tool_reference.md

GNN MCP Tool Quick Reference

All 131 real tools registered by the GNN MCP server (v1.6.0 Engine; reference refreshed 2026-04-20).
Sorted alphabetically by domain. For full per-domain documentation see ../modules/21_mcp.md.

Full Tool Table

Domain	Tool	Description
analysis	compute_complexity_metrics	Compute complexity scores for a GNN model
analysis	get_analysis_results	Retrieve cached analysis results
analysis	list_analysis_tools	List available analysis capabilities
analysis	process_analysis	Run statistical analysis on GNN files
audio	analyze_audio_characteristics	Analyse characteristics of a GNN model for sonification
audio	check_audio_backends	Check which audio backends are available (SAPF, Pedalboard, soundfile)
audio	get_audio_generation_options	List configurable audio generation options
audio	get_audio_module_info	Return audio module version and capabilities
audio	process_audio	Run GNN audio processing pipeline
audio	validate_audio_content	Validate audio content from GNN specs
advanced_visualization	check_visualization_capabilities	Check which advanced visualization libraries are available
advanced_visualization	get_advanced_visualization_module_info	Return module info and capabilities
advanced_visualization	list_d2_visualization_types	List supported D2 diagram types
advanced_visualization	process_advanced_visualization	Process advanced visualization (D2, dashboards)
execute	check_execute_dependencies	Check execution framework dependency availability
execute	execute_gnn_model	Execute a single GNN model file and capture results
execute	execute_pymdp_simulation	Run a PyMDP simulation from a rendered Python script
execute	get_execute_module_info	Return execute module version and capabilities
execute	process_execute	Run GNN execution pipeline across all frameworks
export	list_export_formats	List all supported export formats
export	process_export	Run multi-format export pipeline
export	validate_export_format	Validate an export format specifier
gnn	get_gnn_module_info	Return GNN module version and capabilities
gnn	parse_gnn_content	Parse a GNN specification string
gnn	validate_gnn_content	Validate a GNN specification string
gui	get_gui_module_info	Return GUI module version and feature flags
gui	list_available_guis	List available GUI types
gui	process_gui	Process GNN files for GUI generation
integration	check_integration_dependencies	Check integration dependency availability
integration	list_supported_integrations	List all supported integration targets
integration	process_integration	Run system integration pipeline
intelligent_analysis	get_analysis_capabilities	List intelligent analysis capabilities
intelligent_analysis	get_intelligent_analysis_module_info	Return module version and capabilities
intelligent_analysis	process_intelligent_analysis	Run intelligent analysis on pipeline results
llm	analyze_gnn_with_llm	Analyse a single GNN file with the configured LLM provider
llm	generate_llm_documentation	Generate LLM-powered documentation for a GNN model
llm	get_llm_module_info	Return LLM module version and capabilities
llm	get_llm_providers	List available LLM providers and their status
llm	process_llm	Run LLM analysis pipeline for all GNN files
ml_integration	check_ml_frameworks	Check which ML frameworks are available
ml_integration	get_ml_module_info	Return ML integration module version and capabilities
ml_integration	list_ml_integration_targets	List ML integration targets
ml_integration	process_ml_integration	Process ML integration for GNN files
ontology	extract_ontology_annotations	Extract ontology annotations from a GNN file
ontology	list_standard_ontology_terms	List all standard Active Inference ontology terms
ontology	process_ontology	Run Active Inference ontology processing
ontology	validate_ontology_terms	Validate ontology annotation terms
pipeline	get_pipeline_status	Get current pipeline execution status
pipeline	get_pipeline_steps	List all 25 pipeline steps (0-24) with metadata
render	get_render_module_info	Return render module version and capabilities
render	list_render_frameworks	List supported rendering frameworks
render	process_render	Run code generation for all GNN files
render	render_gnn_to_format	Render a GNN file to a specific framework format
report	generate_report	Generate a comprehensive pipeline report
report	get_report_module_info	Return report module version and capabilities
report	list_report_formats	List available report formats
report	read_report	Read a previously generated report
research	list_research_topics	List active research topics and experimental features
research	process_research	Run research tools pipeline
sapf	get_sapf_module_info	Return SAPF module version and capabilities
sapf	list_audio_artifacts	List generated audio artifacts
sapf	process_sapf	Run SAPF audio pipeline
security	list_security_checks	List all security checks performed
security	process_security	Run security validation pipeline
security	scan_gnn_file	Scan a GNN file for security issues
utils	get_utils_info	Return utils module version and available utilities
validation	check_schema_compliance	Check schema compliance for a GNN file
validation	get_validation_report	Get the latest validation report
validation	process_validation	Run GNN validation pipeline
validation	validate_gnn_file	Validate a single GNN file
visualization	get_visualization_options	List configurable visualization options
visualization	list_visualization_artifacts	List generated visualization artifacts
visualization	process_visualization	Run graph and matrix visualization pipeline
website	build_website_from_pipeline_output	Build website from pipeline artifacts
website	get_website_module_info	Return website module version and capabilities
website	get_website_status	Get current website generation status
website	list_generated_website_pages	List all generated website pages
website	process_website	Generate static HTML website from pipeline output

Total: 131 tools across 38+ domains
Verified by src/tests/test_mcp_audit.py as part of the full src/tests/ suite (current pass/skip counts: repository README.md).