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Galaxy user-defined tool authoring help

Vendored Galaxy authoring guidance for user-defined tools: tool format, expressions, containers, API endpoints, and use in workflows.

draft target/galaxy
Raw
Revised
2026-10-23
Rev
4
Sources
https://github.com/galaxyproject/galaxy/blob/5af1d03c929748006dd53ad451e5cb1fd140399a/client/src/components/Tool/authoringHelp.yml
Related

Vendored from upstream, pinned at SHA 5af1d03 on release_26.1, after galaxyproject/galaxy#23694 merged. One file lives next to this note and is declared in companions: so casting carries it with the note:

  • galaxy-user-tool-authoring-help.yml — Galaxy’s single source of truth for GalaxyUserTool authoring guidance (client/src/components/Tool/authoringHelp.yml). Galaxy renders it twice: as the help panel in the tool editor and as the generated user_defined_tools_authoring page of the Galaxy docs. Sync is manual.

When to consult: as the upstream source for galaxy-user-tool-workflow-binding, which derives the Foundry’s step-binding rule from the file’s workflows section, and for the endpoint table in its api section.

Reading the file

The file is a list of sections, each with an id, a title, a kind, and a CommonMark body. Some bodies contain placeholders ({{quick_start_example}}, {{parameter_type_index}}, {{validator_type_index}}, {{output_type_index}}). Sections with parameter_types, output_types, or validator_types set are filled from Galaxy’s tool source schema at render time. Neither the placeholders nor those sections are expanded here, so the per-type field tables are not in this copy. Links use Galaxy’s own gxdoc:, gxui:, and gxhelp:// targets and do not resolve outside Galaxy.

The sections the Foundry reads:

  • workflows (“Using a tool in a workflow”) — how a format2 workflow step embeds a user-defined tool under run. galaxy-user-tool-workflow-binding is derived from it.
  • api (“API endpoints”) — the /api/unprivileged_tools endpoints, the create payload shape, and running a registered tool by tool_uuid.
  • validation, testing — what Galaxy checks when a tool is created, and that Galaxy stores declared tool tests but does not run them for a tool held in its database.

The field-level rules in tool-format, parameters, outputs, expressions, and containers overlap galaxy-user-tool-authoring, which was derived earlier from Galaxy’s generator prompts. That note remains what author-galaxy-tool-wrapper loads.

Incoming References (1)