Create Tooluniverse Skill

Create ToolUniverse Skill

Systematic workflow for creating production-ready ToolUniverse skills that integrate multiple scientific tools, follow implementation-agnostic standards, and achieve 100% test coverage.

Core Principles (Critical)

CRITICAL - Read devtu-optimize-skills: This skill builds on principles from devtu-optimize-skills. Invoke that skill first or review its 10 pillars:

1. TEST FIRST - Never write documentation without testing tools
2. Verify tool contracts - Don't trust function names
3. Handle SOAP tools - Add operation parameter where needed
4. Implementation-agnostic docs - Separate SKILL.md from code
5. Foundation first - Use comprehensive aggregators
6. Disambiguate carefully - Resolve IDs properly
7. Implement fallbacks - Primary → Fallback → Default
8. Grade evidence - T1-T4 tiers on claims
9. Require quantified completeness - Numeric minimums
10. Synthesize - Models and hypotheses, not just lists

When to Use This Skill

Use this skill when:

• Creating new ToolUniverse skills for specific domains
• Building research workflows using scientific tools
• Developing analysis capabilities (e.g., metabolomics, single-cell, cancer genomics)
• Integrating multiple databases into coherent pipelines
• Following up on "create [domain] skill" requests

Overview: 7-Phase Workflow

Phase 1: Domain Analysis →
Phase 2: Tool Discovery & Testing →
Phase 3: Tool Creation (if needed) →
Phase 4: Implementation →
Phase 5: Documentation →
Phase 6: Testing & Validation →
Phase 7: Packaging

Time per skill: ~1.5-2 hours (tested and documented)

Phase 1: Domain Analysis

Objective: Understand the scientific domain and identify required capabilities

Duration: 15 minutes

1.1 Understand Use Cases

Gather concrete examples of how the skill will be used:

• "What analyses should this skill perform?"
• "Can you give examples of typical queries?"
• "What outputs do users expect?"

Example queries to clarify:

• For metabolomics: "Identify metabolites in a sample" vs "Find pathways for metabolites" vs "Compare metabolite profiles"
• For cancer genomics: "Interpret mutations" vs "Find therapies" vs "Match clinical trials"

1.2 Identify Required Data Types

List what the skill needs to work with:

• Input types: Gene lists, protein IDs, compound names, disease names, etc.
• Output types: Reports, tables, visualizations, data files
• Intermediate data: ID mappings, enrichment results, annotations

1.3 Define Analysis Phases

Break the workflow into logical phases:

Example - Metabolomics Skill:

1. Phase 1: Metabolite identification (name → IDs)
2. Phase 2: Metabolite annotation (properties, pathways)
3. Phase 3: Pathway enrichment (statistical analysis)
4. Phase 4: Comparative analysis (samples/conditions)

Example - Cancer Genomics Skill:

1. Phase 1: Mutation validation (check databases)
2. Phase 2: Clinical significance (actionability)
3. Phase 3: Therapy matching (FDA approvals)
4. Phase 4: Trial matching (clinical trials)

1.4 Review Related Skills

Check existing ToolUniverse skills for relevant patterns:

• Read similar skills in skills/ directory
• Note tool usage patterns
• Identify reusable approaches

Useful related skills:

• tooluniverse-systems-biology - Multi-database integration
• tooluniverse-target-research - Comprehensive profiling
• tooluniverse-drug-research - Pharmaceutical workflows

Phase 2: Tool Discovery & Testing

Objective: Find and verify tools needed for each analysis phase

Duration: 30-45 minutes

CRITICAL: Following test-driven development from devtu-optimize-skills

2.1 Search Available Tools

Tool locations: /src/tooluniverse/data/*.json (186 tool files)

Search strategies:

1. Keyword search: grep -r "keyword" src/tooluniverse/data/*.json
2. Tool listing: List all tools from specific database
3. Function search: Search by domain (metabolomics, genomics, etc.)

Example searches:

# Find metabolomics tools
grep -l "metabol" src/tooluniverse/data/*.json

# Find cancer-related tools
grep -l "cancer\|tumor\|oncology" src/tooluniverse/data/*.json

# Find single-cell tools
grep -l "single.cell\|scRNA" src/tooluniverse/data/*.json

2.2 Read Tool Configurations

For each relevant tool file, read to understand:

• Tool names and descriptions
• Parameters (CRITICAL - don't assume from function names!)
• Return schemas
• Test examples

Check for:

• SOAP tools (require operation parameter)
• Parameter name patterns
• Response format variations

2.3 Create Test Script (REQUIRED)

NEVER skip this step - Testing before documentation is the #1 lesson

Template: See scripts/test_tools_template.py

Test script structure:

#!/usr/bin/env python3
"""
Test script for [Domain] tools
Following TDD: test ALL tools BEFORE creating skill documentation
"""

from tooluniverse import ToolUniverse
import json

def test_database_1():
    """Test Database 1 tools"""
    tu = ToolUniverse()
    tu.load_tools()

    # Test tool 1
    result = tu.tools.TOOL_NAME(param="value")
    print(f"Status: {result.get('status')}")
    # Verify response format
    # Check data structure

def test_database_2():
    """Test Database 2 tools"""
    # Similar structure

def main():
    """Run all tests"""
    tests = [
        ("Database 1", test_database_1),
        ("Database 2", test_database_2),
    ]

    results = {}
    for name, test_func in tests:
        try:
            test_func()
            results[name] = "✅ PASS"
        except Exception as e:
            results[name] = f"❌ FAIL: {e}"

    # Print summary
    for name, result in results.items():
        print(f"{name}: {result}")

if __name__ == "__main__":
    main()

2.4 Run Tests and Document Findings

Execute:

python test_[domain]_tools.py

Document discoveries:

• Response format variations (standard, direct list, direct dict)
• Parameter mismatches (function name ≠ parameter name)
• SOAP tools requiring operation
• Tools that don't work / return errors

Create parameter corrections table:

Phase 3: Tool Creation (If Needed)

Objective: Create missing tools using devtu-create-tool

Duration: 30-60 minutes per tool (if needed)

When to create tools:

• Required functionality not available in existing tools
• Critical analysis step has no tool support
• Alternative tools exist but are inferior

When NOT to create tools:

• Adequate tools already exist
• Analysis can use alternative approach
• Tool would duplicate existing functionality

3.1 Use devtu-create-tool Skill

If tools are missing, invoke the devtu-create-tool skill:

Example invocation:

"I need to create a tool for [database/API]. The API endpoint is [URL],
it takes parameters [list], and returns [format]. Can you help create this tool?"

3.2 Test New Tools

After creating tools, add them to test script:

def test_new_tool():
    """Test newly created tool"""
    tu = ToolUniverse()
    tu.load_tools()

    result = tu.tools.NEW_TOOL_NAME(param="test_value")
    assert result.get('status') == 'success', "New tool failed"
    # Verify data structure matches expectations

3.3 Use devtu-fix-tool If Needed

If new tools fail tests, invoke devtu-fix-tool:

"The tool [TOOL_NAME] is returning errors: [error message].
Can you help fix it?"

Phase 4: Implementation

Objective: Create working Python pipeline with tested tools

Duration: 30-45 minutes

CRITICAL: Build from tested tools, not assumptions

4.1 Create Skill Directory

mkdir -p skills/tooluniverse-[domain-name]
cd skills/tooluniverse-[domain-name]

4.2 Write python_implementation.py

Template: See assets/skill_template/python_implementation.py

Structure:

#!/usr/bin/env python3
"""
[Domain Name] - Python SDK Implementation
Tested implementation following TDD principles
"""

from tooluniverse import ToolUniverse
from datetime import datetime

def domain_analysis_pipeline(
    input_param_1=None,
    input_param_2=None,
    output_file=None
):
    """
    [Domain] analysis pipeline.

    Args:
        input_param_1: Description
        input_param_2: Description
        output_file: Output markdown file path

    Returns:
        Path to generated report file
    """

    tu = ToolUniverse()
    tu.load_tools()

    # Generate output filename
    if output_file is None:
        timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
        output_file = f"domain_analysis_{timestamp}.md"

    # Initialize report
    report = []
    report.append("# [Domain] Analysis Report\n")
    report.append(f"**Generated**: {datetime.now()}\n\n")

    # Phase 1: [Description]
    report.append("## 1. [Phase Name]\n")
    try:
        result = tu.tools.TOOL_NAME(param=value)
        if result.get('status') == 'success':
            data = result.get('data', [])
            # Process and add to report
        else:
            report.append("*[Phase] data unavailable.*\n")
    except Exception as e:
        report.append(f"*Error in [Phase]: {str(e)}*\n")

    # Phase 2, 3, 4... (similar structure)

    # Write report
    with open(output_file, 'w') as f:
        f.write(''.join(report))

    print(f"\n✅ Report generated: {output_file}")
    return output_file

if __name__ == "__main__":
    # Example usage
    domain_analysis_pipeline(
        input_param_1="example",
        output_file="example_analysis.md"
    )

Key principles:

• Use tested tools only
• Handle errors gracefully (try/except)
• Continue if one phase fails
• Progressive report writing
• Clear status messages

4.3 Create test_skill.py

Template: See assets/skill_template/test_skill.py

Test cases:

1. Test each input type
2. Test combined inputs
3. Verify report sections exist
4. Check error handling

#!/usr/bin/env python3
"""Test script for [Domain] skill"""

import sys
import os
sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))

from python_implementation import domain_analysis_pipeline

def test_basic_analysis():
    """Test basic analysis workflow"""
    output = domain_analysis_pipeline(
        input_param_1="test_value",
        output_file="test_basic.md"
    )
    assert os.path.exists(output), "Output file not created"

def test_combined_analysis():
    """Test with multiple inputs"""
    output = domain_analysis_pipeline(
        input_param_1="value1",
        input_param_2="value2",
        output_file="test_combined.md"
    )

    # Verify report has all sections
    with open(output, 'r') as f:
        content = f.read()
        assert "Phase 1" in content
        assert "Phase 2" in content

def main():
    tests = [
        ("Basic Analysis", test_basic_analysis),
        ("Combined Analysis", test_combined_analysis),
    ]

    results = {}
    for name, test_func in tests:
        try:
            test_func()
            results[name] = "✅ PASS"
        except Exception as e:
            results[name] = f"❌ FAIL: {e}"

    for name, result in results.items():
        print(f"{name}: {result}")

    all_passed = all("PASS" in r for r in results.values())
    return 0 if all_passed else 1

if __name__ == "__main__":
    sys.exit(main())

4.4 Run Tests

python test_skill.py

Fix bugs until 100% pass rate

Phase 5: Documentation

Objective: Create implementation-agnostic documentation

Duration: 30-45 minutes

CRITICAL: SKILL.md must have ZERO Python/MCP specific code

5.1 Write SKILL.md

Template: See assets/skill_template/SKILL.md

Structure:

---
name: tooluniverse-[domain-name]
description: [What it does]. [Capabilities]. [Databases used]. Use when [triggers].
---

# [Domain Name] Analysis

[One paragraph overview]

## When to Use This Skill

**Triggers**:
- "Analyze [domain] for [input]"
- "Find [data type] related to [query]"
- "[Domain-specific action]"

**Use Cases**:
1. [Use case 1 with description]
2. [Use case 2 with description]

## Core Databases Integrated

| Database | Coverage | Strengths |
|----------|----------|-----------|
| **Database 1** | [Scope] | [What it's good for] |
| **Database 2** | [Scope] | [What it's good for] |

## Workflow Overview

Input → Phase 1 → Phase 2 → Phase 3 → Report

---

## Phase 1: [Phase Name]

**When**: [Conditions]

**Objective**: [What this phase achieves]

### Tools Used

**TOOL_NAME**:
- **Input**:
  - `parameter1`: Description
  - `parameter2`: Description
- **Output**: Description
- **Use**: What it's used for

### Workflow

1. [Step 1]
2. [Step 2]
3. [Step 3]

### Decision Logic

- **Condition 1**: Action to take
- **Empty results**: How to handle
- **Errors**: Fallback strategy

---

## Phase 2, 3, 4... (similar structure)

---

## Output Structure

[Description of report format]

### Report Format

**Required Sections**:
1. Header with parameters
2. Phase 1 results
3. Phase 2 results
...

---

## Tool Parameter Reference

**Critical Parameter Notes** (from testing):

| Tool | Parameter | CORRECT Name | Common Mistake |
|------|-----------|--------------|----------------|
| TOOL_NAME | `param` | ✅ `actual_param` | ❌ `assumed_param` |

**Response Format Notes**:
- **TOOL_1**: Returns [format]
- **TOOL_2**: Returns [format]

---

## Fallback Strategies

[Document Primary → Fallback → Default for critical tools]

---

## Limitations & Known Issues

### Database-Specific
- **Database 1**: [Limitations]
- **Database 2**: [Limitations]

### Technical
- **Response formats**: [Notes]
- **Rate limits**: [If any]

---

## Summary

[Domain] skill provides:
1. ✅ [Capability 1]
2. ✅ [Capability 2]

**Outputs**: [Description]
**Best for**: [Use cases]

Key principles:

• NO Python/MCP code in SKILL.md
• Describe WHAT to do, not HOW in specific language
• Tool parameters conceptually described
• Decision logic and fallback strategies
• Response format variations documented

5.2 Write QUICK_START.md

Template: See assets/skill_template/QUICK_START.md

Structure:

## Quick Start: [Domain] Analysis

[One paragraph overview]

---

## Choose Your Implementation

### Python SDK

#### Option 1: Complete Pipeline (Recommended)

```python
from skills.tooluniverse_[domain].python_implementation import domain_pipeline

# Example 1
domain_pipeline(
    input_param="value",
    output_file="analysis.md"
)

Option 2: Individual Tools

from tooluniverse import ToolUniverse

tu = ToolUniverse()
tu.load_tools()

# Tool 1
result = tu.tools.TOOL_NAME(param="value")

# Tool 2
result = tu.tools.TOOL_NAME2(param="value")

MCP (Model Context Protocol)

Option 1: Conversational (Natural Language)

"Analyze [domain] for [input]"

"Find [data] related to [query]"

Option 2: Direct Tool Calls

{
  "tool": "TOOL_NAME",
  "parameters": {
    "param": "value"
  }
}

Tool Parameters (All Implementations)

Common Recipes

Recipe 1: [Use Case Name]

Python SDK:

[Code example]

MCP:

[Conversational example]

Recipe 2, 3... (similar)

Expected Output

[Show example report structure]

Troubleshooting

Issue: [Problem]

Solution: [Fix]

Next Steps

After running this skill:

1. [Follow-up action 1]
2. [Follow-up action 2]

**Key principles**:
- Equal treatment of Python SDK and MCP
- Concrete examples for both
- Parameter table applies to both
- Clear recipes

---

## Phase 6: Testing & Validation

**Objective**: Verify skill meets all quality standards through comprehensive testing

**Duration**: 30-45 minutes

**CRITICAL**: This phase is MANDATORY - no skill is complete without passing comprehensive tests

### 6.1 Create Comprehensive Test Suite

**File**: `test_skill_comprehensive.py`

**CRITICAL**: Test ALL use cases from documentation + edge cases

**Test structure**:
```python
#!/usr/bin/env python3
"""
Comprehensive Test Suite for [Domain] Skill
Tests all use cases from SKILL.md + edge cases
"""

import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__)))

from python_implementation import skill_function
from tooluniverse import ToolUniverse

def test_1_use_case_from_skill_md():
    """Test Case 1: [Use case name from SKILL.md]"""
    print("\n" + "="*80)
    print("TEST 1: [Use Case Name]")
    print("="*80)
    print("Expected: [What should happen]")

    tu = ToolUniverse()
    result = skill_function(tu=tu, input_param="value")

    # Validation
    assert isinstance(result, ExpectedType), "Should return expected type"
    assert result.field_name is not None, "Should have required field"

    print(f"\n✅ PASS: [What passed]")
    return result

def test_2_documentation_accuracy():
    """Test Case 2: QUICK_START.md example works exactly as documented"""
    print("\n" + "="*80)
    print("TEST 2: Documentation Accuracy")
    print("="*80)

    # Exact copy-paste from QUICK_START.md
    tu = ToolUniverse()
    result = skill_function(tu=tu, param="value")  # From docs

    # Verify documented attributes exist
    assert hasattr(result, 'documented_field'), "Doc says this field exists"

    print(f"\n✅ PASS: Documentation examples work")
    return result

def test_3_edge_case_invalid_input():
    """Test Case 3: Error handling with invalid inputs"""
    print("\n" + "="*80)
    print("TEST 3: Error Handling")
    print("="*80)

    tu = ToolUniverse()
    result = skill_function(tu=tu, input_param="INVALID")

    # Should handle gracefully, not crash
    assert isinstance(result, ExpectedType), "Should still return result"
    assert len(result.warnings) > 0, "Should have warnings"

    print(f"\n✅ PASS: Handled invalid input gracefully")
    return result

def test_4_result_structure():
    """Test Case 4: Result structure matches documentation"""
    print("\n" + "="*80)
    print("TEST 4: Result Structure")
    print("="*80)

    tu = ToolUniverse()
    result = skill_function(tu=tu, input_param="value")

    # Check all documented fields
    required_fields = ['field1', 'field2', 'field3']
    for field in required_fields:
        assert hasattr(result, field), f"Missing field: {field}"

    print(f"\n✅ PASS: All documented fields present")
    return result

def test_5_parameter_validation():
    """Test Case 5: All documented parameters work"""
    print("\n" + "="*80)
    print("TEST 5: Parameter Validation")
    print("="*80)

    tu = ToolUniverse()
    result = skill_function(
        tu=tu,
        param1="value1",  # All documented params
        param2="value2",
        param3=True
    )

    assert isinstance(result, ExpectedType), "Should work with all params"

    print(f"\n✅ PASS: All parameters accepted")
    return result

def run_all_tests():
    """Run all tests and generate report"""
    print("\n" + "="*80)
    print("[DOMAIN] SKILL - COMPREHENSIVE TEST SUITE")
    print("="*80)

    tests = [
        ("Use Case 1", test_1_use_case_from_skill_md),
        ("Documentation Accuracy", test_2_documentation_accuracy),
        ("Error Handling", test_3_edge_case_invalid_input),
        ("Result Structure", test_4_result_structure),
        ("Parameter Validation", test_5_parameter_validation),
    ]

    results = {}
    passed = 0
    failed = 0

    for test_name, test_func in tests:
        try:
            result = test_func()
            results[test_name] = {"status": "PASS", "result": result}
            passed += 1
        except Exception as e:
            results[test_name] = {"status": "FAIL", "error": str(e)}
            failed += 1
            print(f"\n❌ FAIL: {test_name}")
            print(f"   Error: {e}")

    # Summary
    print("\n" + "="*80)
    print("TEST SUMMARY")
    print("="*80)
    print(f"✅ Passed: {passed}/{len(tests)}")
    print(f"❌ Failed: {failed}/{len(tests)}")
    print(f"📊 Success Rate: {passed/len(tests)*100:.1f}%")

    if failed == 0:
        print("\n🎉 ALL TESTS PASSED! Skill is production-ready.")
    else:
        print("\n⚠️  Some tests failed. Review errors above.")

    return passed, failed

if __name__ == "__main__":
    passed, failed = run_all_tests()
    sys.exit(0 if failed == 0 else 1)

Requirements:

• ✅ Test ALL use cases from SKILL.md (typically 4-6 use cases)
• ✅ Test QUICK_START.md example (exact copy-paste must work)
• ✅ Test error handling (invalid inputs don't crash)
• ✅ Test result structure (all fields present, correct types)
• ✅ Test all parameters (documented params accepted)
• ✅ Test edge cases (empty results, partial failures)

6.2 Run Test Suite & Generate Report

cd skills/tooluniverse-[domain]
python test_skill_comprehensive.py > test_output.txt 2>&1

Requirements:

• ✅ 100% test pass rate
• ✅ All use cases pass
• ✅ Documentation examples work exactly as written
• ✅ No exceptions or crashes
• ✅ Edge cases handled gracefully

6.3 Create Test Report

File: SKILL_TESTING_REPORT.md

Content:

# [Domain] Skill - Testing Report

**Date**: [Date]
**Status**: ✅ PASS / ❌ FAIL
**Success Rate**: X/Y tests passed (100%)

## Executive Summary

[Brief summary of testing results]

## Test Results

### Test 1: [Use Case Name] ✅
**Use Case**: [Description from SKILL.md]
**Result**: [What happened]
**Validation**: [What was verified]

### Test 2-5: [Similar format]

## Quality Metrics
- **Code quality**: [Assessment]
- **Documentation accuracy**: [All examples work / Issues found]
- **Robustness**: [Error handling assessment]
- **User experience**: [Assessment]

## Recommendation
✅ PRODUCTION-READY / ❌ NEEDS FIXES

6.4 Validate Against Checklist

Implementation & Testing:

• All tool calls tested with real ToolUniverse instance
• Test script passes with 100% success
• Working pipeline runs without errors
• ALL use cases from SKILL.md tested
• QUICK_START examples tested (exact copy-paste works)
• Edge cases tested (invalid inputs, empty results)
• Result structure validated (all fields present)
• All parameters tested
• Error cases handled gracefully
• SOAP tools have operation parameter (if applicable)
• Fallback strategies implemented and tested
• Test report created (SKILL_TESTING_REPORT.md)

Documentation:

• SKILL.md is implementation-agnostic (NO Python/MCP code)
• python_implementation.py contains working code
• QUICK_START.md includes both Python SDK and MCP
• Tool parameter table notes "applies to all implementations"
• SOAP tool warnings displayed (if applicable)
• Fallback strategies documented
• Known limitations documented
• Example reports referenced
• Documentation examples verified to work

Quality:

• Reports are readable (not debug logs)
• All sections present even if "no data"
• Source databases clearly attributed
• Completes in reasonable time (<5 min)
• Test suite comprehensive (5+ test cases)
• Test report documents quality metrics

6.5 Manual Verification

Test with fresh environment:

1. Load ToolUniverse
2. Import python_implementation
3. Run exact example from QUICK_START (copy-paste)
4. Verify output matches expectations
5. Verify all documented fields accessible

CRITICAL: If documentation example doesn't work, fix EITHER:

• The documentation (update to match implementation), OR
• The implementation (update to match documentation)

NEVER release with documentation that doesn't work

Phase 7: Packaging & Documentation

Objective: Create distributable skill and summary

Duration: 15 minutes

7.1 Create Summary Document

File: NEW_SKILL_[DOMAIN].md

Content:

# New Skill Created: [Domain] Analysis

**Date**: [Date]
**Status**: ✅ COMPLETE AND TESTED

## Overview

[Brief description]

### Key Features
- [Feature 1]
- [Feature 2]

## Skill Details

**Location**: `skills/tooluniverse-[domain]/`

**Files Created**:
1. ✅ `python_implementation.py` ([lines]) - Working pipeline
2. ✅ `SKILL.md` ([lines]) - Implementation-agnostic docs
3. ✅ `QUICK_START.md` ([lines]) - Multi-implementation guide
4. ✅ `test_skill.py` ([lines]) - Test suite

**Total**: [total lines]

## Tools Integrated

- **Database 1**: [X tools]
- **Database 2**: [Y tools]
**Total**: [N tools]

## Test Results

✅ Test 1 - PASS ✅ Test 2 - PASS ✅ Test 3 - PASS

100% test pass rate

## Capabilities

[List key capabilities]

## Impact & Value

[Describe impact]

## Next Steps

[Suggest enhancements]

7.2 Update Session Tracking

If creating multiple skills in session, update tracking document with:

• Skills created count
• Total tools utilized
• Test coverage metrics
• Time per skill

Tool Parameter Verification Workflow

From devtu-optimize-skills - CRITICAL

Common Parameter Mistakes to Avoid

SOAP Tools Detection

Indicators:

• Error: "Parameter validation failed: 'operation' is a required property"
• Tool name includes: IMGT, SAbDab, TheraSAbDab
• Tool config shows operation in schema

Fix: Add operation parameter as first argument with method name

Response Format Variations

Standard: {status: "success", data: [...]} Direct list: Returns [...] without wrapper Direct dict: Returns {field1: ..., field2: ...} without status

Solution: Handle all three in implementation with isinstance() checks

Extended Reference: For detailed tool tables, examples, and templates, read REFERENCE.md in this skill directory. The agent can access it via: read skills/create-tooluniverse-skill/REFERENCE.md