Galaxy Tool MCP Server

The MCP Server Galaxy Tool Utilities addresses a common bottleneck for bioinformatics developers: the tedious, error‑prone process of creating and validating Galaxy tool definitions. Galaxy, a widely used workflow platform for life‑science data analysis, relies on XML files to describe each tool’s inputs, outputs, and execution logic. Crafting these XML files manually is time‑consuming and prone to schema violations, which can stall deployment or break reproducibility. This MCP server eliminates that friction by providing a lightweight, protocol‑compliant service that validates any Galaxy tool XML against the official schema and can instantly generate a boilerplate template for new tools.

For developers integrating AI assistants—such as Claude or other MCP‑compatible agents—this server offers a direct, programmatic interface to the Galaxy ecosystem. Instead of manually opening editors or running command‑line utilities, an AI assistant can request the server to validate a tool XML string or ask for a fresh template. The assistant can then embed these responses into conversational workflows, guiding users through tool development or automating repetitive tasks like parameter tuning. Because the server operates over standard MCP streams, it fits seamlessly into existing development pipelines and IDE extensions (e.g., Cline in VSCode), allowing developers to invoke validation or template generation with a single prompt.

Key capabilities include:

• Schema Validation: The server parses incoming XML and checks it against the official Galaxy XSD, returning detailed error messages if the file is malformed or non‑conformant.
• Template Generation: A minimal, syntactically correct Galaxy tool XML is produced on demand, providing a scaffold that developers can customize with specific commands or parameters.
• Low‑Latency Interaction: Running locally via and communicating over stdio, the server offers near‑instant responses suitable for interactive development sessions.

Typical use cases span from rapid prototyping of new Galaxy tools—especially when incorporating emerging libraries like PyCaret—to continuous integration pipelines that automatically verify tool definitions before deployment. In a collaborative environment, an AI assistant can surface validation results in real time, reducing the need for manual reviews and ensuring that all contributors adhere to Galaxy’s strict schema requirements.

What sets this MCP server apart is its focus on the tool definition layer of Galaxy, a niche yet critical aspect often overlooked by broader bioinformatics toolchains. By abstracting away XML intricacies, it empowers developers to concentrate on biological logic rather than boilerplate syntax. The integration with MCP means that any agent or IDE plugin capable of speaking the protocol can tap into these utilities, making it a versatile addition to modern AI‑augmented development workflows.