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Tools

List available bioinformatics tools and invoke them directly without going through the agent.

GET/v1/toolstools scope

Returns all available bioinformatics tools with their input schemas. Use this to discover what tools are available before invoking them.

tools = client.tools.list()
for tool in tools:
    print(f"{tool.id}: {tool.description}")
POST/v1/tools/:toolId/runtools scope

Invoke a specific tool with input parameters. Returns the tool output synchronously. Use GET /v1/tools to discover available tool IDs and their required parameters.

Request body

ParameterTypeDescription
inputobjectTool-specific input parameters. See tool schema from GET /v1/tools.
workspace_idstringOptional workspace context for file-aware tools.
result = client.tools.run(
    tool_id="ncbi_search",
    input={
        "database": "pubmed",
        "query": "BRCA1 mutations breast cancer",
        "maxResults": 5,
    }
)
for article in result["results"]:
    print(article["title"])
Tip: For complex, multi-step analysis, use the Query endpoint instead — the agent will automatically select and chain the right tools based on your prompt.