If you want to run tests in atom, you have to install nuclide-test-runner also:
apm install nuclide-test-runner
You do not need other nuclide packages.
For best experience, you also should install language-ansi:
apm install language-ansi
The shipped ANSI highlighting of nuclide test runner has bugs.
Good catch. Let us know what about this package looks wrong to you, and we'll investigate right away.