What is already happening is that users independently run fragment insertion for several microbiome studies. If they then decide to do a meta-analysis it is not necessary to run fragment insertion on a merged biom table. Instead, to save some compute, the user could collect all his/her placement files and merge them into one, from which one unified insertion tree can be computed - as long as all individual runs used the same reference tree.
Another use case is to chunk your input to distribute it across a grid, but that is more of an edge case. (Since it is cluster specific and trivial, I don’t want to add explicit support with the plugin to chunk input and execute them)
In the end, I don’t have control over the number or names of the placement files a user wants to merge.