# cwl-summary-to-galaxy-data-flow scenarios

Concrete cases for `cwl-summary-to-galaxy-data-flow`, exercised against the
abstract properties in `eval.md`. Each case binds a fixture shape and states its
expected values; the `eval.md` oracle is applied to whatever the case produces.

## Case: secondaryFiles plumbing visible

- fixture: a summary where at least one step input or workflow output requires `secondaryFiles`.
- expect: draft either keeps required secondaryFiles traveling with their primary
  file across steps, or flags the gap as an open question. They must not silently
  vanish between nodes.

## Case: no invented Tool Shed IDs

- fixture: any non-trivial summary with multiple `CommandLineTool` steps.
- expect: each CWL `CommandLineTool` appears as a placeholder with enough source
  context (baseCommand, key inputs, expected outputs) for later tool discovery.
  Concrete Tool Shed IDs, owners, or version revisions must not be fabricated.

## Case: pickValue is not silently dropped

- fixture: a summary with `pickValue:*` on a workflow output or step input (e.g. `first_non_null`, `the_only_non_null`, `all_non_null`).
- expect: every `pickValue` marker appears in the draft — as a native
  `pick_value` workflow step, a sibling-workflow note, or an open question. A
  draft that omits the marker fails this case even if it looks plausible
  otherwise.

## Case: ExpressionTool steps surface as placeholders

- fixture: a summary containing at least one `ExpressionTool` step (or a subworkflow that uses one).
- expect: each `ExpressionTool` appears as a flagged placeholder with the source
  expression intent noted for review. They must not be absorbed silently into
  wiring, since Galaxy has no native equivalent.

## Case: template Mold can consume the draft

- fixture: source summary, interface brief, and data-flow brief.
- expect: `cwl-summary-to-galaxy-template` can turn the draft into workflow
  inputs, placeholder steps, rough connections, and TODO notes without asking for
  missing basics such as step names, source CWL tools, or open branching
  questions.