Coerce input data into phyloseq-class objects

[tfaits]

We want to let users submit a range of data formats to PathoStat, but we want all of the processing, analyses, and outputs to be of a standard format. If we can coerce input data types (PathoScope reports, .biom files, Qiime output, etc) into phyloseq objects, it will make everything easier to work with. This carries the added advantage of compatibility with a bunch of outside packages/tools.