NAME

       add_metadata - Script to add sample and/or observation metadata to BIOM-formatted files.

SYNOPSIS

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

DESCRIPTION

       Script to add sample and/or observation metadata to 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 BIOM filepath

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

              Optional Options:

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

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

       --sc_separated=SC_SEPARATED
              comma-separated list of  the  metadata  fields  to  split  on  semi-colons.  this  is  useful  for
              hierarchical data such as taxonomy or functional category [default: none]

       --int_fields=INT_FIELDS
              comma-separated  list  of the metadata fields to cast to integers. this is useful for integer data
              such as "DaysSinceStart" [default: none]

       --float_fields=FLOAT_FIELDS
              comma-separated list of the metadata fields to cast to floating point numbers. this is useful  for
              real number data such as "pH" [default: none]

       --observation_header=OBSERVATION_HEADER
              comma-separated  list  of the observation metadata field names. this is useful if a header line is
              not provided with the metadata, if you want to rename the fields, or if you want to  include  only
              the  first  n  fields  where  n  is  the number of entries provided here [default: use header from
              observation_mapping_fp]

       --sample_header=SAMPLE_HEADER
              comma-separated list of the sample metadata field names. this is useful if a header  line  is  not
              provided  with  the metadata, if you want to rename the fields, or if you want to include only the
              first n fields where n  is  the  number  of  entries  provided  here  [default:  use  header  from
              sample_mapping_fp]

add_metadata 1.1.2                                October 2013                                   ADD_METADATA(1)