galaxy-tool-refactor-mcp 0.3.5

MCP server exposing the Galaxy tool refactoring facade to AI agents.

galaxy-tool-refactor-mcp

An MCP server that exposes the Galaxy tool refactoring framework to AI coding agents. A tier-4 sibling of galaxy-tool-refactor-cli: both wrap the galaxy-tool-refactor-registry facade (tier 3.6) for a different audience — the CLI for humans at a terminal, this for agents over the Model Context Protocol.

Shape

The facade is library-first (structured args in, structured results out, no disk writes unless asked, introspectable), so the server is a thin adapter:

• service.py — protocol-agnostic. Pure functions that take XML as a str (plus rulesets / select / ignore) and return JSON-able dicts by calling the facade. No mcp import; fully unit-tested.
• server.py — the FastMCP binding. A small handler per tool delegates to service, and is the error boundary (facade UnknownRuleset / UnknownRuleCode / UnknownProfile and tier-1 ToolXmlSyntaxError → a clean MCP tool error).

Tools

MCP tool	What it does
format_tool	Apply a ruleset's fixable rules then format; returns canonical XML + advisory notes.
upgrade_tool	Repair then profile placement then format; minimal-bump by default (profile= moves only when strictly needed for validity; modernize opts into the behavior-preserving walk, capped at the lower of the behaviour ceiling and the deployment ceiling, the newest profile every major public Galaxy server runs; allow_behavior_change lifts the walk's behaviour gate only, target_profile caps the walk and may exceed the deployment ceiling); returns upgraded XML, steps applied, the behavior-preserving verdict, baseline_profile/reached_profile/stopped_at/blocking_codes/auto_fixed_codes, and notes.
check_tool	Report-only detect over the selected rules; returns the findings (each flagged fixable vs advisory).
convert_help_tool	Convert an RST <help> body to Markdown when provable (profile ≥ 24.2 + render-equivalence gate); returns converted XML or a skip reason.
tokenize_version_tool	Factor a literal version="<base>+galaxy<suffix>" into @TOOL_VERSION@/@VERSION_SUFFIX@ tokens when the expansion-equality gate proves it byte-identical; returns tokenized XML or a skip reason.
find_references_tool	Read-only: every Cheetah $name reference site across the tool's templated sections (returns {name, occurrences}). Single-document — references inside imported macro files are the CLI find-references.
rename_param_tool	Rename a parameter across the tool atomically (returns {old, new, changed, renamed, reason, formatted}; formatted is null on a bail). Single-document — the cross-file/imported-macro rename is the CLI rename-param.
list_rulesets	The baked-in rulesets (name / codes / is_default / description).
list_rules	The baked-in rules (code / summary / family / fixable / rulesets).

Agents supply content and receive content — the server never writes to disk.

Run

uv run galaxy-tool-refactor-mcp   # serves over stdio

Point an MCP client (e.g. a coding agent) at that command. list_rulesets / list_rules let the agent discover the available rulesets and rule codes at runtime instead of hardcoding them.

See docs/decisions.md D1 for the design, and docs/vision.md for the longer-horizon agent-authored-rules direction (Goal 2, still future).