How this complements planemo

TL;DR. planemo is the community’s command-line companion for developing, linting, testing, and deploying Galaxy (and CWL) tools and workflows. galaxy-tool-refactor doesn’t replace any of that. It adds the part planemo doesn’t focus on: automatically fixing and upgrading tool XML, in a canonical IUC style, with an agent-callable interface. They’re siblings in the Galaxy family, meant to be used together.

Where they overlap, and where they don’t

planemo

galaxy-tool-refactor

Lint / report problems

✅ (broad: tools, workflows, CWL)

✅ advisory check (tool XML, IUC best practices)

Auto-fix style/structure

limited

✅ canonical format (idempotent, behaviour-preserving)

Upgrade a tool’s profile= with safe repairs

-

✅ upgrade (bounded by soundness)

Run tool tests

✅

-

Serve / deploy, ToolShed publishing

✅

-

Workflows & CWL

✅

- (tool XML only)

Agent / MCP interface

-

✅ MCP server + library

Evidence base

-

tuned against 9,373 real tools

planemo tells you what’s wrong; galaxy-tool-refactor can also make the fix and move the tool forward. The overlap is only in detection, and even there the two have different emphases (planemo is broad across artifact types; this project goes deep on tool-XML structure and profile upgrades).

The detection overlap is deliberate: the check tier reimplements the mechanically-reimplementable planemo lint tool-XML linters, the generated parity table maps all 146 planemo linters to their GTR coverage rule-by-rule, and the CLI accepts planemo linter names as rule aliases (--select HelpMissing, case-insensitive), so a planemo user can select rules by the names they already know.

How they fit together

  • A maintainer can keep using planemo for testing and deployment, and reach for format/upgrade to do the mechanical cleanup and version bump.

  • The most natural future link is for this engine to act as a fix/upgrade backend behind planemo or the planemo CI action, see the leverage map. That integration is not built yet; it’s a direction, not a claim.

On positioning

planemo is a core Galaxy-community project maintained by people we work alongside. This project is built to strengthen that ecosystem, same family, complementary job, not to compete with it.