NAME

       format_input - determine features of organisms, clades, taxonomic units, genes

SYNOPSIS

       format_input   [-h]   [--output_table  OUTPUT_TABLE]  [-f  {c,r}]  [-c  [1..n_feats]]  [-s
       [1..n_feats]] [-o float] [-u  [1..n_feats]]  [-m  {f,s}]  [-n  int]  [-biom_c  BIOM_CLASS]
       [-biom_s BIOM_SUBCLASS] INPUT_FILE OUTPUT_FILE

DESCRIPTION

       LEfSe formatting modules

OPTIONS

   positional arguments:
       INPUT_FILE
              the  input  file, feature hierarchical level can be specified with | or . and those
              symbols must not be present for other reasons in the input file.

       OUTPUT_FILE
              the output file containing the data for LEfSe

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

       --output_table OUTPUT_TABLE
              the formatted table in txt format

       -f {c,r}
              set whether the features are on rows (default) or on columns

       -c [1..n_feats]
              set which feature use as class (default 1)

       -s [1..n_feats]
              set which feature use as subclass (default -1 meaning no subclass)

       -o float
              set the normalization value (default -1.0 meaning no normalization)

       -u [1..n_feats]
              set which feature use as subject (default -1 meaning no subject)

       -m {f,s}
              set the policy to adopt with missin values: f removes  the  features  with  missing
              values, s removes samples with missing values (default f)

       -n int set  the  minimum  cardinality  of each subclass (subclasses with low cardinalities
              will be grouped together, if the cardinality is still low, no  pairwise  comparison
              will be performed with them)

       -biom_c BIOM_CLASS
              For biom input files: Set which feature use as class

       -biom_s BIOM_SUBCLASS
              For biom input files: set which feature use as subclass

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.