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

-t, --output_ena_table <output_ena_table>: path to ENA table output file

-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

Note: When supplying a pre-filtered libraries table with –libraries, the corresponding sample table is still required!

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

--libraries <libraries>: (Optional) Path to a pre-filtered libraries table NOTE: This argument is mutually exclusive with arguments: [librarymetadata].

--librarymetadata: Generate AncientMetagenomeDir libraries table of all samples in input table NOTE: This argument is mutually exclusive with arguments: [libraries].

-o, --output <output>

conversion output directory

Default:: '.'

--bibliography: Generate BibTeX file of all publications 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

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

--sratoolkit: Generate bash script with SRA Toolkit fasterq-dump based download commands for all libraries of samples in input table

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

download

Download a table from the amdirt repository

amdirt download [OPTIONS]

Options

-t, --table <table>

AncientMetagenomeDir table to download

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

-y, --table_type <table_type>

Type of table to download

Default:: 'samples'
Options:: samples | libraries

-r, --release <release>

Release tag to download

Default:: 'v24.12.0'
Options:: v24.12.0 | v24.09.0 | v24.06.0 | v24.03.0 | v23.12.0 | v23.09.0 | v23.06.0 | v23.03.0 | v22.12.0 | v22.09.2 | v22.09.1 | v22.09

-o, --output <output>

Output directory

Default:: '.'

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

-l, --local_json_schema <local_json_schema>: path to folder with local JSON schemas

-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