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

convert_biom 1.1.2                                October 2013                                   CONVERT_BIOM(1)