reference as input or parameter about q2-fragment-insertion HOT 3 CLOSED

Sounds good. Unsure about optional inputs but I think not. What about instead of optional inputs, a method for establishing a reference which uses the types you propose, and a method which can take a reference that has been established?

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Greg says that optional inputs are possible:

gregcaporaso: @Stefan, yes - see the phylogeny input here: https://github.com/qiime2/q2-diversity/blob/master/q2_diversity/_alpha/_visualizer.py#L266

I am building that in at the moment. I think that is easier than coming up with a new Semantic type of a "Reference"

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Now implemented as optional inputs in PR #7

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