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Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable.
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基于 SOC 职业分类
Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan.
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
Assemble Galaxy workflow test fixtures and assertions.
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
| name | author-galaxy-tool-wrapper |
| description | Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
summary-nextflow. Schema: summary-nextflow. Produced by summarize-nextflow. Source pipeline summary from summarize-nextflow; provides process command, inputs, outputs, and container or conda evidence for UDT authoring.galaxy-user-tool-definition as galaxy-user-tool.yml. Format: yaml. Galaxy GalaxyUserTool YAML definition for a tool not present on the Tool Shed.references/prompts/custom-tool-structured.md: prompt reference copied verbatim into the bundle. Generate a schema-shaped GalaxyUserTool YAML definition from missing-wrapper requirements and source-derived process evidence.references/schemas/summary-nextflow.schema.json: Schema file copied verbatim into the bundle. Read process tool, container, conda, inputs, outputs, script summary, and test fixture evidence from the source pipeline summary.references/prompts/custom-tool-critic.md: prompt reference copied verbatim into the bundle. Run the mandatory fuzzy quality review after structural validation passes. Use when: after the drafted GalaxyUserTool passes structural validation and before emitting galaxy-user-tool.yml.references/notes/component-nextflow-containers-and-envs.md: Research note copied verbatim into the bundle. Map Nextflow container/conda evidence to Galaxy UDT container and package provenance. Use when: a missing Galaxy user-defined tool must be authored from a Nextflow process with container or conda directives.references/notes/component-nextflow-containers-and-envs.yml: Companion file copied verbatim into the bundle. Sibling of references/notes/component-nextflow-containers-and-envs.md; read it where that note directs.Author a Galaxy user-defined tool (UDT) YAML definition when discover-shed-tool cannot produce an acceptable existing Tool Shed wrapper. This skill owns the author-on-fallthrough path only; do not duplicate existing wrappers unless discovery evidence is weak or missing.
The output is a single GalaxyUserTool YAML document, not Galaxy XML. Preserve source evidence and unresolved assumptions in the emitted artifact or companion notes rather than inventing command flags, containers, datatypes, or package names.
Use the source summary and branch fallthrough context to identify:
Read the discovery result before authoring. Continue only when discovery returned miss, or when the selected hit was weak enough that the harness explicitly fell through.
If the missing tool need is under-specified, ask for clarification or emit an unresolved assumption. Do not create a plausible-looking UDT from absent command or container evidence.
Extract the minimum executable contract:
shell_command intent and every referenced input/output token.from_work_dir / discovery rules.Prefer BioContainers or directly evidenced containers. If only Conda/package evidence exists, record what is known and avoid guessing an image tag.
Use references/prompts/custom-tool-structured.md to generate a GalaxyUserTool YAML draft from the requirements brief.
The draft must use class: GalaxyUserTool. Every variable referenced by shell_command must have a declared input or output. Escape shell variables that are not Galaxy expressions.
Validate the draft against the available Galaxy user-tool validator or schema surface before critique. Treat structural validation failures as authoring failures, not critic feedback.
Fix validation errors directly. Do not run the critic until the draft passes structural validation.
After structural validation passes, use references/prompts/custom-tool-critic.md with the original request, requirements brief, and drafted YAML.
Apply every concrete clarity or idiomaticity issue when should_refine is true. Re-validate the refined draft structurally after edits. If critic feedback conflicts with source evidence, keep the source evidence and record the conflict.
Write galaxy-user-tool.yml with the validated and critic-reviewed GalaxyUserTool definition.
The artifact should be ready for the downstream harness or Galaxy runtime to load as a user-defined tool. Include unresolved assumptions only when they are truthful and actionable; otherwise fail instead of emitting a misleading tool.