Claude skill · cast

implement-galaxy-workflow-test

Assemble Galaxy workflow test fixtures and assertions.

Install

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Then invoke as:

/foundry-skills:implement-galaxy-workflow-test

Skill Bundle

/ packaged cast

attached files: 9
upfront: 3
on demand: 6
cast rev: n/a
validated: 0

Produces: 1 artifact.

Consumes: 3 artifacts.

Artifact Contract

/ skill handoff

Produces

galaxy-workflow-test

Galaxy workflow test file (tests-format) with job inputs, expected outputs, assertions; passes static schema + label cross-check. Named as the workflow basename + `-tests.yml` so Planemo discovers it as the companion of `galaxy-workflow.gxwf.yml`.

yamlgalaxy-workflow.gxwf-tests.yml

Raw artifact contract

{
  "id": "galaxy-workflow-test",
  "kind": "yaml",
  "default_filename": "galaxy-workflow.gxwf-tests.yml",
  "description": "Galaxy workflow test file (tests-format) with job inputs, expected outputs, assertions; passes static schema + label cross-check. Named as the workflow basename + `-tests.yml` so Planemo discovers it as the companion of `galaxy-workflow.gxwf.yml`."
}

Consumes

galaxy-test-plan

Schema-valid Galaxy test plan ([[galaxy-workflow-test-plan]]) from a *-test-to-galaxy-test-plan Mold; carries job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions.

Raw artifact contract

{
  "id": "galaxy-test-plan",
  "description": "Schema-valid Galaxy test plan ([[galaxy-workflow-test-plan]]) from a *-test-to-galaxy-test-plan Mold; carries job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions.",
  "inherited_schema": "[[galaxy-workflow-test-plan]]",
  "producers": [
    "cwl-test-to-galaxy-test-plan",
    "freeform-summary-to-galaxy-test-plan",
    "nextflow-test-to-galaxy-test-plan"
  ]
}

galaxy-workflow

Concrete gxformat2 workflow being tested — the loop-endstate `galaxy-workflow.gxwf.yml` from [[advance-galaxy-draft-step]] (`class: GalaxyWorkflow`); provides the real input/output labels, outputs, and collection shapes the test must assert against.

Raw artifact contract

{
  "id": "galaxy-workflow",
  "description": "Concrete gxformat2 workflow being tested — the loop-endstate `galaxy-workflow.gxwf.yml` from [[advance-galaxy-draft-step]] (`class: GalaxyWorkflow`); provides the real input/output labels, outputs, and collection shapes the test must assert against.",
  "producers": [
    "advance-galaxy-draft-step"
  ]
}

test-data-refs

Resolved test data references (URLs, paths, expected shapes) from paper-to-test-data or find-test-data.

Raw artifact contract

{
  "id": "test-data-refs",
  "description": "Resolved test data references (URLs, paths, expected shapes) from paper-to-test-data or find-test-data.",
  "producers": [
    "find-test-data",
    "paper-to-test-data"
  ]
}

Attached Files

/ runtime references

Load upfront

cli-tool

planemo

packaged

Runtime for workflow_test_init / workflow_test_on_invocation; install before authoring tests against a live invocation.

upfront runtime verbatim corpus-observed deterministic 1.9 KB

bundle: references/cli/planemo.md
source: content/cli/planemo/index.md

Preview md

---
type: cli-tool
tool: planemo
origin: pypi
package: planemo
package_version: "0.75.44"
invoke: planemo
invoke_fallback: "uvx --from planemo==0.75.44 planemo"
availability_check: "planemo --version"
docs_url: "https://planemo.readthedocs.io/"
tags:
  - cli-tool
  - cli/planemo
status: draft
created: 2026-05-10
revised: 2026-06-18
revision: 4
ai_generated: true
summary: "Galaxy tool/workflow runtime testing CLI; used by run-workflow-test and friends."
---

# planemo

Galaxy's runtime testing and authoring CLI. Foundry Molds invoke `planemo test`, `planemo lint`, and friends for end-to-end workflow validation; the cast skill consumes structured JSON output from `--test_output_json` and validates it against [[planemo-test-report]].

## Pin

`package_version` pins to the released `planemo==0.75.44` from PyPI — base upstream planemo, no fork.

Released 0.75.44 carries the merged [galaxyproject/planemo#1636](https://github.com/galaxyproject/planemo/pull/1636), so `planemo cli_metadata` and `planemo output_schema` ship in the base release. Every Foundry consumer now runs off this base pin: the workflow-test phases ([[run-workflow-test]], [[implement-galaxy-workflow-test]]) which need only `planemo test --test_output_json`, the convergence loop in [[convert-nfcore-module-to-galaxy-tool]], and the vendored-artifact regeneration story (`packages/planemo-cli-meta/`, `packages/planemo-test-report-schema/`). No fork pin is required.

## Install

```sh
uvx --from planemo==0.75.44 planemo --version
```

For a persistent install:

```sh
uv tool install planemo==0.75.44
```

Contributor laptops only need planemo when **regenerating** vendored artifacts (the schema JSON in `packages/planemo-test-report-schema/`, the planemo CLI manual pages under `content/cli/planemo/`). Normal Foundry
...

schema

galaxy-workflow-test-plan

packaged

Input contract: read the schema-valid Galaxy test plan (job inputs, expected outputs, assertion intent, tolerances, label assumptions, unresolved mappings, omissions) and convert it into tests-format output, reconciling assumed labels and fixtures against the real draft.

upfront runtime verbatim hypothesis deterministic 17.8 KB

bundle: references/schemas/galaxy-workflow-test-plan.schema.json
source: package://@galaxy-foundry/foundry#galaxyWorkflowTestPlanSchema

Preview json

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://galaxyproject.org/foundry/schemas/galaxy-workflow-test-plan.schema.json",
  "$comment": "Canonical source: packages/foundry/src/schemas/galaxy-workflow-test-plan/galaxy-workflow-test-plan.schema.json in galaxyproject/foundry. Mold frontmatter cites this schema via [[galaxy-workflow-test-plan]] wiki-links; the cast pipeline imports the `galaxyWorkflowTestPlanSchema` runtime export and serializes it into cast bundles. The on-disk artifact is YAML; validate it with `foundry validate-galaxy-workflow-test-plan`.",
  "title": "Galaxy Workflow Test Plan",
  "description": "Intermediate, reviewable Galaxy workflow test-plan handoff produced by a *-test-to-galaxy-test-plan Mold (nextflow, cwl, or freeform) and consumed by implement-galaxy-workflow-test. It preserves test intent, fixture provenance, assertion intent, tolerances, label assumptions, unresolved mappings, and intentional omissions before any concrete tests-format `*-tests.yml` is authored. It is NOT the final test artifact: assertion vocabulary is referenced by family name from the tests-format schema, not duplicated here.",
  "type": "object",
  "additionalProperties": false,
  "required": [
    "plan_version",
    "source",
    "workflow",
    "test_cases",
    "unresolved",
    "omissions",
    "warnings"
  ],
  "properties": {
    "plan_version": {
      "type": "string",
      "enum": [
        "1"
      ],
      "description": "Test-plan schema major version."
    },
    "source": {
      "$ref": "#/$defs/SourceRecord"
    },
    "workflow": {
      "$ref": "#/$defs/WorkflowRef"
    },
    "test_cases": {
      "type": "array",
      "description": "One entry per planned Galaxy workflow test (each becomes one tests-format test entry downstream).",
      "items": {
        "$ref": "#/$defs/TestCase"
      }
    },
    "unresolved": {
      "type": "array",
      "description": "Mappings the plan could not resolve and that implement-galaxy-workflow-test (or a reviewer) must settle before authoring the final test file.",
      "items": {
        "$ref": "#/$defs/UnresolvedItem"
      }
    },
    "omissions": {
      "type": "array",
      "description": "Outputs or behaviors deliberately left unasserted, with rationale, so the gap is a recorded decision rather than an oversight.",
      "items": {
        "$ref": "#/$defs/Omis
...

schema

tests-format

packaged

JSON Schema contract for the Galaxy workflow test format. Output of this Mold must validate against it.

upfront runtime verbatim corpus-observed deterministic 201.1 KB

bundle: references/schemas/tests-format.schema.json
source: package://@galaxy-foundry/foundry#testsFormatSchema

Preview json

{
  "$defs": {
    "Collection": {
      "additionalProperties": false,
      "properties": {
        "class": {
          "const": "Collection",
          "title": "Class",
          "type": "string"
        },
        "collection_type": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Collection Type"
        },
        "elements": {
          "anyOf": [
            {
              "items": {
                "oneOf": [
                  {
                    "oneOf": [
                      {
                        "$ref": "#/$defs/LocationFile"
                      },
                      {
                        "$ref": "#/$defs/PathFile"
                      },
                      {
                        "$ref": "#/$defs/ContentsFile"
                      },
                      {
                        "$ref": "#/$defs/CompositeDataFile"
                      }
                    ]
                  },
                  {
                    "$ref": "#/$defs/Collection"
                  }
                ]
              },
              "type": "array"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Elements"
        },
        "identifier": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Identifier"
        },
        "name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Name"
        },
        "rows": {
          "anyOf": [
            {
              "additionalProperties": {
                "items": {},
                "type": "array"
              },
              "type": "object"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Rows"
        }
      },
      "required": [
        "class"
      ],
      "title": "Collection",
      "type": "object"
    },
    "CollectionAttributes": {
      "additionalProperties": false,
...

Load on demand

cli-command

validate-tests

packaged

Run the cheap static workflow-test validation and workflow-label cross-check before Planemo execution.

Trigger: After authoring or editing a Galaxy workflow test file and before Planemo invocation.

on-demand runtime sidecar corpus-observed deterministic 2.6 KB

bundle: references/cli/validate-tests.json
source: content/cli/gxwf/validate-tests.md

Preview json

{
  "type": "cli-command",
  "tool": "gxwf",
  "command": "validate-tests",
  "summary": "Validate Galaxy workflow test files and optionally cross-check labels against their workflow.",
  "source_path": "content/cli/gxwf/validate-tests.md",
  "source_revision": 3,
  "package": "@galaxy-tool-util/cli",
  "description": "Validate a workflow-test file (*-tests.yml, *.gxwf-tests.yml) against the Galaxy Tests schema",
  "synopsis": "gxwf validate-tests [options] <file>",
  "args": [
    {
      "raw": "file",
      "name": "file",
      "required": true,
      "variadic": false,
      "description": "Tests file (*-tests.yml)"
    }
  ],
  "options": [
    {
      "flags": "--json",
      "name": "json",
      "description": "Output structured JSON report",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--workflow <path>",
      "name": "workflow",
      "description": "Cross-check job inputs + output assertions against a workflow (.ga / .gxwf.yml)",
      "takesArgument": true,
      "argumentPlaceholder": "<path>",
      "optionalArgument": false,
      "negatable": false
    }
  ],
  "body": "# `gxwf validate-tests`\n\nValidate a Galaxy workflow test file (`*-tests.yml` or `*.gxwf-tests.yml`) against the Galaxy tests schema. Optionally cross-check the test file against a workflow so missing input labels, missing output labels, and type mismatches fail before a slow Planemo run.\n\n`<file>` is a workflow test YAML file, usually named `<workflow>-tests.yml` or `<workflow>.gxwf-tests.yml`.\n\n## Output\n\nDefault output is human-readable validation diagnostics.\n\nWith `--json`, the command emits a structured report describing schema errors and, when `--workflow` is supplied, workflow-coherence errors such as missing labels or incompatible input values.\n\n## Examples\n\n```bash\ngxwf validate-tests workflow-tests.yml\ngxwf validate-tests workflow-tests.yml --json\ngxwf validate-tests workflow-tests.yml --workflow workflow.gxwf.yml --json\n```\n\n## Gotchas\n\n- This is the cheap static gate before Planemo. It does not execute the workflow and does not prove assertions pass on real outputs.\n- Use `--workflow` whenever the workflow file is available. Schema-valid tests can still reference stale input/output labels after workflow edits.\n- Run this before `planemo workflow_test_on_invocation` or 
...

research

galaxy-workflow-testability-design

packaged

Revise workflow inputs, outputs, labels, checkpoints, and collection identifiers so meaningful tests can be authored.

Trigger: When test authoring reveals missing labels, omitted workflow-level outputs, unstable collection identifiers, weakly assertable final outputs, or fixture-shape pressure on workflow inputs.

on-demand runtime verbatim corpus-observed deterministic 11.4 KB

bundle: references/notes/galaxy-workflow-testability-design.md
source: content/research/galaxy-workflow-testability-design.md

Preview md

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-05-03
revised: 2026-05-06
revision: 2
ai_generated: true
related_notes:
  - "[[iwc-workflow-testability-survey]]"
  - "[[iwc-test-data-conventions]]"
  - "[[planemo-asserts-idioms]]"
  - "[[iwc-shortcuts-anti-patterns]]"
  - "[[planemo-workflow-test-architecture]]"
  - "[[implement-galaxy-workflow-test]]"
  - "[[gxformat2-schema]]"
  - "[[gxformat2-workflow-inputs]]"
  - "[[galaxy-datatypes-conf]]"
summary: "Design guidance for Galaxy workflow inputs, outputs, and checkpoints that make IWC-style workflow tests possible."
---

# Galaxy workflow testability design

Use this note when authoring or translating a Galaxy workflow **before** the `-tests.yml` file exists. It covers workflow structure choices that make later IWC-style tests meaningful: labels, promoted checkpoints, collection identifiers, and fixture-compatible inputs.

This is not a `content/patterns/` page. It is cross-cutting design guidance for Molds that need testable Galaxy workflows. Assertion syntax lives in [[planemo-asserts-idioms]]. Test YAML fixture shapes live in [[iwc-test-data-conventions]]. Accepted shortcut vs smell calls live in [[iwc-shortcuts-anti-patterns]]. Corpus evidence trail lives in [[iwc-workflow-testability-survey]].

## 1. Treat labels as API

Workflow input and output labels are not cosmetic. Planemo and IWC tests address workflow inputs and outputs by label, and the survey found exact label matches for every asserted output across 114 matched workflow/test pairs. A generated workflow should therefore pick stable, descriptive labels before test authoring starts.

Rules:

- Label every output that may need a test assertion.
- Treat input/output renames as breaking changes
...

research

iwc-shortcuts-anti-patterns

packaged

Flag assertion shortcuts that are acceptable in IWC versus shortcuts that should be avoided.

Trigger: When considering existence-only, size-only, image-only, checksum, output-label, or negative-test patterns.

on-demand runtime verbatim corpus-observed deterministic 23.9 KB

bundle: references/notes/iwc-shortcuts-anti-patterns.md
source: content/research/iwc-shortcuts-anti-patterns.md

Preview md

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-04-30
revised: 2026-05-03
revision: 2
ai_generated: true
related_notes:
  - "[[galaxy-workflow-testability-design]]"
  - "[[iwc-test-data-conventions]]"
  - "[[planemo-asserts-idioms]]"
  - "[[implement-galaxy-workflow-test]]"
  - "[[tests-format]]"
  - "[[iwc-conditionals-survey]]"
  - "[[iwc-map-over-lifecycle-survey]]"
  - "[[iwc-tabular-operations-survey]]"
  - "[[iwc-transformations-survey]]"
summary: "What IWC test suites cut corners on (accepted) vs what's a code smell — existence-only probes, sim_size deltas, image dim checks, label coupling."
---

# IWC test-suite shortcuts and anti-patterns

## Purpose

When an agent translates or authors a Galaxy workflow for IWC submission, the test suite it writes will be reviewed against IWC's *de facto* style — not against an idealized assertion ladder. That style routinely tolerates assertions that look weak in isolation. This note distinguishes the corner-cutting that is **normal and accepted** in the corpus from the patterns that an agent should treat as **smells** worth flagging.

This note owns accepted-vs-smell calls. For positive workflow-structure guidance behind label stability, checkpoint promotion, and collection identifier design, use [[galaxy-workflow-testability-design]].

Grounding: 115 `*-tests.yml` files under `workflow-fixtures/iwc-src/workflows/` (mirror of `galaxyproject/iwc`), prior synthesis in `galaxy-brain/vault/projects/workflow_state/skills/COMPONENT_GALAXY_WORKFLOW_TESTING.md`. Path citations below are relative to `iwc-src/workflows/` unless absolute.

## TL;DR rules of thumb

1. **Default to tolerant assertions.** `compare: sim_size` + `delta:`, `has_image_*` + `delta:`, `has_text` s
...

research

iwc-test-data-conventions

packaged

Assemble job input fixtures, remote URLs, hashes, collection shapes, and test-data layout in IWC style.

Trigger: When writing or revising the job/input side of a Galaxy workflow test file.

on-demand runtime verbatim corpus-observed deterministic 21.1 KB

bundle: references/notes/iwc-test-data-conventions.md
source: content/research/iwc-test-data-conventions.md

Preview md

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-04-30
revised: 2026-05-03
revision: 3
ai_generated: true
related_notes:
  - "[[galaxy-workflow-testability-design]]"
  - "[[iwc-shortcuts-anti-patterns]]"
  - "[[planemo-asserts-idioms]]"
  - "[[implement-galaxy-workflow-test]]"
  - "[[tests-format]]"
  - "[[iwc-tabular-operations-survey]]"
summary: "How IWC workflows organize and reference test data — Zenodo-first, SHA-1 integrity, collection shapes, CVMFS gotchas."
---

# IWC test data conventions

Reference for an agent implementing or editing a `<workflow>-tests.yml` in IWC style. All evidence cited from `/Users/jxc755/projects/repositories/workflow-fixtures/iwc-src/workflows/` (raw IWC clone) and `workflows/README.md`. Authoritative spec: [planemo.readthedocs.io/en/latest/test_format.html](https://planemo.readthedocs.io/en/latest/test_format.html). The companion analysis at `/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/skills/COMPONENT_GALAXY_WORKFLOW_TESTING.md` is the synthesized source for several normative claims here.

This note owns **test YAML fixture shapes**. For workflow-structure choices that make those fixtures possible before the test file exists, use [[galaxy-workflow-testability-design]].

## 1. Where does test data live? Remote vs in-repo

Two storage patterns. They mix freely inside one job.

**Remote `location:` (default for any non-trivial input).** Strongly preferred for anything bigger than a toy fixture. Order of preference, observed in the corpus:

- **Zenodo** — overwhelming default, persistent DOI-backed URL.
  - `read-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml:13,17` — `https://zenodo.org/records/11484
...

research

planemo-asserts-idioms

packaged

Choose assertion families, tolerance magnitudes, and the static/Planemo validation loop.

Trigger: When writing or revising output assertions for a Galaxy workflow test file.

on-demand runtime verbatim corpus-observed deterministic 18.2 KB

bundle: references/notes/planemo-asserts-idioms.md
source: content/research/planemo-asserts-idioms.md

Preview md

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-04-30
revised: 2026-05-11
revision: 6
ai_generated: true
related_notes:
  - "[[galaxy-workflow-testability-design]]"
  - "[[iwc-test-data-conventions]]"
  - "[[iwc-shortcuts-anti-patterns]]"
  - "[[implement-galaxy-workflow-test]]"
  - "[[tests-format]]"
  - "[[planemo-workflow-test-architecture]]"
  - "[[validate-tests]]"
  - "[[iwc-tabular-operations-survey]]"
  - "[[galaxy-discover-datasets]]"
summary: "Decision and idiom guide for picking planemo workflow-test assertions: which family per output type, how to size tolerances, when to validate."
---

# Planemo asserts: idiom and decision guide

Companion to [[iwc-test-data-conventions]] (input shapes), [[galaxy-workflow-testability-design]] (workflow structure before test YAML exists), and [[iwc-shortcuts-anti-patterns]] (what's accepted vs smell). This note is forward-looking: when authoring a new `<workflow>-tests.yml`, which assertion family fits which output, and what the recommended tolerances and operators are.

The **vocabulary itself is not restated here** — every assertion's parameter list, types, defaults, required fields, and Python docstring is rendered from the test-format JSON Schema at [[tests-format]]. Assertion names below deep-link into that page (e.g. [[tests-format#has_text_model|has_text]] jumps straight to that `$def`).

## 1. Choose by output type

The single most useful decision table. Pick the row that matches the file format the workflow emits; default to the recommended assertion family.

| Output type | Default assertion family | Why | Fallback |
|---|---|---|---|
| **Plain text reports / logs** (FastQC summary, MultiQC text section) | [[tests-format#has_text_model|has_text]] (su
...

research

planemo-workflow-test-architecture

packaged

Write tests with stable labels and artifacts that Planemo can connect back to Galaxy invocations, jobs, and outputs.

Trigger: When adding or revising workflow tests that will be iterated with Planemo or generated from existing invocations.

on-demand runtime verbatim corpus-observed deterministic 7.8 KB

bundle: references/notes/planemo-workflow-test-architecture.md
source: content/research/planemo-workflow-test-architecture.md

Preview md

---
type: research
subtype: component
title: "Planemo workflow-test architecture"
tags:
  - research/component
  - tool/planemo
  - target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-11
revision: 3
ai_generated: true
related_notes:
  - "[[galaxy-workflow-testability-design]]"
  - "[[galaxy-tool-job-failure-reference]]"
  - "[[galaxy-workflow-invocation-failure-reference]]"
  - "[[planemo-asserts-idioms]]"
related_molds:
  - "[[run-workflow-test]]"
  - "[[debug-galaxy-workflow-output]]"
  - "[[implement-galaxy-workflow-test]]"
sources:
  - "~/projects/repositories/planemo/planemo/commands/cmd_test.py"
  - "~/projects/repositories/planemo/planemo/commands/cmd_run.py"
  - "~/projects/repositories/planemo/planemo/galaxy/activity.py"
  - "~/projects/repositories/planemo/planemo/galaxy/invocations"
  - "~/projects/repositories/planemo/planemo/galaxy/config.py"
summary: "Reference for Planemo workflow test/run architecture, Galaxy modes, API polling, and noisy failure boundaries."
---

# Planemo Workflow-Test Architecture

This note describes Planemo architecture relevant to workflow tests and workflow runs. It is reference material for Molds that need to run tests or interpret Planemo artifacts, not a command-selection recipe.

## Main Commands

| User action | Command | Core behavior |
|---|---|---|
| Full workflow test | `planemo test <workflow>` ([[planemo-test]]) | Finds test definitions, starts or targets Galaxy, stages inputs, invokes workflow, checks assertions, writes reports. |
| Direct run | `planemo run <workflow> <job.yml>` | Runs one workflow/job pair and can download outputs without assertion checks. |
| Recheck assertions | `planemo workflow_test_on_invocation <tests.yml> <invocation_id>` ([[planemo-workflow_test_on_invocation]]) | Runs test asser
...

SKILL.md


# implement-galaxy-workflow-test

Follow the procedure below and use the artifact/reference sections as the runtime contract.

## When To Use

- Assemble Galaxy workflow test fixtures and assertions.

## Inputs

- Read artifact `galaxy-test-plan`. Schema: galaxy-workflow-test-plan. Produced by `cwl-test-to-galaxy-test-plan`, `freeform-summary-to-galaxy-test-plan`, `nextflow-test-to-galaxy-test-plan`. Schema-valid Galaxy test plan (galaxy-workflow-test-plan) from a *-test-to-galaxy-test-plan Mold; carries job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions.
- Read artifact `galaxy-workflow`. Produced by `advance-galaxy-draft-step`. Concrete gxformat2 workflow being tested — the loop-endstate `galaxy-workflow.gxwf.yml` from advance-galaxy-draft-step (`class: GalaxyWorkflow`); provides the real input/output labels, outputs, and collection shapes the test must assert against.
- Read artifact `test-data-refs`. Produced by `find-test-data`, `paper-to-test-data`. Resolved test data references (URLs, paths, expected shapes) from paper-to-test-data or find-test-data.

## Outputs

- Write artifact `galaxy-workflow-test` as `galaxy-workflow.gxwf-tests.yml`. Format: `yaml`. Galaxy workflow test file (tests-format) with job inputs, expected outputs, assertions; passes static schema + label cross-check. Named as the workflow basename + `-tests.yml` so Planemo discovers it as the companion of `galaxy-workflow.gxwf.yml`.

## Required Tools

- **`gxwf`** (gxwf). `npm install -g @galaxy-tool-util/cli@^1.8.1`.
  Ephemeral run: `npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf`.
  Check: `gxwf --help | grep -q draft-validate`.
  Docs: https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli
- **`planemo`** (planemo). `uv tool install planemo==0.75.44` (or `pip install planemo==0.75.44`).
  Ephemeral run: `uvx --from planemo==0.75.44 planemo`.
  Check: `planemo --version`.
  Docs: https://planemo.readthedocs.io/
  Bundled reference: `references/cli/planemo.md`.

## Load Upfront

- `references/cli/planemo.md`: CLI tool reference copied verbatim into the bundle. Runtime for workflow_test_init / workflow_test_on_invocation; install before authoring tests against a live invocation.
- `references/schemas/galaxy-workflow-test-plan.schema.json`: Schema file copied verbatim into the bundle. Input contract: read the schema-valid Galaxy test plan (job inputs, expected outputs, assertion intent, tolerances, label assumptions, unresolved mappings, omissions) and convert it into tests-format output, reconciling assumed labels and fixtures against the real draft.
- `references/schemas/tests-format.schema.json`: Schema file copied verbatim into the bundle. JSON Schema contract for the Galaxy workflow test format. Output of this Mold must validate against it.

## Load On Demand

- `references/cli/validate-tests.json`: CLI command reference packaged as a sidecar. Run the cheap static workflow-test validation and workflow-label cross-check before Planemo execution. Use when: after authoring or editing a Galaxy workflow test file and before Planemo invocation.
- `references/notes/galaxy-workflow-testability-design.md`: Research note copied verbatim into the bundle. Revise workflow inputs, outputs, labels, checkpoints, and collection identifiers so meaningful tests can be authored. Use when: test authoring reveals missing labels, omitted workflow-level outputs, unstable collection identifiers, weakly assertable final outputs, or fixture-shape pressure on workflow inputs.
- `references/notes/iwc-shortcuts-anti-patterns.md`: Research note copied verbatim into the bundle. Flag assertion shortcuts that are acceptable in IWC versus shortcuts that should be avoided. Use when: considering existence-only, size-only, image-only, checksum, output-label, or negative-test patterns.
- `references/notes/iwc-test-data-conventions.md`: Research note copied verbatim into the bundle. Assemble job input fixtures, remote URLs, hashes, collection shapes, and test-data layout in IWC style. Use when: writing or revising the job/input side of a Galaxy workflow test file.
- `references/notes/planemo-asserts-idioms.md`: Research note copied verbatim into the bundle. Choose assertion families, tolerance magnitudes, and the static/Planemo validation loop. Use when: writing or revising output assertions for a Galaxy workflow test file.
- `references/notes/planemo-workflow-test-architecture.md`: Research note copied verbatim into the bundle. Write tests with stable labels and artifacts that Planemo can connect back to Galaxy invocations, jobs, and outputs. Use when: adding or revising workflow tests that will be iterated with Planemo or generated from existing invocations.

## Validation

- None declared.

## Procedure

Assemble a Galaxy workflow test file (`tests-format`) from the schema-valid Galaxy test plan (galaxy-workflow-test-plan), the concrete gxformat2 workflow (`galaxy-workflow.gxwf.yml`), and the resolved test-data refs. One invocation produces the companion test file whose job inputs come from the workflow inputs and whose assertions come from the plan's assertion intent. The output must validate against tests-format and pass the workflow-label cross-check before any Planemo run.

**Name the companion off the workflow's basename.** Planemo discovers the test file by stripping only the workflow's final extension and appending `-tests.yml`, so the companion of `galaxy-workflow.gxwf.yml` is `galaxy-workflow.gxwf-tests.yml` (keep the `.gxwf`) — not `galaxy-workflow-tests.yml`. Derive the name from whatever the workflow file is actually called; a `.ga` workflow would instead pair with `<basename>-tests.yml`.

The workflow is the contract: input and output labels in the test file must address real workflow input/output labels. The test plan's bindings may be `assumed` or `unresolved` — especially for synthesized (freeform-sourced) plans whose `workflow.label_source` is `interface-brief` — so reconcile each plan binding against the real workflow labels here, and resolve `unresolved[]` entries and `storage: unresolved` fixtures against the workflow and the resolved test-data refs. When authoring reveals a missing label, an omitted workflow output, or an unstable collection identifier, treat it as testability pressure on the workflow itself — surface it per galaxy-workflow-testability-design rather than asserting around it.

### Sequence

1. **Bootstrap.** Prefer generating the test skeleton from a real invocation, not from scratch:
   - **`planemo workflow_test_init --from_invocation <id>`** (planemo-workflow_test_init) — preferred bootstrap for new test files; reviewer convention. See planemo-asserts-idioms §7.
   - **`planemo workflow_test_on_invocation <tests.yml> <id>`** (planemo-workflow_test_on_invocation) — fast assertion-iteration loop without re-running the workflow.
2. **Author job inputs and stage their data.** Wire each workflow input to a `test-data-refs` entry, and make the data the test references actually exist on disk before any Planemo run:
   - **Prefer a bare remote `location:`** (iwc-test-data-conventions, remote-URL-first) whenever the ref is a single fetchable artifact — Galaxy fetches it at upload time, so nothing is staged locally. Record the hash when known.
   - **Materialize a local `test-data/` layout only when the ref needs prep a URL can't express** — a concatenation (e.g. per-isolate chromosome+plasmid into one FASTA), a subset (one chromosome, selected loci), or a column split into named collection elements. In that case the test file's `path:` entries point at files this skill writes: fetch from the ref's verified source URLs, run the documented prep, and lay the result out in the `test-data/` directory addressed by the `*-tests.yml`, relative to the workflow. The collection element identifiers in the staged layout must match the test file and the workflow labels exactly.
   - Never emit a `path:` (or `location:`) the test references but no source produces — an un-materialized path passes the static cross-check and fails only at upload, far from here. If a ref is `resolved: false`, surface the gap rather than authoring a path to a file that does not exist.

   Inputs must match the workflow's collection shapes and datatypes.
3. **Author assertions.** Materialize the plan's assertion intent into concrete output assertions. Choose assertion families and tolerances per planemo-asserts-idioms; check each shortcut against iwc-shortcuts-anti-patterns so an existence-only or size-only assertion is a deliberate choice, not an evasion. Honor the plan's `omissions[]` and treat low-`confidence` synthesized intent as a starting point to tighten against the real invocation.
4. **Validate static.** Run validate-tests for the schema gate, then the workflow-label cross-check (`checkTestsAgainstWorkflow`): zero missing input labels, zero missing output labels, no collection/datatype mismatches. Fix before spending a Planemo run.
5. **Run green.** Drive planemo `test` with the staged data. "Managed Galaxy" here means **Planemo-managed**: `planemo test` bootstraps its own Galaxy and installs the workflow's tools from the Tool Shed/conda — it does **not** require a pre-provisioned external server, so absence of a running Galaxy is not a reason to skip this gate (cost/runtime of heavy tool or reference-DB installs may be, but that is a deliberate deferral, not an impossibility). On green, hand off the test file plus enough invocation/job/assertion context for run-workflow-test and debug-galaxy-workflow-output to use if a later run fails.

Author tests with stable labels and artifacts that Planemo can connect back to Galaxy invocations, jobs, and outputs (planemo-workflow-test-architecture) — that traceability is what makes the downstream debug skill able to locate failure evidence.

## 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.