.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH QIIME2LEFSE "1" "September 2019" "qiime2lefse 1.0.8" "User Commands"
.SH NAME
qiime2lefse \- determine features of organisms, clades, taxonomic units, genes
.SH SYNOPSIS
.B qiime2lefse
[\-h] [\-\-in [INPUT_FILE]] [\-\-md [METADATA_FILE]]
[\-\-out [OUTPUT_FILE]] [\-c class attribute]
[\-s subclass attribute] [\-u subject attribute]
.SH DESCRIPTION
Script will convert QIIME TSV BIOM table for use with lefse. It is imperative
that this table has taxa metadata associated with it named 'Consensus
Lineage', this can be down with e.g. the follow biom convert script: \fB\-\-\-\-\fR biom
convert \fB\-i\fR otu.biom \fB\-o\fR otu.txt \fB\-\-to\-tsv\fR \fB\-\-header\-key\fR Taxonomy \fB\-\-outputmetadata\-id\fR 'Consensus Lineage'
.SH OPTIONS
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-in\fR [INPUT_FILE]
the Qiime OTU table file [ stdin if not present ]
.TP
\fB\-\-md\fR [METADATA_FILE]
the Qiime OTU table file [ only OTU table without
metadata if not present ]
.TP
\fB\-\-out\fR [OUTPUT_FILE]
the output file [stdout if not present]
.TP
\fB\-c\fR class attribute
the attribute to use as class
.TP
\fB\-s\fR subclass attribute
the attribute to use as subclass
.TP
\fB\-u\fR subject attribute
the attribute to use as subject
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.