Decide whether to go by train or by plane.

Literal

Train [by-で] go [question-のか] plane [by-で] go [question-のか] decide [imperative].

The pattern ~のか~のか ('whether X or Y') forms an alternative question. The のか on each side feels slightly more explanatory and deliberative than plain か. 決めなさい is the ~なさい polite imperative, often used by teachers or parents to children — softer than the bare imperative, but still directive.