Add agent based AI tool recommendation

lib/galaxy/agents/__init__.py

@@ -15,6 +15,7 @@
 from .orchestrator import WorkflowOrchestratorAgent
 from .registry import AgentRegistry
 from .router import QueryRouterAgent
+from .tools import ToolRecommendationAgent
 
 __all__ = [
     "AgentType",
@@ -25,6 +26,7 @@
     "ErrorAnalysisAgent",
     "CustomToolAgent",
     "WorkflowOrchestratorAgent",
+    "ToolRecommendationAgent",
 ]
 
 # Global agent registry instance
@@ -35,3 +37,4 @@
 agent_registry.register(AgentType.ERROR_ANALYSIS, ErrorAnalysisAgent)
 agent_registry.register(AgentType.CUSTOM_TOOL, CustomToolAgent)
 agent_registry.register(AgentType.ORCHESTRATOR, WorkflowOrchestratorAgent)
+agent_registry.register(AgentType.TOOL_RECOMMENDATION, ToolRecommendationAgent)

lib/galaxy/agents/base.py

@@ -166,6 +166,7 @@ class AgentType:
     ERROR_ANALYSIS = "error_analysis"
     CUSTOM_TOOL = "custom_tool"
     ORCHESTRATOR = "orchestrator"
+    TOOL_RECOMMENDATION = "tool_recommendation"
 
 
 # Internal agent response model (simplified for internal use)

lib/galaxy/agents/prompts/router.md

@@ -24,12 +24,17 @@ For off-topic questions (general coding, non-scientific topics, unrelated softwa
 ## How to Respond
 
 **Answer directly** for:
-- Galaxy platform questions ("How do I run BWA?", "What is a workflow?")
-- Tool discovery ("What tools analyze RNA-seq data?")
-- Usage guidance ("How do I upload files?")
+- Galaxy platform questions ("What is a workflow?", "How do I upload files?")
+- How to USE a specific tool ("How do I run BWA?", "What parameters does HISAT2 need?")
 - Scientific analysis best practices
 - Galaxy features and capabilities
 
+**Use `hand_off_to_tool_recommendation`** when user:
+- Asks what tool to use for a task ("What tool should I use to align reads?")
+- Wants to find/discover tools ("Is there a tool that converts BAM to FASTQ?")
+- Needs help choosing between tools for an analysis type
+- Asks "what tools are available for X?"
+
 **Use `hand_off_to_error_analysis`** when user:
 - Has a failed job with error messages or exit codes
 - Is asking about stderr/stdout from a tool run
@@ -43,8 +48,10 @@ For off-topic questions (general coding, non-scientific topics, unrelated softwa
 
 ## Important Distinctions
 
-- "What tool does X?" → Answer directly (tool discovery)
+- "What tool should I use for X?" → Use hand_off_to_tool_recommendation
+- "Is there a tool that does X?" → Use hand_off_to_tool_recommendation
 - "How do I use tool X?" → Answer directly (usage help)
+- "What parameters does X need?" → Answer directly (usage help)
 - "Create a tool that does X" → Use hand_off_to_custom_tool
 - "My job failed" → Use hand_off_to_error_analysis
 

lib/galaxy/agents/prompts/tool_recommendation.md

@@ -0,0 +1,42 @@
+# Galaxy Tool Recommendation Agent
+
+You are a Galaxy Project expert specializing in tool discovery and recommendation.
+
+Your goal is to help users find the right tools for their bioinformatics tasks by providing practical recommendations with clear reasoning.
+
+## CRITICAL: Tool Availability
+
+**This Galaxy server only has certain tools installed. You MUST verify tools exist before recommending them.**
+
+1. **ALWAYS call `search_galaxy_tools` FIRST** before making any recommendations
+2. **ONLY recommend tools that appear in the search results** - if a tool doesn't show up in the search, it is NOT installed on this server
+3. If your search returns no results for a common tool (like BWA, HISAT2, etc.), that means it's not installed
+4. When a well-known tool is not installed, tell the user: "While [tool name] would typically be recommended for this task, it doesn't appear to be installed on this Galaxy server. You may want to contact your administrator to request its installation."
+
+## Available Tools
+
+- **`search_galaxy_tools(query)`** - Search for tools by keyword. Always start here.
+- **`get_galaxy_tool_details(tool_id)`** - Get detailed info (inputs, outputs, version) for a specific tool. Use after searching to provide better recommendations.
+- **`get_galaxy_tool_categories()`** - List available tool categories. Use when user asks "what kinds of tools are available?" or to understand the server's capabilities.
+
+## Recommendation Process
+
+1. Understand the user's task and data types
+2. **Call `search_galaxy_tools` with relevant keywords** (e.g., "alignment", "mapping", "fastq")
+3. Optionally call `get_galaxy_tool_details` on promising candidates to get input/output format info
+4. Recommend tools from the search results, using their exact IDs
+5. If no suitable tools are found, be honest about the limitation
+
+## Tool IDs
+
+- Use ONLY the exact `id` field from search results
+- Never guess or fabricate tool IDs based on your training knowledge
+- If you know a tool exists in Galaxy generally but it's not in the search results, it's NOT available on this server
+
+## Best Practices
+
+- Prioritize tools that are well-maintained and widely used
+- Consider the user's experience level
+- Explain why you're recommending specific tools
+- Mention important parameters or configuration options
+- Suggest workflows when multiple tools are needed

lib/galaxy/agents/router.py

@@ -5,6 +5,7 @@
 - Answer general Galaxy questions directly (returns str)
 - Hand off to error_analysis for job debugging
 - Hand off to custom_tool for explicit tool creation requests
+- Hand off to tool_recommendation for tool discovery
 """
 
 import logging
@@ -58,13 +59,15 @@ def _create_agent(self) -> Agent[GalaxyAgentDependencies, str]:
         # Create output functions for specialist handoff
         error_handoff = self._create_error_analysis_handoff()
         tool_handoff = self._create_custom_tool_handoff()
+        tool_rec_handoff = self._create_tool_recommendation_handoff()
 
         return Agent(
             self._get_model(),
             deps_type=GalaxyAgentDependencies,
             output_type=[
                 error_handoff,
                 tool_handoff,
+                tool_rec_handoff,
                 str,  # Default: answer directly
             ],
             system_prompt=self.get_system_prompt(),
@@ -166,6 +169,43 @@ async def hand_off_to_custom_tool(
 
         return hand_off_to_custom_tool
 
+    def _create_tool_recommendation_handoff(self):
+        """Create output function for tool recommendation handoff."""
+
+        async def hand_off_to_tool_recommendation(
+            ctx: RunContext[GalaxyAgentDependencies],
+            query: str,
+        ) -> str:
+            """Route to tool recommendation agent for finding Galaxy tools.
+
+            Use this when the user:
+            - Asks what tool to use for a task ("what tool aligns reads?")
+            - Wants to find tools for a specific analysis type
+            - Needs help discovering available tools
+            - Asks "is there a tool that does X?"
+
+            Do NOT use for:
+            - How to USE a specific tool (answer directly)
+            - Creating NEW tools (use hand_off_to_custom_tool)
+            - Job errors (use hand_off_to_error_analysis)
+
+            Args:
+                query: The tool discovery question
+            """
+            from .tools import ToolRecommendationAgent
+
+            log.info(f"Router handing off to tool_recommendation: '{query[:100]}...'")
+
+            try:
+                agent = ToolRecommendationAgent(ctx.deps)
+                result = await agent.process(query)
+                return result.content
+            except Exception as e:
+                log.error(f"Tool recommendation handoff failed: {e}")
+                return f"I encountered an issue while searching for tools. Please try again or browse the tool panel directly. Error: {e}"
+
+        return hand_off_to_tool_recommendation
+
     async def process(self, query: str, context: Optional[dict[str, Any]] = None) -> AgentResponse:
         """
         Process a query and return the response.