Agentic Tools ============= **Configuration File**: ``agentic_tools.json`` **Tool Type**: Local **Tools Count**: 25 This page contains all tools defined in the ``agentic_tools.json`` configuration file. Available Tools --------------- **AdvancedCodeQualityAnalyzer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Performs deep analysis of code quality including complexity, security, performance, and maintaina... .. dropdown:: AdvancedCodeQualityAnalyzer tool specification **Tool Information:** * **Name**: ``AdvancedCodeQualityAnalyzer`` * **Type**: ``AgenticTool`` * **Description**: Performs deep analysis of code quality including complexity, security, performance, and maintainability metrics with domain-specific expertise **Parameters:** * ``source_code`` (string) (required) The source code to analyze for quality assessment * ``language`` (string) (optional) Programming language (python, javascript, etc.) * ``analysis_depth`` (string) (optional) Level of analysis depth to perform * ``domain_context`` (string) (optional) Domain context for specialized analysis (e.g., bioinformatics, web development) **Example Usage:** .. code-block:: python query = { "name": "AdvancedCodeQualityAnalyzer", "arguments": { "source_code": "example_value" } } result = tu.run(query) **DataAnalysisValidityReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Checks statistical choices, assumption testing, and reporting transparency. .. dropdown:: DataAnalysisValidityReviewer tool specification **Tool Information:** * **Name**: ``DataAnalysisValidityReviewer`` * **Type**: ``AgenticTool`` * **Description**: Checks statistical choices, assumption testing, and reporting transparency. **Parameters:** * ``analysis_section`` (string) (required) No description **Example Usage:** .. code-block:: python query = { "name": "DataAnalysisValidityReviewer", "arguments": { "analysis_section": "example_value" } } result = tu.run(query) **DescriptionAnalyzer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Analyzes a tool's original description and the results of multiple test cases, then suggests an i... .. dropdown:: DescriptionAnalyzer tool specification **Tool Information:** * **Name**: ``DescriptionAnalyzer`` * **Type**: ``AgenticTool`` * **Description**: Analyzes a tool's original description and the results of multiple test cases, then suggests an improved description that is more accurate, comprehensive, and user-friendly. Optionally provides a rationale for the changes. **Parameters:** * ``original_description`` (string) (required) The original description of the tool. * ``test_results`` (string) (required) A JSON string containing a list of test case input/output pairs. **Example Usage:** .. code-block:: python query = { "name": "DescriptionAnalyzer", "arguments": { "original_description": "example_value", "test_results": "example_value" } } result = tu.run(query) **DescriptionQualityEvaluator** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Evaluates the quality of tool descriptions and parameter descriptions, providing a score and spec... .. dropdown:: DescriptionQualityEvaluator tool specification **Tool Information:** * **Name**: ``DescriptionQualityEvaluator`` * **Type**: ``AgenticTool`` * **Description**: Evaluates the quality of tool descriptions and parameter descriptions, providing a score and specific feedback for improvements. **Parameters:** * ``tool_description`` (string) (required) The tool description to evaluate. * ``parameter_descriptions`` (string) (required) JSON string of parameter names and their descriptions. * ``test_results`` (string) (required) JSON string containing test case results. **Example Usage:** .. code-block:: python query = { "name": "DescriptionQualityEvaluator", "arguments": { "tool_description": "example_value", "parameter_descriptions": "example_value", "test_results": "example_value" } } result = tu.run(query) **DomainExpertValidator** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Provides domain-specific validation and expert recommendations for tools with deep expertise acro... .. dropdown:: DomainExpertValidator tool specification **Tool Information:** * **Name**: ``DomainExpertValidator`` * **Type**: ``AgenticTool`` * **Description**: Provides domain-specific validation and expert recommendations for tools with deep expertise across scientific and technical domains **Parameters:** * ``tool_config`` (string) (required) JSON string of tool configuration to validate * ``domain`` (string) (required) Domain expertise area for validation * ``validation_aspects`` (string) (optional) JSON array string of specific aspects to validate * ``implementation_code`` (string) (optional) Implementation code to validate (optional) **Example Usage:** .. code-block:: python query = { "name": "DomainExpertValidator", "arguments": { "tool_config": "example_value", "domain": "example_value" } } result = tu.run(query) **EthicalComplianceReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Checks adherence to ethical standards and disclosure practices. .. dropdown:: EthicalComplianceReviewer tool specification **Tool Information:** * **Name**: ``EthicalComplianceReviewer`` * **Type**: ``AgenticTool`` * **Description**: Checks adherence to ethical standards and disclosure practices. **Parameters:** * ``ethics_section`` (string) (required) No description **Example Usage:** .. code-block:: python query = { "name": "EthicalComplianceReviewer", "arguments": { "ethics_section": "example_value" } } result = tu.run(query) **ExperimentalDesignScorer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Assesses a proposed experimental design by assigning scores and structured feedback on hypothesis... .. dropdown:: ExperimentalDesignScorer tool specification **Tool Information:** * **Name**: ``ExperimentalDesignScorer`` * **Type**: ``AgenticTool`` * **Description**: Assesses a proposed experimental design by assigning scores and structured feedback on hypothesis clarity, variable definitions, sample size, controls, randomization, measurement methods, statistical analysis, bias mitigation, ethical considerations, and overall feasibility. **Parameters:** * ``hypothesis`` (string) (required) A clear statement of the research hypothesis to be tested. * ``design_description`` (string) (required) A detailed description of the proposed experimental design, including variables, methods, sample details, and planned analyses. **Example Usage:** .. code-block:: python query = { "name": "ExperimentalDesignScorer", "arguments": { "hypothesis": "example_value", "design_description": "example_value" } } result = tu.run(query) **HypothesisGenerator** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Generates research hypotheses based on provided background context, domain, and desired format. U... .. dropdown:: HypothesisGenerator tool specification **Tool Information:** * **Name**: ``HypothesisGenerator`` * **Type**: ``AgenticTool`` * **Description**: Generates research hypotheses based on provided background context, domain, and desired format. Uses AI to propose novel, testable hypotheses for scientific exploration. **Parameters:** * ``context`` (string) (required) Background information, observations, or data description from which to derive hypotheses. * ``domain`` (string) (required) Field of study or research area (e.g., 'neuroscience', 'ecology', 'materials science'). * ``number_of_hypotheses`` (string) (required) Number of hypotheses to generate (e.g., '3', '5'). * ``hypothesis_format`` (string) (optional) Optional directive on how to structure each hypothesis. Choose from one of the following formats: 1. If–Then Statements: "If [independent variable condition], then [expected outcome]." 2. Null and Alternative (Statistical): • H₀ (Null): "There is no difference/effect/association between X and Y." • H₁ (Alt): "There is a difference/effect/association between X and Y." 3. Associative (Correlation-Focused): "There is a relationship/association between [Variable A] and [Variable B]." 4. Directional (Non-If–Then): "Increasing/decreasing [Variable A] will lead to [directional change] in [Variable B]." 5. Comparative (Group Comparison): "Group A will show higher/lower [dependent measure] compared to Group B under [condition]." 6. Mechanistic: "Because [mechanism or process], [Variable A] will cause [Variable B]." 7. Descriptive (Exploratory/Pattern-Oriented): "Population X exhibits pattern Y in context Z." If omitted, defaults to concise declarative sentences. **Example Usage:** .. code-block:: python query = { "name": "HypothesisGenerator", "arguments": { "context": "example_value", "domain": "example_value", "number_of_hypotheses": "example_value" } } result = tu.run(query) **LabelGenerator** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Generates relevant keyword labels for tools based on their name, description, parameters, and cat... .. dropdown:: LabelGenerator tool specification **Tool Information:** * **Name**: ``LabelGenerator`` * **Type**: ``AgenticTool`` * **Description**: Generates relevant keyword labels for tools based on their name, description, parameters, and category. Creates a comprehensive list of tags for tool discovery and categorization. **Parameters:** * ``tool_name`` (string) (required) The name of the tool * ``tool_description`` (string) (required) Detailed description of what the tool does * ``tool_parameters`` (string) (required) JSON string describing the tool's input parameters and their types * ``category`` (string) (required) The general category or domain the tool belongs to * ``existing_labels`` (string) (optional) JSON array string of existing labels to consider reusing (optional) **Example Usage:** .. code-block:: python query = { "name": "LabelGenerator", "arguments": { "tool_name": "example_value", "tool_description": "example_value", "tool_parameters": "example_value", "category": "example_value" } } result = tu.run(query) **LiteratureContextReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Reviews coverage, relevance, and critical synthesis of prior scholarship. .. dropdown:: LiteratureContextReviewer tool specification **Tool Information:** * **Name**: ``LiteratureContextReviewer`` * **Type**: ``AgenticTool`` * **Description**: Reviews coverage, relevance, and critical synthesis of prior scholarship. **Parameters:** * ``paper_title`` (string) (required) No description * ``literature_review`` (string) (required) Full literature-review text **Example Usage:** .. code-block:: python query = { "name": "LiteratureContextReviewer", "arguments": { "paper_title": "example_value", "literature_review": "example_value" } } result = tu.run(query) **MedicalLiteratureReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Conducts systematic reviews of medical literature on specific topics. Synthesizes findings from m... .. dropdown:: MedicalLiteratureReviewer tool specification **Tool Information:** * **Name**: ``MedicalLiteratureReviewer`` * **Type**: ``AgenticTool`` * **Description**: Conducts systematic reviews of medical literature on specific topics. Synthesizes findings from multiple studies and provides evidence-based conclusions with structured analysis and quality assessment. **Parameters:** * ``research_topic`` (string) (required) The specific medical/research topic for literature review (e.g., 'efficacy of drug X in treating condition Y'). * ``literature_content`` (string) (required) The literature content, abstracts, full studies, or research papers to review and synthesize. * ``focus_area`` (string) (required) Primary focus area for the review (e.g., 'therapeutic efficacy', 'safety profile', 'diagnostic accuracy', 'biomarker validation'). * ``study_types`` (string) (required) Types of studies to prioritize in the analysis (e.g., 'randomized controlled trials', 'meta-analyses', 'cohort studies', 'case-control studies'). * ``quality_level`` (string) (required) Minimum evidence quality level to include (e.g., 'high quality only', 'moderate and above', 'all available evidence'). * ``review_scope`` (string) (required) Scope of the review (e.g., 'comprehensive systematic review', 'rapid review', 'scoping review', 'narrative review'). **Example Usage:** .. code-block:: python query = { "name": "MedicalLiteratureReviewer", "arguments": { "research_topic": "example_value", "literature_content": "example_value", "focus_area": "example_value", "study_types": "example_value", "quality_level": "example_value", "review_scope": "example_value" } } result = tu.run(query) **MedicalTermNormalizer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Identifies and corrects misspelled drug or disease names, returning a list of plausible standardi... .. dropdown:: MedicalTermNormalizer tool specification **Tool Information:** * **Name**: ``MedicalTermNormalizer`` * **Type**: ``AgenticTool`` * **Description**: Identifies and corrects misspelled drug or disease names, returning a list of plausible standardized terms. **Parameters:** * ``raw_terms`` (string) (required) A comma- or whitespace-separated string containing one misspelled drug or disease name. **Example Usage:** .. code-block:: python query = { "name": "MedicalTermNormalizer", "arguments": { "raw_terms": "example_value" } } result = tu.run(query) **MethodologyRigorReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Evaluates design appropriateness, sampling, and procedural transparency. .. dropdown:: MethodologyRigorReviewer tool specification **Tool Information:** * **Name**: ``MethodologyRigorReviewer`` * **Type**: ``AgenticTool`` * **Description**: Evaluates design appropriateness, sampling, and procedural transparency. **Parameters:** * ``methods_section`` (string) (required) Full Methods text **Example Usage:** .. code-block:: python query = { "name": "MethodologyRigorReviewer", "arguments": { "methods_section": "example_value" } } result = tu.run(query) **NoveltySignificanceReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Provides a structured peer-review of the work's originality and potential impact. .. dropdown:: NoveltySignificanceReviewer tool specification **Tool Information:** * **Name**: ``NoveltySignificanceReviewer`` * **Type**: ``AgenticTool`` * **Description**: Provides a structured peer-review of the work's originality and potential impact. **Parameters:** * ``paper_title`` (string) (required) Manuscript title * ``abstract`` (string) (required) Manuscript abstract * ``manuscript_text`` (string) (required) Full manuscript text **Example Usage:** .. code-block:: python query = { "name": "NoveltySignificanceReviewer", "arguments": { "paper_title": "example_value", "abstract": "example_value", "manuscript_text": "example_value" } } result = tu.run(query) **ProtocolOptimizer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Reviews an initial protocol and delivers targeted revisions that improve clarity, feasibility, ri... .. dropdown:: ProtocolOptimizer tool specification **Tool Information:** * **Name**: ``ProtocolOptimizer`` * **Type**: ``AgenticTool`` * **Description**: Reviews an initial protocol and delivers targeted revisions that improve clarity, feasibility, risk-management, and evaluation rigor. **Parameters:** * ``initial_protocol`` (string) (required) No description **Example Usage:** .. code-block:: python query = { "name": "ProtocolOptimizer", "arguments": { "initial_protocol": "example_value" } } result = tu.run(query) **QuestionRephraser** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Generates three distinct paraphrases of a given question while ensuring answer options remain val... .. dropdown:: QuestionRephraser tool specification **Tool Information:** * **Name**: ``QuestionRephraser`` * **Type**: ``AgenticTool`` * **Description**: Generates three distinct paraphrases of a given question while ensuring answer options remain valid and applicable. **Parameters:** * ``question`` (string) (required) The original question text to be rephrased * ``options`` (string) (optional) Answer options (e.g., multiple choice options) that should remain valid for the rephrased questions. Leave empty if no options are provided. **Example Usage:** .. code-block:: python query = { "name": "QuestionRephraser", "arguments": { "question": "example_value" } } result = tu.run(query) **ReproducibilityTransparencyReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Evaluates data, code, and protocol availability for replication. .. dropdown:: ReproducibilityTransparencyReviewer tool specification **Tool Information:** * **Name**: ``ReproducibilityTransparencyReviewer`` * **Type**: ``AgenticTool`` * **Description**: Evaluates data, code, and protocol availability for replication. **Parameters:** * ``availability_statement`` (string) (required) No description **Example Usage:** .. code-block:: python query = { "name": "ReproducibilityTransparencyReviewer", "arguments": { "availability_statement": "example_value" } } result = tu.run(query) **ResultsInterpretationReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Judges whether conclusions are data-justified and limitations addressed. .. dropdown:: ResultsInterpretationReviewer tool specification **Tool Information:** * **Name**: ``ResultsInterpretationReviewer`` * **Type**: ``AgenticTool`` * **Description**: Judges whether conclusions are data-justified and limitations addressed. **Parameters:** * ``results_section`` (string) (required) No description * ``discussion_section`` (string) (required) No description **Example Usage:** .. code-block:: python query = { "name": "ResultsInterpretationReviewer", "arguments": { "results_section": "example_value", "discussion_section": "example_value" } } result = tu.run(query) **ScientificTextSummarizer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Summarizes biomedical research texts, abstracts, or papers with specified length and focus areas.... .. dropdown:: ScientificTextSummarizer tool specification **Tool Information:** * **Name**: ``ScientificTextSummarizer`` * **Type**: ``AgenticTool`` * **Description**: Summarizes biomedical research texts, abstracts, or papers with specified length and focus areas. Uses AI to extract key findings, methodology, and conclusions from complex biomedical literature. **Parameters:** * ``text`` (string) (required) The biomedical text, abstract, or paper content to be summarized. * ``summary_length`` (string) (required) Desired length of summary (e.g., '50', '100', '200 words'). * ``focus_area`` (string) (required) What to focus on in the summary (e.g., 'methodology', 'results', 'clinical implications', 'drug interactions'). **Example Usage:** .. code-block:: python query = { "name": "ScientificTextSummarizer", "arguments": { "text": "example_value", "summary_length": "example_value", "focus_area": "example_value" } } result = tu.run(query) **ToolMetadataGenerator** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Generates a JSON structure with the metadata of a tool in ToolUniverse, given the JSON configurat... .. dropdown:: ToolMetadataGenerator tool specification **Tool Information:** * **Name**: ``ToolMetadataGenerator`` * **Type**: ``AgenticTool`` * **Description**: Generates a JSON structure with the metadata of a tool in ToolUniverse, given the JSON configuration of the tool. **Parameters:** * ``tool_config`` (string) (required) JSON string of the tool configuration to extract metadata from * ``tool_type_mappings`` (object) (optional) A mapping from a simplified toolType to a list of tool_config.type that fall under the toolType (e.g., {'Databases': ['XMLTool']}) **Example Usage:** .. code-block:: python query = { "name": "ToolMetadataGenerator", "arguments": { "tool_config": "example_value" } } result = tu.run(query) **ToolMetadataStandardizer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Standardizes and groups semantically equivalent metadata strings (e.g., sources, tags) into canon... .. dropdown:: ToolMetadataStandardizer tool specification **Tool Information:** * **Name**: ``ToolMetadataStandardizer`` * **Type**: ``AgenticTool`` * **Description**: Standardizes and groups semantically equivalent metadata strings (e.g., sources, tags) into canonical forms for consistent downstream usage. **Parameters:** * ``metadata_list`` (array) (required) List of raw metadata strings (e.g., sources, tags) to standardize and group. * ``limit`` (integer) (optional) If provided, the maximum number of canonical strings to return. The LLM will group terms more aggressively to meet this limit, ensuring all raw strings are mapped. **Example Usage:** .. code-block:: python query = { "name": "ToolMetadataStandardizer", "arguments": { "metadata_list": ["item1", "item2"] } } result = tu.run(query) **ToolQualityEvaluator** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Evaluates the quality of tool configurations and implementations. Provides detailed scoring and f... .. dropdown:: ToolQualityEvaluator tool specification **Tool Information:** * **Name**: ``ToolQualityEvaluator`` * **Type**: ``AgenticTool`` * **Description**: Evaluates the quality of tool configurations and implementations. Provides detailed scoring and feedback for improvement. **Parameters:** * ``tool_config`` (string) (required) JSON string of the tool configuration * ``test_cases`` (string) (required) JSON string of test cases * ``evaluation_aspects`` (array) (required) Aspects to evaluate (functionality, usability, completeness, best_practices) **Example Usage:** .. code-block:: python query = { "name": "ToolQualityEvaluator", "arguments": { "tool_config": "example_value", "test_cases": "example_value", "evaluation_aspects": ["item1", "item2"] } } result = tu.run(query) **ToolRelationshipDetector** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Analyzes a primary tool against a list of other tools to identify meaningful, directional data fl... .. dropdown:: ToolRelationshipDetector tool specification **Tool Information:** * **Name**: ``ToolRelationshipDetector`` * **Type**: ``AgenticTool`` * **Description**: Analyzes a primary tool against a list of other tools to identify meaningful, directional data flow compatibilities for scientific workflows. Returns a list of compatible pairs with direction and rationale. **Parameters:** * ``tool_a`` (string) (required) JSON string for the primary tool configuration (Tool A). * ``other_tools`` (string) (required) JSON string of a list of other tool configurations to compare against Tool A. **Example Usage:** .. code-block:: python query = { "name": "ToolRelationshipDetector", "arguments": { "tool_a": "example_value", "other_tools": "example_value" } } result = tu.run(query) **WritingPresentationReviewer** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Assesses clarity, organization, grammar, and visual presentation quality. .. dropdown:: WritingPresentationReviewer tool specification **Tool Information:** * **Name**: ``WritingPresentationReviewer`` * **Type**: ``AgenticTool`` * **Description**: Assesses clarity, organization, grammar, and visual presentation quality. **Parameters:** * ``manuscript_text`` (string) (required) No description **Example Usage:** .. code-block:: python query = { "name": "WritingPresentationReviewer", "arguments": { "manuscript_text": "example_value" } } result = tu.run(query) **call_agentic_human** (Type: AgenticTool) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Produces a concise, practical answer that emulates how a well-informed human would respond to the... .. dropdown:: call_agentic_human tool specification **Tool Information:** * **Name**: ``call_agentic_human`` * **Type**: ``AgenticTool`` * **Description**: Produces a concise, practical answer that emulates how a well-informed human would respond to the question. **Parameters:** * ``question`` (string) (required) The user's question to be answered in a human-like manner. **Example Usage:** .. code-block:: python query = { "name": "call_agentic_human", "arguments": { "question": "example_value" } } result = tu.run(query) Navigation ---------- * :doc:`tools_config_index` - Back to Tools Overview * :doc:`../guide/loading_tools` - Loading Local Tools