cat. 

If I were trying to do this, and being able (using DYohn's info) to figure out the short and long sides of the ellipse, I would still find it difficult to draw the correct arcs between each of the four points.  Since we are talking about a wood enclosure, a miscut ruins the project.

So what I would try is to construct a cardboard replica of the wedge box.  Then, "walk" the tube into the angled side, snipping away the cardboard as you walk it in.  The pressure of the tube will cause a slight dimple in the cardboard as you work it slowly in, and so it's a process of snugging the razor blade along the tube wall and cutting the cardboard along the pressure points.  Eventually you will have it walked all the way through.

When the tube is inserted where you want it, double check the angle of the tube in relation to the bottom of the box (right angle?).  Use tape to smooth the cutout in the cardboard so that you can reinsert the tube and see no air gaps.

The face of the cardboard replica box will serve as the template for your cutout.

One thing of note:  the thickness of the MDF will inhibit the tube from proper insertion, since the wood would be cut perpendicular to its surface (which is angled in relation to the tube).  You will have to back cut the lower half of the ellipse, which can be a time-consuming endeavor.  Sort of shaving the hole out from the backside but being careful not to cut all the way to the surface.  A coping saw might be the tool to use for this.

Length 1  +  Length 2    =   X      X divided by 2 = the length in which you use as the length of the cylinder.