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 astr(plusrulesets/select/ignore) and return JSON-abledicts by calling the facade. Nomcpimport; fully unit-tested.server.py— the FastMCP binding. A small handler per tool delegates toservice, and is the error boundary (facadeUnknownRuleset/UnknownRuleCode/UnknownProfileand tier-1ToolXmlSyntaxError→ 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).
1 maintainer
Metadata
1 maintainer
Release files for galaxy-tool-refactor-mcp 0.3.9
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