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.
  --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)
  --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)
  --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.