CLI Reference

Clarid-Tools has 3 subcommands:

code, qrcode and validate.

📦 `clarid-tools code` Options¶

clarid-tools [-h] [long options ...]

--action: String
encode | decode
--age_group: String
Age group
--assay: String
Assay key
--batch: String
Batch
--clar_id: String
ID to decode (use --clar_id or --stub_id)
--codebook: String
Path to codebook.yaml
--condition: String
Condition key or ICD-10 code
--duration: String
Duration: P[0-9][D|W|M|Y] or P0N (Not Available)
--entity: String
biosample | subject
(accepts synonyms: biospecimen -> biosample; individual -> subject)
--format: String
human | stub
--icd10_map: String
Path to ICD-10 map JSON
--icd10_order: String
Path to icd10_order.json
--infile: String
Bulk input CSV/TSV
--max_conditions: Int Maximum number of ICD-10 codes allowed
--outfile: String
Bulk output file
--project: String
Project key
--replicate: Int
Replicate number
--sample_type: String
Sample type key
--sep: String
Separator
--sex: String
Sex
--species: String
Species key
--study: String
Study
--subject_id: Int
Subject ID
--subject_id_base62_width: Int
Number of Base-62 characters to use for subject ID stubs
--subject_id_pad_length: Int
Decimal padding width for subject IDs in biosample/subject human format
--timepoint: String
Timepoint
--tissue: String
Tissue key
--type: String
Type
--with_condition_name:
Append human-readable condition_name on decode
--usage, -h, --help, --man:
Show help messages or manual

clarid-tools validate [-h] [long options ...]

clarid-tools qrcode [-h] [long options ...]

--action: String
encode | decode
--column: String
Column name to read (defaults to clar_id or stub_id, encode only)
--input: String
CSV file (encode) or directory of PNGs, or single PNG file (decode)
--outdir: String
Where to write PNGs (encode only)
--outfile: String
Where to write CSV (decode directory mode only)
--sep: String
CSV separator
--size: Int
Module size for qrencode (-s flag)
--usage, -h, --help, --man:
Show help messages or manual