$ micca tabletotax --help
usage: micca tabletotax [-h] -i FILE -t FILE [-o DIR]

Given an OTU table and a taxonomy file, micca tabletotax
creates in the output directory a table for each taxonomic
level (taxtable1.txt, ..., taxtableN.txt). OTU counts are
summed together if they have the same taxonomy at the
considered level.

The OTU table must be an OTU x sample, TAB-separated OTU table
file (see 'micca otu'). The taxonomy file must be a
tab-delimited file where where rows are either in the form
(see 'micca classify'):

1. SEQID[TAB]k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;
2. SEQID[TAB]Bacteria;Firmicutes;Clostridia;Clostridiales;;;
3. SEQID[TAB]Bacteria;Firmicutes;Clostridia;Clostridiales

optional arguments:
  -h, --help            show this help message and exit

  -i FILE, --input FILE
                        input OTU table file (required).
  -t FILE, --tax FILE   input taxonomy file (required).
  -o DIR, --output DIR  output directory (default .).


    micca tabletotax -i otutable.txt -t tax.txt -o taxtables