Usage: biom convert [OPTIONS]:

Convert to/from the BIOM table format.

Convert between BIOM table formats. See examples here: http://biom-format.org/documentation/biom_conversion.html

Example usage:

Convert a "classic" BIOM file (tab-separated text) to an HDF5 BIOM formatted OTU table:

$ biom convert -i table.txt -o table.biom --to-hdf5

Options:

-i, --input-fp PATH
	The input BIOM table [required]
-o, --output-fp PATH
	The output BIOM table [required]
-m, --sample-metadata-fp PATH
	The sample metadata mapping file (will add sample metadata to the input BIOM table, if provided).
--observation-metadata-fp PATH
	The observation metadata mapping file (will add observation metadata to the input BIOM table, if provided).
--to-json	Output as JSON-formatted table.
--to-hdf5	Output as HDF5-formatted table.
--to-tsv	Output as TSV-formatted (classic) table. table is a BIOM table with collapsed samples, this will update the sample metadata of the table to the supported HDF5 collapsed format.
--collapsed-observations
	If --to_hdf5 is passed and the original table is a BIOM table with collapsed observations, this will update the supported HDF5 collapsed format.
--header-key TEXT
	The observation metadata to include from the input BIOM table file when creating a tsv table file. By default no observation metadata will be included.
--output-metadata-id TEXT
	The name to be given to the observation metadata column when creating a tsv table file if the column should be renamed.
--table-type	OTU table,Pathway table,Function table,Ortholog table,Gene table,Metabolite table,Taxon table,Table The type of the table.
--process-obs-metadata
	taxonomy,naive,sc_separated Process metadata associated with observations when converting from a classic table.
--tsv-metadata-formatter
	naive,sc_separated Method for formatting the observation
--help	Show this message and exit.