Quick Reference

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: AMDirT development team and the SPAAM community
Homepage & Documentation: https://github.com/SPAAM-community/AMDirT

AMDirT [OPTIONS] COMMAND [ARGS]...

Options

--version: Show the version and exit.

--verbose: Verbose mode

autofill

Autofills library and/or sample table(s) using ENA API and accession numbers

ACCESSION: ENA accession(s). Multiple accessions can be space separated (e.g. PRJNA123 PRJNA456)

AMDirT autofill [OPTIONS] [ACCESSION]...

Options

-n, --table_name <table_name>

Default:: ancientmetagenome-hostassociated
Options:: ancientmetagenome-environmental | ancientmetagenome-hostassociated | ancientsinglegenome-hostassociated | test

-l, --library_output <library_output>: path to library output table file

-s, --sample_output <sample_output>: path to sample output table file

Arguments

ACCESSION: Optional argument(s)

convert

Converts filtered samples and libraries tables to eager, ameta, taxprofiler, 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:: .

--bibliography: Generate BibTeX file of all publications in input table

--librarymetadata: Generate AncientMetagenomeDir libraries table of all samples in input table

--curl: Generate bash script with curl-based download commands for all libraries of samples in input table

--aspera: Generate bash script with Aspera-based download commands for all libraries of samples in input table

--eager: Convert filtered samples and libraries tables to eager input tables

--fetchngs: Convert filtered samples and libraries tables to nf-core/fetchngs input tables

--ameta: Convert filtered samples and libraries tables to aMeta input tables

--mag: Convert filtered samples and libraries tables to nf-core/mag input tables

--taxprofiler: Convert filtered samples and libraries tables to nf-core/taxprofiler input tables

Arguments

SAMPLES: Required argument

TABLE_NAME: Required argument

merge

Merges new dataset with existing table

DATASET: path to tsv file of new dataset to merge

AMDirT merge [OPTIONS] DATASET

Options

-n, --table_name <table_name>

Default:: ancientmetagenome-hostassociated
Options:: ancientmetagenome-environmental | ancientmetagenome-hostassociated | ancientsinglegenome-hostassociated | test

-t, --table_type <table_type>

Default:: libraries
Options:: samples | libraries

-m, --markdown: Output is in markdown format

-o, --outdir <outdir>

path to sample output table file

Default:: .

Arguments

DATASET: Required argument

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

-s, --schema_check: Turn on schema checking.

-d, --line_dup: 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.

-a, --online_archive: Turn on ENA accession validation

--remote <remote>: [Optional] Path/URL to remote reference sample table for archive accession validation

-m, --markdown: Output is in markdown format

Arguments

DATASET: Required argument

SCHEMA: Required argument

viewer

Launch interactive filtering tool

AMDirT viewer [OPTIONS]

Options

-t, --tables <tables>: JSON file listing AncientMetagenomeDir tables