I do not teach courses (I am a Canvas administrator for our school), but I believe it was @kona who gave me some information similar to what @KristinL posted above:
I have two assignments that my students can pick from, but I'll only be grading one of the assignments. How do I set this up in Canvas?
Create two assignments in your course like normal []. You can place these two assignments in their own Assignment Group (How do I add an assignment group in a course?), but you don't have to. When it comes time to grade either of the submitted assignments, don't put a grade in for the assignment that the students didn't do. As long as the grade is left blank (no zero) then it doesn't count against the student. ANY assignment that is left blank for the grade (no zero or other score entered in) will NOT be counted against the student. This is why it is so important to put zeros in for assignments that the students should have submitted, but didn't. If you don't put the zero in, then the assignment doesn't count against the student, and their grade looks much higher than it really is.
As an alternate solution, instead of leaving the grade blank, you can use EX (excused). This way, both you and your student know for sure that the grade is excused and shouldn't be marked as a zero. Review How do I excuse an assignment for a student in the Gradebook? for additional information.
I hope this will help, Leland.
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