rename the qiita object names

[antgonza]

Currently, the names of the Qiita file objects are confusing cause the objects are upper case and the files are lower case but it's not clear in the name that they are different. A more specific example: the Qiita object BIOM can contain a biom and a preprocessed_fasta.

This is not a fast change but neither difficult.

cc - @wasade