NAME

       convert_biom - Script to convert biom formatted files

SYNOPSIS

       Detailed      usage      examples      can      be      found      here:      http://biom-
       format.org/documentation/biom_conversion.html

DESCRIPTION

       Script to convert biom formatted files.

OPTIONS

       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

              Required Options:

       -i INPUT_FP, --input_fp=INPUT_FP
              the input filepath

       -o OUTPUT_FP, --output_fp=OUTPUT_FP
              the output filepath

              Optional Options:

       -t BIOM_TYPE, --biom_type=BIOM_TYPE
              Type of biom file to write (dense or sparse) when passed a classic table  [default:
              sparse]

       -b, --biom_to_classic_table
              Convert  biom  file  to  classic table file [default: convert classic table file to
              biom file]

       --sparse_biom_to_dense_biom
              Convert sparse biom file to a dense biom file [default: convert classic table  file
              to biom file]

       --dense_biom_to_sparse_biom
              Convert  dense biom file to a sparse biom file [default: convert classic table file
              to biom file]

       -m SAMPLE_MAPPING_FP, --sample_mapping_fp=SAMPLE_MAPPING_FP
              The mapping filepath (will add sample metadata to biom file, if provided) [default:
              none]

       --observation_mapping_fp=OBSERVATION_MAPPING_FP
              The  mapping  filepath  (will  add  observation metadata to biom file, if provided)
              [default: none]

       --header_key=HEADER_KEY
              Pull this key from observation metadata within a biom file when writing  a  classic
              table [default: no observation metadata will be written]

       --output_metadata_id=OUTPUT_METADATA_ID
              Name  for  the  observation  metadata  column when writing a biom file as a classic
              table [default: same name as in biom-formatted table]

       --process_obs_metadata=PROCESS_OBS_METADATA
              Process metadata associated with observations when converting from a classic table.
              Must be one of: taxonomy, naive, sc_separated [default: naive]

       --biom_table_type=BIOM_TABLE_TYPE
              The biom table type to get converted into. Required when converting a classic table
              file to biom file.  Must be one  of:  metabolite  table,  gene  table,  otu  table,
              pathway table, function table, ortholog table, taxon table