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These are sort of an error in the workflow definition but we don't have a means to competently display this information to the user via the UI so I think we need to just allow this to happen. I've attached a test case that exhibits this behavior and passes under 17.09 but fails under the current dev branch without these fixes. This was broken in https://github.com/galaxyproject/galaxy/commit/d5f98f49045bca351e982f17cac9386308089eeb when we started to actually persist pointers to workflow invocation outputs (as part of https://github.com/galaxyproject/galaxy/pull/5013).