Issues

• API Docs Maybe Should Have Corresponding MCP entrypoints

  agent/implementdocumentationneeds-triageroadmap/offupstream/galaxy
  galaxyproject/foundry#624 · Filter by author jmchilton opened on Sep 26, 2026

• Apply Rules Tutorial Patterns

  agent/researchpriority/v2roadmap/off
  galaxyproject/foundry#621 · Filter by author jmchilton opened on Sep 26, 2026

• Augment freeform-to-Workflow Brief scenarios with real source artifacts

  needs-triage
  galaxyproject/foundry#592 · Filter by author jmchilton opened on Sep 20, 2026

• download?style=ga emits unversioned tool_ids, producing workflows that save but cannot be invoked

  needs-triage
  galaxyproject/foundry#591 · Filter by author scottcain opened on Sep 18, 2026

• Authoring never checks a wrapped script's own declared input-ordering assumption against the tool it will consume from

  needs-triage
  galaxyproject/foundry#590 · Filter by author scottcain opened on Sep 18, 2026

• PUT /api/workflows/{id} defaults exact_tools to true and discards the per-step detail it already computed

  needs-triage
  galaxyproject/foundry#589 · Filter by author scottcain opened on Sep 18, 2026

• A sample_sheet column was wired onto a plain scalar tool port, a binding that can never work

  needs-triage
  galaxyproject/foundry#588 · Filter by author scottcain opened on Sep 18, 2026

• gxformat2 has no tool_uuid, so a step bound to a registered UDT imports unresolved

  needs-triage
  galaxyproject/foundry#587 · Filter by author scottcain opened on Sep 18, 2026

• Galaxy's unprivileged-tool lint fails opaquely on an integer input with value: 0

  needs-triage
  galaxyproject/foundry#586 · Filter by author scottcain opened on Sep 18, 2026

• The real UDT registration endpoint is /api/unprivileged_tools, not the admin-only /api/dynamic_tools

  needs-triage
  galaxyproject/foundry#585 · Filter by author scottcain opened on Sep 18, 2026

• Invocation-failure reference has no tell for a stale toolbox read vs. a real install failure

  needs-triage
  galaxyproject/foundry#584 · Filter by author scottcain opened on Sep 18, 2026

• replacement_collection indexes rows unconditionally, crashing Planemo staging for a sample_sheet input without rows

  needs-triage
  galaxyproject/foundry#583 · Filter by author scottcain opened on Sep 18, 2026

• No documented path for an authored GalaxyUserTool to reach a Planemo-managed toolbox

  needs-triage
  galaxyproject/foundry#582 · Filter by author scottcain opened on Sep 18, 2026

• gxwf validate --connections crashes on an ordinary format2 dict-shaped step.in

  needs-triage
  galaxyproject/foundry#581 · Filter by author scottcain opened on Sep 18, 2026

• comments: type: frame authored without position/size is rejected by real Galaxy import

  needs-triage
  galaxyproject/foundry#580 · Filter by author scottcain opened on Sep 18, 2026

• No packaged note documents the sample_sheet + rows: job-input shape

  needs-triage
  galaxyproject/foundry#579 · Filter by author scottcain opened on Sep 18, 2026

• tests-format has no way to put a value on an intermediate step's input port

  needs-triage
  galaxyproject/foundry#578 · Filter by author scottcain opened on Sep 18, 2026

• freeform-summary-to-galaxy-test-plan is silent on being handed a concrete draft and resolved test-data refs

  needs-triage
  galaxyproject/foundry#577 · Filter by author scottcain opened on Sep 18, 2026

• Test-plan schema requires a file-shaped fixture for plain scalar workflow parameters

  needs-triage
  galaxyproject/foundry#576 · Filter by author scottcain opened on Sep 18, 2026

• paper-to-test-data has no scoping or upstream-fixture guidance, and is the weaker half of its own fallback chain

  needs-triage
  galaxyproject/foundry#575 · Filter by author scottcain opened on Sep 18, 2026

• gxwf tool-search returns zero hits for a literal Tool Shed repo slug

  needs-triage
  galaxyproject/foundry#574 · Filter by author scottcain opened on Sep 18, 2026

• implement-galaxy-tool-step documents no binding convention for an authored UDT

  needs-triage
  galaxyproject/foundry#573 · Filter by author scottcain opened on Sep 18, 2026

• ToolShed-fetch decoder rejects a real IUC wrapper's filtered list-collection output

  needs-triage
  galaxyproject/foundry#572 · Filter by author scottcain opened on Sep 18, 2026

• gxformat2-schema documents nested state but not nested in: key addressing

  needs-triage
  galaxyproject/foundry#571 · Filter by author scottcain opened on Sep 18, 2026

• Pattern MOCs are cast without the pattern pages they point at

  needs-triage
  galaxyproject/foundry#570 · Filter by author scottcain opened on Sep 18, 2026