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other versions
- bullseye 1.0.8-3
FORMAT_INPUT(1) | User Commands | FORMAT_INPUT(1) |
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.
September 2019 | format_input 1.0.8 |