.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH LEFSE_RUN.PY "1" "September 2021" "lefse_run.py 1.1.2" "User Commands"
.SH NAME
lefse_run.py \- determine features of organisms, clades, taxonomic units, genes
.SH DESCRIPTION
usage: lefse_run.py [\-h] [\-o str] [\-a float] [\-w float] [\-l float]
.TP
[\-\-nlogs int] [\-\-verbose int] [\-\-wilc int] [\-r str]
[\-\-svm_norm int] [\-b int] [\-e int] [\-c int] [\-f float]
[\-s {0,1,2}] [\-\-min_c int] [\-t str] [\-y {0,1}]
INPUT_FILE OUTPUT_FILE
.PP
LEfSe 1.1.01
.SS "positional arguments:"
.TP
INPUT_FILE
the input file
.TP
OUTPUT_FILE
the output file containing the data for the visualization
module
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR str
set the file for exporting the result (only concise textual
form)
.TP
\fB\-a\fR float
set the alpha value for the Anova test (default 0.05)
.TP
\fB\-w\fR float
set the alpha value for the Wilcoxon test (default 0.05)
.TP
\fB\-l\fR float
set the threshold on the absolute value of the logarithmic
LDA score (default 2.0)
.TP
\fB\-\-nlogs\fR int
max log ingluence of LDA coeff
.TP
\fB\-\-verbose\fR int
verbose execution (default 0)
.TP
\fB\-\-wilc\fR int
wheter to perform the Wicoxon step (default 1)
.TP
\fB\-r\fR str
select LDA or SVM for effect size (default LDA)
.TP
\fB\-\-svm_norm\fR int
whether to normalize the data in [0,1] for SVM feature
waiting (default 1 strongly suggested)
.TP
\fB\-b\fR int
set the number of bootstrap iteration for LDA (default 30)
.TP
\fB\-e\fR int
set whether perform the wilcoxon test only among the
subclasses with the same name (default 0)
.TP
\fB\-c\fR int
set whether perform the wilcoxon test ing the Curtis's
approach [BETA VERSION] (default 0)
.TP
\fB\-f\fR float
set the subsampling fraction value for each bootstrap
iteration (default 0.66666)
.TP
\fB\-s\fR {0,1,2}
set the multiple testing correction options. 0 no correction
(more strict, default), 1 correction for independent
comparisons, 2 correction for dependent comparison
.TP
\fB\-\-min_c\fR int
minimum number of samples per subclass for performing
wilcoxon test (default 10)
.TP
\fB\-t\fR str
set the title of the analysis (default input file without
extension)
.TP
\fB\-y\fR {0,1}
(for multiclass tasks) set whether the test is performed in
a one\-against\-one ( 1 \- more strict!) or in a one\-againstall setting ( 0 \- less strict) (default 0)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.