qiime/qiime — pull request #782 by lkursell (2013-03-25 17:49:12+00:00)
Title: Otu category significance

otu_category_significance.py previously had the option to read in a directory of otu tables and collate the results into a single file - this option was most useful for passing in a directory of rarefied otu tables at the same depth to develop a "confidence" for the p-values you were seeing.

When the user passes in a directory of otu tables, they now have the option to write out a unique results file for every table that was in the directory.

I've created a new optional parameter called -w --collate_results, that is default False, to handle these situations. Simply pass the -w to collate the results, else an individual results file is written for every input otu table. Also, the output parameter is now required rather than optional. This is because the script now has the ability to write out more than one output results file, and coming up with a default could lead to too much confusion.

A corresponding pull request in qiime-test-data has been added for inputing a directory of otu tables and writing out an individual results file for every table.