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cwl-test-to-galaxy-test-plan

Translate CWL test fixtures into a Galaxy workflow test plan.

draft

Mold health

ok
  • Source layout

    Every file beside index.md is one the mold kind declares.

  • Axis fields

    source-specific fields are coherent.

  • Eval plan

    Abstract oracle: the properties any cast of this Mold must satisfy.

    eval.md declares properties and check type.

    eval.md ↗
  • Scenarios

    Concrete cases bound to fixtures, run against the eval properties.

    scenarios.md declares cases bound to fixtures.

    scenarios.md ↗
  • Typed refs

    8 typed references; 0 resolver issues.

  • On-demand triggers

    All on-demand references describe triggers.

  • Evidence checks

    Hypothesis references include verification.

axis
source-specific
source
cwl
name
cwl-test-to-galaxy-test-plan
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Schema galaxy-workflow-test-plan

Structured contract copied for validation or lookup.

Purpose
Output contract: the emitted plan conforms to [[galaxy-workflow-test-plan]]. Cast bundles the JSON Schema; validate with `foundry validate-galaxy-workflow-test-plan`.
Verify
Cast the skill on a CWL summary carrying tests and confirm the emitted YAML validates and downstream [[implement-galaxy-workflow-test]] consumes it.
Schema tests-format

Structured contract copied for validation or lookup.

Purpose
Use the Galaxy workflow tests schema as the assertion-family vocabulary when translating CWL test evidence into a Galaxy test plan.
Trigger
When mapping expected outputs, tolerances, or fixture assertions into Galaxy workflow-test assertion intent.
Research iwc-test-data-conventions

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose
Emit Galaxy/IWC-style job input fixtures, remote locations, hashes, and collection input shapes.
Trigger
When writing job inputs or deciding whether fixtures belong in test-data, Zenodo, ENA/SRA, or CVMFS.

Cast artifacts

How to install →

Artifact handoffs

/ pipeline contract

Produces

Consumes

  • Structured CWL summary from [[summarize-cwl]]; lists discovered test cases, job-file paths, and expected-output references.

    produced by

cwl-test-to-galaxy-test-plan

Turn the CWL summary’s discovered test cases into a reviewable Galaxy test plan. Preserve each case’s job-file and expected-output provenance so implement-galaxy-workflow-test can author the final test against the concrete Galaxy workflow. The plan records assertion intent and open mappings, not a tests-format test file.

For each tests[] case, open its job_path when available. Map the declared CWL input values onto the Galaxy inputs the summary and translation imply. Keep File locations, Directory contents, secondaryFiles, arrays, and collection element identifiers visible where they affect the fixture or its Galaxy shape. Record the source path or URL and any known checksum. If a job file is missing or an input cannot be mapped, leave the fixture or label unresolved with a reason. A job_path in the summary is a pointer to inputs, not the inputs themselves.

Translate each recorded expected output into a Galaxy output to check. Use the CWL output id and any supplied path, URL, checksum, or assertion as evidence for an appropriate tests-format assertion family. Record what the assertion should establish, its expected value and tolerance when supported, and the source of that expectation. Do not infer a passing value from an output name or turn a checksum into a Galaxy assertion without confirming that the translated output can be compared that way. For collections and sidecars, identify the element or file that the check actually addresses.

Bind input and output labels to a concrete Galaxy draft only if one is available to inspect. Otherwise mark inferred labels as assumed or unresolved, set workflow.label_source accordingly, and record the mapping that implement-galaxy-workflow-test must confirm. Set source.derived_from: test-evidence for a plan based on discovered CWL tests, and evidence: test-evidence only for assertions supported by those tests. If a useful Galaxy check must instead be inferred from workflow intent, mark that assertion evidence: intent and explain its lower confidence.

Record unavailable fixtures, expression-dependent shapes, untranslatable assertions, and missing label or datatype mappings in unresolved[] or warnings[] as appropriate. Put outputs deliberately left unasserted in omissions[] with a reason. If the summary has no usable test case, report that coverage gap rather than presenting a fabricated case as translated evidence. Validate the emitted galaxy-test-plan.yml with foundry validate-galaxy-workflow-test-plan before handing it to implement-galaxy-workflow-test.

Incoming References (4)

  • CWL → GALAXY phase of pipeline — Translate a CWL Workflow into a Galaxy gxformat2 workflow, then assemble and run a Galaxy workflow test.
  • Galaxy workflow test plan related note — JSON Schema for the intermediate Galaxy workflow test-plan handoff produced by the test-plan Molds and consumed by implement-galaxy-workflow-test.
  • CWL workflow summary related note — JSON Schema for the structured summary emitted by the summarize-cwl Mold.
  • Galaxy workflow test format related note — JSON Schema for the planemo workflow test format (`<workflow>-tests.yml`), vendored from `@galaxy-tool-util/schema`.