Agent Skill · cast freeform-summary-to-galaxy-interface
Map a free-form source summary into a Galaxy workflow interface design brief.
← All cast skills · Source mold →
SKILL.md
# freeform-summary-to-galaxy-interface
Follow the procedure below and use the artifact/reference sections as the runtime contract.
## When To Use
- Map a free-form source summary into a Galaxy workflow interface design brief.
## Inputs
- Read artifact `freeform-summary`. Produced by `interview-to-freeform-summary`, `summarize-paper`. Free-form source summary emitted by summarize-paper or interview-to-freeform-summary; methods, tools, sample data, references, and workflow intent with explicit uncertainty.
- Read artifact `open-requirements-ledger`. Produced by `advance-galaxy-draft-step`, `apply-galaxy-workflow-changeset`, `compare-against-iwc-exemplar`, `cwl-summary-to-galaxy-data-flow`, `cwl-summary-to-galaxy-interface`, `cwl-summary-to-galaxy-template`, `freeform-summary-to-galaxy-data-flow`, `freeform-summary-to-galaxy-interface`, `freeform-summary-to-galaxy-template`, `implement-galaxy-tool-step`, `interview-to-galaxy-workflow-changeset`, `nextflow-summary-to-galaxy-data-flow`, `nextflow-summary-to-galaxy-interface`, `nextflow-summary-to-galaxy-reference-data`, `nextflow-summary-to-galaxy-template`, `repair-galaxy-draft-topology`. Carried obligations ledger open-requirements-ledger: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.
## Outputs
- Write artifact `freeform-galaxy-interface` as `freeform-galaxy-interface.md`. Format: `markdown`. Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source-summary provenance, confidence, open questions.
- Write artifact `open-requirements-ledger` as `open-requirements.ledger.yml`. Format: `yaml`. Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.
## Required Tools
- None declared. Procedure should not assume external CLIs are present.
## Load Upfront
- `references/notes/open-requirements-ledger.md`: Research note copied verbatim into the bundle. Inherit open entries rather than re-deriving them, close the ones this brief's input, output, and label decisions settle, and append interface obligations the narrative never settles — an output the source names but never specifies, a parameter stated only qualitatively, a collection shape the prose doesn't determine.
## Load On Demand
- `references/notes/galaxy-collection-semantics.md`: Research note copied verbatim into the bundle. Choose Galaxy collection input shapes (File / list / paired / list:paired / record) from the source's per-sample, paired, grouped, or nested data descriptions. Use when: the free-form summary describes paired reads, per-sample groups, nested or grouped inputs, or any input that should become a Galaxy dataset collection.
- `references/notes/galaxy-collection-semantics.yml`: Companion file copied verbatim into the bundle. Sibling of `references/notes/galaxy-collection-semantics.md`; read it where that note directs.
- `references/notes/galaxy-sample-sheet-collections.md`: Research note copied verbatim into the bundle. Pick the right sample_sheet variant and translate described per-sample column metadata into Galaxy column_definitions when the source describes sample-sheet-shaped inputs. Use when: the free-form summary describes a sample sheet, a per-sample/per-record table, or any table mapping samples to files that should become a Galaxy collection or sample-sheet input.
- `references/notes/galaxy-workflow-testability-design.md`: Research note copied verbatim into the bundle. Choose stable workflow input/output labels and promoted checkpoint outputs that future tests can address. Use when: deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.
## Validation
- None declared.
## Procedure
Read a free-form source summary and emit a reviewable Markdown interface brief for a Galaxy workflow. Capture workflow inputs, workflow outputs, labels, Galaxy collection shapes, checkpoint outputs worth exposing for tests, source-summary provenance, confidence, and open questions.
Free-form sources are narrative- or interview-derived and carry explicit uncertainty. Translate what the summary supports into interface decisions; carry unresolved interface choices forward as open questions rather than inventing precise inputs, outputs, or labels.
The output is not a gxformat2 skeleton and not a workflow schema. It is a design handoff consumed by freeform-summary-to-galaxy-data-flow, freeform-summary-to-galaxy-template, and later test-plan work.
## Feedback Mode
- Feedback mode is off unless the caller explicitly enables `--feedback` or supplies a feedback-ledger path.
- When enabled, read `_feedback.md` before doing the work and use its registered `foundry-feedback.ledger.yml` protocol.
- Preserve harness-owned run and phase state. Append only concrete observations about a canonical Foundry source asset or a related project that this run showed to be at fault; do not put ordinary workflow requirements in this ledger.
- Before reporting completion, make one explicit pass over the work you just did. Do not ask yourself whether anything was unclear — recall what happened: where you guessed at something the instructions should have settled, needed information this bundle does not carry, hit an instruction that contradicted another or contradicted the artifacts in front of you, used a packaged reference that did not cover your case, or did something the procedure never describes.
- Append an entry for each such event that clears the protocol's bar. If none do, append nothing and report `no feedback` explicitly. Silence and a clean pass are not the same thing, and nothing downstream can tell them apart unless you say which one it was.
- Pass the same ledger path to any subagent used for this work, and merge updates serially so one writer cannot overwrite another.
## Runtime Notes
- Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
- Preserve declared artifact filenames unless the user or harness supplies explicit paths.
- Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.