Claude skill · cast

freeform-summary-to-galaxy-test-plan

Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.

Install

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

Then invoke as:

/foundry-skills:freeform-summary-to-galaxy-test-plan

Skill Bundle

/ packaged cast

attached files: 7
upfront: 1
on demand: 6
cast rev: n/a
validated: 0

Produces: 1 artifact.

Consumes: 5 artifacts.

Artifact Contract

/ skill handoff

Produces

galaxy-test-plan

Reviewable Galaxy workflow test plan (see [[galaxy-workflow-test-plan]]): synthesized test cases with job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions.

yamlgalaxy-test-plan.yml[[galaxy-workflow-test-plan]]

Raw artifact contract

{
  "id": "galaxy-test-plan",
  "kind": "yaml",
  "default_filename": "galaxy-test-plan.yml",
  "schema": "[[galaxy-workflow-test-plan]]",
  "description": "Reviewable Galaxy workflow test plan (see [[galaxy-workflow-test-plan]]): synthesized test cases with job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions."
}

Consumes

freeform-summary

Free-form source summary from [[summarize-paper]] or [[interview-to-freeform-summary]]; carries methods, sample data, parameters, and expected outputs that seed test intent.

Raw artifact contract

{
  "id": "freeform-summary",
  "description": "Free-form source summary from [[summarize-paper]] or [[interview-to-freeform-summary]]; carries methods, sample data, parameters, and expected outputs that seed test intent.",
  "producers": [
    "interview-to-freeform-summary",
    "summarize-paper"
  ]
}

freeform-galaxy-interface

Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins workflow inputs, outputs, and labels the plan binds assertions to.

Raw artifact contract

{
  "id": "freeform-galaxy-interface",
  "description": "Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins workflow inputs, outputs, and labels the plan binds assertions to.",
  "producers": [
    "freeform-summary-to-galaxy-interface"
  ]
}

freeform-galaxy-data-flow

Galaxy data-flow brief from [[freeform-summary-to-galaxy-data-flow]] that pins abstract operations and collection choices the plan must respect.

Raw artifact contract

{
  "id": "freeform-galaxy-data-flow",
  "description": "Galaxy data-flow brief from [[freeform-summary-to-galaxy-data-flow]] that pins abstract operations and collection choices the plan must respect.",
  "producers": [
    "freeform-summary-to-galaxy-data-flow"
  ]
}

iwc-comparison-notes

Structural diff guidance from [[compare-against-iwc-exemplar]]; steers the plan toward IWC-aligned testable checkpoints and fixture shapes.

Raw artifact contract

{
  "id": "iwc-comparison-notes",
  "description": "Structural diff guidance from [[compare-against-iwc-exemplar]]; steers the plan toward IWC-aligned testable checkpoints and fixture shapes.",
  "producers": [
    "compare-against-iwc-exemplar"
  ]
}

iwc-exemplar-gxformat2

Cleaned gxformat2 view of the nearest IWC exemplar from [[compare-against-iwc-exemplar]]; pattern-match its labels, collection identifiers, and tested checkpoints. Absent when no nearest exemplar was found.

Raw artifact contract

{
  "id": "iwc-exemplar-gxformat2",
  "description": "Cleaned gxformat2 view of the nearest IWC exemplar from [[compare-against-iwc-exemplar]]; pattern-match its labels, collection identifiers, and tested checkpoints. Absent when no nearest exemplar was found.",
  "producers": [
    "compare-against-iwc-exemplar"
  ]
}

Attached Files

/ runtime references

Load upfront

schema

galaxy-workflow-test-plan

packaged

Output contract: the emitted plan conforms to [[galaxy-workflow-test-plan]]. Cast bundles the JSON Schema so the skill carries its output shape; validate with `foundry validate-galaxy-workflow-test-plan`.

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
...

Load on demand

research

galaxy-workflow-testability-design

packaged

Choose which workflow outputs and promoted checkpoints make meaningful assertions when no upstream test evidence exists.

Trigger: When deciding which outputs to assert, which checkpoints to promote, and which labels the plan should assume.

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

Distinguish accepted IWC-style test shortcuts from assertion smells while synthesizing assertions from intent.

Trigger: When considering existence-only, size-only, image-dimension, or tolerant output checks, or recording an omission.

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

Describe job-input fixtures, remote-URL-first locations, hashes, and collection input shapes the plan should record as fixture provenance.

Trigger: When recording job inputs or fixture provenance, or deciding whether a fixture belongs in test-data, Zenodo, ENA/SRA, or CVMFS.

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

Pick the assertion family and tolerance that fit each synthesized expected output by output type.

Trigger: When turning an expected output into assertion intent and a tolerance.

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

Keep the plan addressable by stable labels and artifacts Planemo can connect back to invocations, jobs, and outputs.

Trigger: When recording the labels and checkpoints the downstream test must address.

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
...

schema

tests-format

packaged

Use the Galaxy workflow tests schema as the assertion-family vocabulary referenced by the plan's assertion intent.

Trigger: When naming an assertion family or compare operator for a synthesized expected output.

on-demand 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,
...

SKILL.md


# freeform-summary-to-galaxy-test-plan

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

## When To Use

- Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.

## Inputs

- Read artifact `freeform-summary`. Produced by `interview-to-freeform-summary`, `summarize-paper`. Free-form source summary from summarize-paper or interview-to-freeform-summary; carries methods, sample data, parameters, and expected outputs that seed test intent.
- Read artifact `freeform-galaxy-interface`. Produced by `freeform-summary-to-galaxy-interface`. Galaxy interface brief from freeform-summary-to-galaxy-interface that pins workflow inputs, outputs, and labels the plan binds assertions to.
- Read artifact `freeform-galaxy-data-flow`. Produced by `freeform-summary-to-galaxy-data-flow`. Galaxy data-flow brief from freeform-summary-to-galaxy-data-flow that pins abstract operations and collection choices the plan must respect.
- Read artifact `iwc-comparison-notes`. Produced by `compare-against-iwc-exemplar`. Structural diff guidance from compare-against-iwc-exemplar; steers the plan toward IWC-aligned testable checkpoints and fixture shapes.
- Read artifact `iwc-exemplar-gxformat2`. Produced by `compare-against-iwc-exemplar`. Cleaned gxformat2 view of the nearest IWC exemplar from compare-against-iwc-exemplar; pattern-match its labels, collection identifiers, and tested checkpoints. Absent when no nearest exemplar was found.

## Outputs

- Write artifact `galaxy-test-plan` as `galaxy-test-plan.yml`. Format: `yaml`. Schema: galaxy-workflow-test-plan. Reviewable Galaxy workflow test plan (see galaxy-workflow-test-plan): synthesized test cases with job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions.

## Required Tools

- None declared. Procedure should not assume external CLIs are present.

## Load Upfront

- `references/schemas/galaxy-workflow-test-plan.schema.json`: Schema file copied verbatim into the bundle. Output contract: the emitted plan conforms to galaxy-workflow-test-plan. Cast bundles the JSON Schema so the skill carries its output shape; validate with `foundry validate-galaxy-workflow-test-plan`.

## Load On Demand

- `references/notes/galaxy-workflow-testability-design.md`: Research note copied verbatim into the bundle. Choose which workflow outputs and promoted checkpoints make meaningful assertions when no upstream test evidence exists. Use when: deciding which outputs to assert, which checkpoints to promote, and which labels the plan should assume.
- `references/notes/iwc-shortcuts-anti-patterns.md`: Research note copied verbatim into the bundle. Distinguish accepted IWC-style test shortcuts from assertion smells while synthesizing assertions from intent. Use when: considering existence-only, size-only, image-dimension, or tolerant output checks, or recording an omission.
- `references/notes/iwc-test-data-conventions.md`: Research note copied verbatim into the bundle. Describe job-input fixtures, remote-URL-first locations, hashes, and collection input shapes the plan should record as fixture provenance. Use when: recording job inputs or fixture provenance, or deciding whether a fixture belongs in test-data, Zenodo, ENA/SRA, or CVMFS.
- `references/notes/planemo-asserts-idioms.md`: Research note copied verbatim into the bundle. Pick the assertion family and tolerance that fit each synthesized expected output by output type. Use when: turning an expected output into assertion intent and a tolerance.
- `references/notes/planemo-workflow-test-architecture.md`: Research note copied verbatim into the bundle. Keep the plan addressable by stable labels and artifacts Planemo can connect back to invocations, jobs, and outputs. Use when: recording the labels and checkpoints the downstream test must address.
- `references/schemas/tests-format.schema.json`: Schema file copied verbatim into the bundle. Use the Galaxy workflow tests schema as the assertion-family vocabulary referenced by the plan's assertion intent. Use when: naming an assertion family or compare operator for a synthesized expected output.

## Validation

- Validate `galaxy-test-plan.yml` before returning it: run `foundry galaxy-test-plan.yml` from `@galaxy-foundry/foundry`. If the command is not on PATH, run `npx --package @galaxy-foundry/foundry foundry galaxy-test-plan.yml`. This checks artifact `galaxy-test-plan` against the galaxy-workflow-test-plan schema.

## Procedure

Synthesize a Galaxy workflow test plan from a free-form source summary and the Galaxy interface and data-flow briefs. The output is a reviewable handoff conforming to galaxy-workflow-test-plan, not a concrete `tests-format` file: it records test cases, job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and intentional omissions so implement-galaxy-workflow-test can author the final Galaxy test artifact.

### Synthesized, not translated

This is the structural difference from nextflow-test-to-galaxy-test-plan and cwl-test-to-galaxy-test-plan. Those skills **translate** existing upstream test evidence — nf-test snapshots, CWL job files and expected outputs — into a Galaxy plan. A free-form source has no upstream test fixtures to convert, so this skill **synthesizes** the plan from workflow intent and scenario-level expected outputs: the methods, sample data, parameters, and "expected results" recorded in the free-form summary, plus the testable structure the interface/data-flow briefs and the nearest IWC exemplar imply.

Set the plan's `source.derived_from` to `intent` (not `test-evidence`) and each synthesized assertion's `evidence` to `intent`; most synthesized assertions are `confidence: medium` or `low`. Where the summary does carry a concrete expected value (a known count, a named output token, a published figure), record it as `expected_value` and raise the confidence.

### Labels and fixtures are assumed, not bound

This skill consumes the template-era briefs, not the concrete workflow draft or the resolved test-data refs — those exist in the harness run-state by the time the plan is authored, but they are reconciled downstream rather than here. So:

- Bind assertions to the labels the interface brief pins, and set `label_status` to `assumed` (or `unresolved` when even the brief is silent) and the plan's `workflow.label_source` to `interface-brief`. implement-galaxy-workflow-test reconciles these against the real draft labels and the workflow-label cross-check.
- Record fixtures with `storage: unresolved` and `location: null` when the free-form summary names test data only by description; capture what is known (a dataset name, an accession, a Zenodo DOI, a rough size) in `fixture.provenance` so test-data resolution and the implement skill can act on it. Use iwc-test-data-conventions for the storage classes and the remote-URL-first convention.

When a binding or fixture cannot be settled from the briefs, add an `unresolved[]` entry (with `blocking: true` when the final test cannot be authored without it) rather than inventing a label or a URL.

### Choosing assertions from intent

For each expected output the briefs expose, pick the assertion family by output type per planemo-asserts-idioms and a defensible tolerance. When the only exposed output is weakly assertable (a stochastic plot, an opaque binary), consult galaxy-workflow-testability-design: prefer recording assertion intent against a stronger promoted checkpoint, and when you settle for a weak check, record the weaker outputs in `omissions[]` with a rationale rather than asserting around them. Check each shortcut against iwc-shortcuts-anti-patterns so an existence-only or size-only intent is a deliberate choice.

Keep the plan addressable by stable labels and artifacts (planemo-workflow-test-architecture) so the downstream test, run, and debug skills can connect assertions back to invocations and outputs.

## 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.