CLI Reference
The reference below is generated from the Click application so it stays aligned with the current command definitions.
cli
Autonima: Automated Neuroimaging Meta-Analysis
Usage:
cli [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
cli create-sample-config
Create a sample configuration file.
This command generates a sample configuration file that can be used as a starting point for your systematic review.
Example: autonima create-sample-config > config.yaml
Usage:
cli create-sample-config [OPTIONS]
Options:
--help Show this message and exit.
cli meta
Run meta-analyses on Autonima output using NiMARE.
This command runs coordinate-based meta-analyses on the results from an Autonima systematic review pipeline.
Arguments: OUTPUT_FOLDER Output folder containing NiMADS files
Options: --estimator CBMA estimator to use (ale, mkdadensity, kda) --estimator-args JSON string of arguments for the estimator --corrector Corrector to use (fdr, montecarlo, bonferroni) --corrector-args JSON string of arguments for the corrector --include-ids Path to newline-delimited study IDs/PMIDs for post-hoc filtering --run-reports Generate NiMARE HTML reports (default: off) --fail-fast Stop on the first failing annotation column --debug Enable fail-fast post-mortem debugging (ipdb/pdb)
Examples: autonima meta results/outputs autonima meta results/outputs --estimator ale --corrector montecarlo autonima meta results/outputs --estimator-args '{"n_iters": 1000}' --corrector-args '{"alpha": 0.01}'
Usage:
cli meta [OPTIONS] OUTPUT_FOLDER
Options:
--estimator [ale|mkdadensity|kda]
CBMA estimator to use (default: mkdadensity)
--estimator-args TEXT JSON string of arguments for the estimator
(default: {})
--corrector [fdr|montecarlo|bonferroni]
Corrector to use (default: fdr)
--corrector-args TEXT JSON string of arguments for the corrector
(default: {})
--include-ids FILE Path to text file with study IDs/PMIDs to
include (one per line)
--run-reports Generate NiMARE HTML reports (disabled by
default to reduce memory use)
--fail-fast Stop at the first failing annotation column
--debug Enable debug mode; fail fast and enter post-
mortem debugging on errors
--help Show this message and exit.
cli run
Run the Autonima systematic review pipeline.
This command executes the complete systematic review workflow: 1. Literature search via PubMed 2. Abstract screening with LLMs 3. Full-text retrieval 4. Full-text screening 5. Output generation with PRISMA compliance
Arguments: CONFIG Path to YAML configuration file OUTPUT_FOLDER Optional output folder for all results and intermediary files
Options: -v, --verbose Enable verbose logging --dry-run Validate configuration without running pipeline --force-reextract-incomplete-fulltext Re-run full-text screening for cached fulltext_incomplete studies
Examples: autonima run config.yaml autonima run config.yaml results --verbose autonima run config.yaml --dry-run
Usage:
cli run [OPTIONS] CONFIG [OUTPUT_FOLDER]
Options:
-v, --verbose Enable verbose logging
--dry-run Validate configuration without running
pipeline
--debug Enable debug mode with post-mortem debugging
on errors
-j, --num-workers INTEGER Number of parallel workers for screening
(default: 1)
--force-reextract-incomplete-fulltext
Re-run full-text screening for studies
cached as fulltext_incomplete using current
full-text files.
--cache-policy [auto|ignore|trust-legacy]
How Autonima should treat existing cache
artifacts. [default: auto]
--clear-cache [abstract|all|annotation|fulltext|output|parsing|retrieval|search]
Delete selected stage cache before running.
Repeat for multiple stages.
--copy-valid-cache-from DIRECTORY
Copy signature-matching cache artifacts from
another output folder.
--help Show this message and exit.
cli run-abstract
Run Autonima through abstract screening.
This command executes: 1. Literature search via PubMed 2. Abstract screening with LLMs
It stops before full-text retrieval and downstream stages.
Usage:
cli run-abstract [OPTIONS] CONFIG [OUTPUT_FOLDER]
Options:
-v, --verbose Enable verbose logging
--dry-run Validate configuration without running
pipeline
--debug Enable debug mode with post-mortem debugging
on errors
-j, --num-workers INTEGER Number of parallel workers for screening
(default: 1)
--cache-policy [auto|ignore|trust-legacy]
How Autonima should treat existing cache
artifacts. [default: auto]
--clear-cache [abstract|all|annotation|fulltext|output|parsing|retrieval|search]
Delete selected stage cache before running.
Repeat for multiple stages.
--copy-valid-cache-from DIRECTORY
Copy signature-matching cache artifacts from
another output folder.
--help Show this message and exit.
cli run-search
Run Autonima through the search stage only.
This command executes: 1. Literature search via PubMed
It stops before abstract screening and downstream stages.
Usage:
cli run-search [OPTIONS] CONFIG [OUTPUT_FOLDER]
Options:
-v, --verbose Enable verbose logging
--dry-run Validate configuration without running
pipeline
--debug Enable debug mode with post-mortem debugging
on errors
-j, --num-workers INTEGER Number of parallel workers for screening
(default: 1)
--cache-policy [auto|ignore|trust-legacy]
How Autonima should treat existing cache
artifacts. [default: auto]
--clear-cache [abstract|all|annotation|fulltext|output|parsing|retrieval|search]
Delete selected stage cache before running.
Repeat for multiple stages.
--copy-valid-cache-from DIRECTORY
Copy signature-matching cache artifacts from
another output folder.
--help Show this message and exit.
cli ui
Launch the local Autonima web UI.
This command starts a localhost FastAPI + React web app for: - project management - YAML spec creation and validation - interactive run orchestration with live progress and logs - secrets setup via ~/.autonima.env
Usage:
cli ui [OPTIONS]
Options:
--workspace DIRECTORY Workspace root directory for .autonima-ui state
--host TEXT Host interface to bind the web app [default:
127.0.0.1]
--port INTEGER Port to bind the web app [default: 8765]
--open / --no-open Open the app in a browser after launch [default:
open]
--help Show this message and exit.
cli validate
Validate a configuration file without running the pipeline.
This command checks if the configuration file is valid and all required parameters are present.
Arguments: CONFIG Path to YAML configuration file OUTPUT_FOLDER Optional output folder for all results and intermediary files
Examples: autonima validate config.yaml autonima validate config.yaml results
Usage:
cli validate [OPTIONS] CONFIG [OUTPUT_FOLDER]
Options:
--debug Enable debug mode with post-mortem debugging on errors
--help Show this message and exit.