Galaxy MCP vs Medplum MCP

Galaxy MCP tools 48

• connectConnect to Galaxy server
• search_tools_by_nameSearch Galaxy tools whose name, ID, or description contains the given query (substring match). Results are paginated. pagination.total_items is how many tools matched in total; pagination.next_offset is where the next page starts (None on the last page). RECOMMENDED WORKFLOW: 1. Use this function to find tools by name/keyword 2. Review the returned tool IDs and names 3. Call get_tool_details(tool_id) for full input parameters 4. Call run_tool() with the correct inputs
• get_tool_detailsGet detailed information about a specific tool including its input parameters. RECOMMENDED WORKFLOW: 1. First find tools using search_tools_by_name() or get_tool_panel() 2. Call this function with io_details=True to see all input parameters 3. Use the inputs schema to construct the inputs dict for run_tool()
• get_tool_run_examplesReturn the exact XML test definitions (inputs, outputs, assertions, required files) for a Galaxy tool so an LLM can study real, working run configurations.
• get_tool_input_templateReturn a ready-to-fill ``inputs`` skeleton for a tool, plus a compact schema. Call this before run_tool when you are unsure how to shape ``inputs``. Replace placeholders (e.g. ``<dataset_id>``) with real values. Repeats show one instance (``name_0|...``); duplicate with ``name_1|...`` to add more. The flattened-key convention is ``section|param``, ``cond|selector``, ``repeat_0|param``.
• get_tool_citationsGet citation information for a specific tool
• run_toolRun a Galaxy tool on datasets in a history. RECOMMENDED WORKFLOW: 1. Create or select a history: create_history() or get_histories() 2. Upload data: upload_file() or upload_file_from_url() 3. Get tool parameters: get_tool_details(tool_id, io_details=True) 4. Call this function with properly formatted inputs 5. Monitor job: get_job_details() or check history contents
• get_tool_panelBrowse the Galaxy tool panel (toolbox) one level at a time. The whole panel is megabytes on a production server, so it is never returned whole. Called with no arguments this lists the top-level entries - each section with the number of tools in it, plus any tools that sit outside a section. Pass section_id to list the tools in one section.
• create_historyCreate a new history to organize datasets and analyses. A history is the primary workspace in Galaxy. Create a new history for each distinct project or analysis to keep your work organized. RECOMMENDED WORKFLOW: 1. Create a history with a descriptive name 2. Upload your input data: upload_file() or upload_file_from_url() 3. Run tools on the data: run_tool() 4. View results: get_history_contents()
• update_historyUpdate an existing Galaxy history's metadata. Any combination of name, annotation, tags, deleted, and published can be updated in a single call. Fields left as None are not modified.
• search_tools_by_keywordsRecommend Galaxy tools based on a list of keywords. Matches on name and description first, then on accepted input formats, and keeps that order so paging is stable. Results are paginated: pagination.total_items is the full match count, pagination.next_offset is where the next page starts. Expensive: finding the format matches costs one detail lookup per tool that did not match by name, and every page repeats the whole scan. Prefer search_tools_by_name when a name or description substring will do.
• get_server_infoGet Galaxy server information including version, URL, and configuration details Also reports which tools this server is too old to run, in `unsupported_tools`, and whether its version could be read at all, in `version_known` -- an empty `unsupported_tools` means nothing is ruled out only when `version_known` is true. Returns: GalaxyResult with server information in data field
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Medplum MCP tools

No tool names declared yet. Check the project README from the listing page.