CLI

To access the help menu:

$ AMDirT --help

The list of arguments of options is detailed below

AMDirT

AMDirT: Performs validity check of ancientMetagenomeDir datasets
Authors: Maxime Borry, Jasmin Frangenberg, Nikolay Oskolov
Contact: <maxime_borry[at]eva.mpg.de>

AMDirT [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

--verbose

Verbose mode

convert

Converts filtered samples and libraries tables to eager and fetchNGS input tables

SAMPLES: path to filtered ancientMetagenomeDir samples tsv file
TABLE_NAME: name of table to convert
AMDirT convert [OPTIONS] SAMPLES TABLE_NAME

Options

-t, --tables <tables>

(Optional) JSON file listing AncientMetagenomeDir tables

-o, --output <output>

conversion output directory

Default

.

Arguments

SAMPLES

Required argument

TABLE_NAME

Required argument

filter

Launch interactive filtering tool

AMDirT filter [OPTIONS]

Options

-t, --tables <tables>

JSON file listing AncientMetagenomeDir tables

validate

Run validity check of ancientMetagenomeDir datasets

DATASET: path to tsv file of dataset to check
SCHEMA: path to JSON schema file
AMDirT validate [OPTIONS] DATASET SCHEMA

Options

-v, --validity

Turn on schema checking.

-d, --duplicate

Turn on line duplicate line checking.

-c, --columns

Turn on column presence/absence checking.

-i, --doi

Turn on DOI duplicate checking.

--multi_values <multi_values>

Check multi-values column for duplicate values

-m, --markdown

Output is in markdown format

Arguments

DATASET

Required argument

SCHEMA

Required argument