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name: workflows-and-tools description: "Author, validate, test, and troubleshoot Galaxy tool wrappers, tool tests, workflow Format2 YAML, CWL conversion surfaces, tool dependency hints, and tool-util CLIs." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Galaxy Workflows and Tools

Use this sub-skill when a task involves Galaxy tool XML or YAML wrappers, tool tests, workflow framework tests, Format2 workflow YAML, CWL conversion surfaces, tool panel loading, dependency requirements, mulled helpers, or galaxy-tool-util command-line utilities.

Start Here

• For tool wrappers and tests, read Tool Development.
• For Format2 workflow YAML, workflow framework tests, inline user-defined tools, and CWL boundaries, read Workflow Development.
• For safe CLI checks and installed galaxy-tool-util entry points, read CLI Reference and use scripts/inspect_tool_util.py.
• For parser, validation, dependency, workflow conversion, and tool panel failures, read Troubleshooting.

Boundaries

• Stay here for tool XML structure, <tests> blocks, YAML test files, galaxy-tool-test, galaxy-tool-format, galaxy-tool-upgrade-advisor, validate-test-format, workflow framework tests, Format2 YAML, CWL conversion surfaces, tool panel behavior, and mulled/dependency command hints.
• Route datatype definitions, persistent tool data tables, .loc files, and deep data-manager table behavior to Data and Storage. Data managers appear here only as special Galaxy tools with admin-only behavior and tool-test implications.
• Route API import/invocation of already-authored workflows to API Automation.
• Route Tool Shed publishing, repository metadata, installation, and distribution operations to Tool Shed Operations.

Safe Default Workflow

1. Identify whether the artifact is a tool wrapper, tool test file, workflow definition, workflow test file, CWL conversion case, dependency/mulled check, or tool panel configuration issue.
2. Run local, non-network static checks first: XML parse/format diff, test-format schema validation, import/help checks for galaxy-tool-util, and upgrade advice.
3. Use server-backed commands such as galaxy-tool-test only when the user supplies a Galaxy URL and API key or explicitly asks to use a running local Galaxy.
4. Treat conda, container registry, BioContainers, and mulled build/list/search operations as external dependency management: explain network/runtime requirements before running them.

Quick Commands

python scripts/inspect_tool_util.py --check-imports --help-checks
python scripts/inspect_tool_util.py --tool-xml path/to/tool.xml --test-file path/to/tests.yml
python -m galaxy.tool_util.format --diff path/to/tool.xml
python -m galaxy.tool_util.validate_test_format path/to/tests.yml
python -m galaxy.tool_util.upgrade.script path/to/tool.xml --profile-version 24.2

Use galaxy-tool-test only with a running Galaxy target, for example: galaxy-tool-test --galaxy-url http://localhost:8080 --key "$GALAXY_API_KEY" --tool-id TOOL_ID --test-index 0.