.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH LEFSE_FORMAT_INPUT.PY "1" "September 2021" "lefse_format_input.py 1.1.2" "User Commands"
.SH NAME
lefse_format_input.py \- determine features of organisms, clades, taxonomic units, genes
.SH DESCRIPTION
usage: lefse_format_input.py [\-h] [\-\-output_table OUTPUT_TABLE] [\-f {c,r}]
.TP
[\-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
.PP
LEfSe formatting modules
.SS "positional arguments:"
.TP
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.
.TP
OUTPUT_FILE
the output file containing the data for LEfSe
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-output_table\fR OUTPUT_TABLE
the formatted table in txt format
.TP
\fB\-f\fR {c,r}
set whether the features are on rows (default) or on
columns
.TP
\fB\-c\fR [1..n_feats]
set which feature use as class (default 1)
.TP
\fB\-s\fR [1..n_feats]
set which feature use as subclass (default \fB\-1\fR meaning
no subclass)
.TP
\fB\-o\fR float
set the normalization value (default \fB\-1\fR.0 meaning no
normalization)
.TP
\fB\-u\fR [1..n_feats]
set which feature use as subject (default \fB\-1\fR meaning
no subject)
.TP
\fB\-m\fR {f,s}
set the policy to adopt with missing values: f removes
the features with missing values, s removes samples
with missing values (default f)
.TP
\fB\-n\fR 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)
.TP
\fB\-biom_c\fR BIOM_CLASS
For biom input files: Set which feature use as class
.TP
\fB\-biom_s\fR BIOM_SUBCLASS
For biom input files: set which feature use as
subclass
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.