Agent Skill · cast

summarize-galaxy-workflow

Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps.

Install with Claude Code

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

Then invoke as:

/foundry-skills:summarize-galaxy-workflow

Install with Codex

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

Then select with /skills or invoke explicitly as:

$summarize-galaxy-workflow

Skill Bundle

/ packaged cast

attached files: 4
upfront: 3
on demand: 1
cast rev: n/a
validated: 0

Produces: 2 artifacts.

Artifact Contract

/ skill handoff

Produces

summary-galaxy-workflow

Structured summary of an existing Galaxy workflow: source/format provenance, inputs, outputs, per-step tool_id/version/tool_state, edge graph, and any existing tests as a regression baseline.

jsonsummary-galaxy-workflow.json[[summary-galaxy-workflow]]

Raw artifact contract

{
  "id": "summary-galaxy-workflow",
  "kind": "json",
  "default_filename": "summary-galaxy-workflow.json",
  "schema": "[[summary-galaxy-workflow]]",
  "description": "Structured summary of an existing Galaxy workflow: source/format provenance, inputs, outputs, per-step tool_id/version/tool_state, edge graph, and any existing tests as a regression baseline."
}

starting-galaxy-workflow

The normalized concrete gxformat2 workflow this summary describes — passthrough when the input was already gxformat2, the `.ga`→gxformat2 conversion otherwise. The substrate [[apply-galaxy-workflow-changeset]] edits; distinct from the summary JSON, which is only context.

yamlstarting-galaxy-workflow.gxwf.yml

Raw artifact contract

{
  "id": "starting-galaxy-workflow",
  "kind": "yaml",
  "default_filename": "starting-galaxy-workflow.gxwf.yml",
  "description": "The normalized concrete gxformat2 workflow this summary describes — passthrough when the input was already gxformat2, the `.ga`→gxformat2 conversion otherwise. The substrate [[apply-galaxy-workflow-changeset]] edits; distinct from the summary JSON, which is only context."
}

Attached Files

/ runtime references

Load upfront

cli-command

gxwf validate

packaged

Validate the gxformat2 workflow before extraction and record diagnostics under documents.validation.

Trigger: Before extracting structure from the workflow document.

upfront runtime sidecar hypothesis deterministic 4.9 KB

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

Preview json

{
  "type": "cli-command",
  "tool": "gxwf",
  "command": "validate",
  "summary": "Validate Galaxy workflow structure, tool state, and optional connection compatibility before runtime execution.",
  "source_path": "content/cli/gxwf/validate.md",
  "source_revision": 3,
  "package": "@galaxy-tool-util/cli",
  "description": "Validate Galaxy workflow files (structure + optional tool state)",
  "synopsis": "gxwf validate [options] <file>",
  "args": [
    {
      "raw": "file",
      "name": "file",
      "required": true,
      "variadic": false,
      "description": "Workflow file (.ga, .gxwf.yml)"
    }
  ],
  "options": [
    {
      "flags": "--format <fmt>",
      "name": "format",
      "description": "Force format: native or format2 (auto-detected by default)",
      "takesArgument": true,
      "argumentPlaceholder": "<fmt>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--no-tool-state",
      "name": "toolState",
      "description": "Skip tool state validation",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": true
    },
    {
      "flags": "--cache-dir <dir>",
      "name": "cacheDir",
      "description": "Tool cache directory",
      "takesArgument": true,
      "argumentPlaceholder": "<dir>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--mode <mode>",
      "name": "mode",
      "description": "Validation backend: effect (default) or json-schema",
      "takesArgument": true,
      "argumentPlaceholder": "<mode>",
      "optionalArgument": false,
      "negatable": false,
      "defaultValue": "effect"
    },
    {
      "flags": "--tool-schema-dir <dir>",
      "name": "toolSchemaDir",
      "description": "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)",
      "takesArgument": true,
      "argumentPlaceholder": "<dir>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--json",
      "name": "json",
      "description": "Output structured JSON report",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--report-html [file]",
      "name": "reportHtml",
      "description": "Write HTML report to file (or stdout if omitted)",
      "takesArgument": true,
      "argumentPlaceholder": "[file]",
  
...

cli-tool

foundry

packaged

Schema-check summary-galaxy-workflow.json with `foundry validate-summary-galaxy-workflow` before returning it from the skill.

upfront runtime verbatim cast-validated deterministic 939 B

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

Preview md

---
type: cli-tool
tool: foundry
origin: npm
package: "@galaxy-foundry/foundry"
invoke: foundry
invoke_fallback: "npx --package @galaxy-foundry/foundry foundry"
availability_check: "foundry --help"
docs_url: "https://github.com/galaxyproject/foundry/blob/main/packages/foundry/README.md"
tags:
  - cli-tool
  - cli/foundry
status: draft
created: 2026-05-11
revised: 2026-05-11
revision: 1
ai_generated: true
summary: "Foundry CLI: bundles all Mold IO validators and a summarize-nextflow subcommand."
---

# foundry

Unified Foundry CLI. Subcommands cover every Mold IO validator plus a `summarize-nextflow` wrapper around the standalone `@galaxy-foundry/summarize-nextflow` package. Per-subcommand synopsis, args, and options are rendered from `@galaxy-foundry/foundry/meta`.

## Install

`npx --package @galaxy-foundry/foundry foundry <subcommand>` runs without a global install. For repeat use, `npm install -g @galaxy-foundry/foundry`.

schema

summary-galaxy-workflow

packaged

Validate the emitted Galaxy workflow summary JSON and provide downstream consumers the output contract.

upfront both verbatim cast-validated deterministic 16.6 KB

bundle: references/schemas/summary-galaxy-workflow.schema.json
source: package://@galaxy-foundry/foundry#summaryGalaxyWorkflowSchema

Preview json

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://galaxyproject.org/foundry/schemas/summary-galaxy-workflow.schema.json",
  "$comment": "Canonical source: packages/foundry/src/schemas/summary-galaxy-workflow/summary-galaxy-workflow.schema.json in galaxyproject/foundry. Mold frontmatter cites this schema via [[summary-galaxy-workflow]] wiki-links; the cast pipeline imports the `summaryGalaxyWorkflowSchema` runtime export and serializes it into cast bundles.",
  "title": "Galaxy Workflow Summary",
  "description": "Structured summary emitted by the summarize-galaxy-workflow Mold. Galaxy gxformat2 is already a typed workflow language, so this schema records validated and normalized workflow structure (inputs, outputs, steps, edges, existing tests) rather than inferred pipeline semantics. When the user supplies a legacy .ga workflow it is converted to gxformat2 first and the conversion is recorded under documents.",
  "type": "object",
  "additionalProperties": false,
  "required": [
    "summary_version",
    "source",
    "documents",
    "workflow_inputs",
    "workflow_outputs",
    "steps",
    "graph",
    "tests",
    "warnings"
  ],
  "properties": {
    "summary_version": {
      "type": "string",
      "enum": [
        "1"
      ],
      "description": "Summary schema major version."
    },
    "source": {
      "$ref": "#/$defs/SourceRecord"
    },
    "documents": {
      "$ref": "#/$defs/DocumentSet"
    },
    "workflow_inputs": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/WorkflowInput"
      }
    },
    "workflow_outputs": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/WorkflowOutput"
      }
    },
    "steps": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/WorkflowStep"
      }
    },
    "graph": {
      "$ref": "#/$defs/WorkflowGraph"
    },
    "tests": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/TestCase"
      }
    },
    "warnings": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/Warning"
      }
    }
  },
  "$defs": {
    "SourceRecord": {
      "type": "object",
      "additionalProperties": false,
      "required": [
        "ecosystem",
        "workflow",
        "url",
        "version",
        "license",
        "slug",
        "format",
        "original_format",
        "release",
        "annotat
...

Load on demand

cli-command

convert

packaged

Convert a legacy `.ga` workflow to gxformat2 before summarizing, and record the conversion under documents.converted_path.

Trigger: When the supplied workflow is native `.ga` rather than gxformat2.

on-demand runtime sidecar hypothesis deterministic 4.3 KB

bundle: references/cli/convert.json
source: content/cli/gxwf/convert.md

Preview json

{
  "type": "cli-command",
  "tool": "gxwf",
  "command": "convert",
  "summary": "Convert a Galaxy workflow between native (.ga) and format2 (.gxwf.yml) representations.",
  "source_path": "content/cli/gxwf/convert.md",
  "source_revision": 2,
  "package": "@galaxy-tool-util/cli",
  "description": "Convert between native (.ga) and format2 (.gxwf.yml) formats",
  "synopsis": "gxwf convert [options] <file>",
  "args": [
    {
      "raw": "file",
      "name": "file",
      "required": true,
      "variadic": false,
      "description": "Workflow file (.ga, .gxwf.yml)"
    }
  ],
  "options": [
    {
      "flags": "--to <format>",
      "name": "to",
      "description": "Target format: native or format2 (infers opposite by default)",
      "takesArgument": true,
      "argumentPlaceholder": "<format>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--output <file>",
      "name": "output",
      "description": "Write result to file (default: stdout)",
      "takesArgument": true,
      "argumentPlaceholder": "<file>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--compact",
      "name": "compact",
      "description": "Omit position info in format2 output",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--json",
      "name": "json",
      "description": "Force JSON output",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--yaml",
      "name": "yaml",
      "description": "Force YAML output",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--format <fmt>",
      "name": "format",
      "description": "Force source format (auto-detected by default)",
      "takesArgument": true,
      "argumentPlaceholder": "<fmt>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--stateful",
      "name": "stateful",
      "description": "Use cached tool definitions for schema-aware state re-encoding",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--cache-dir <dir>",
      "name": "cacheDir",
      "description": "Tool cache directory (for --stateful)",
      "takesArgument": tru
...

SKILL.md


# summarize-galaxy-workflow

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

## When To Use

- Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps.

## Inputs

- No upstream artifact inputs declared. See the procedure for user-supplied runtime inputs.

## Outputs

- Write artifact `summary-galaxy-workflow` as `summary-galaxy-workflow.json`. Format: `json`. Schema: summary-galaxy-workflow. Structured summary of an existing Galaxy workflow: source/format provenance, inputs, outputs, per-step tool_id/version/tool_state, edge graph, and any existing tests as a regression baseline.
- Write artifact `starting-galaxy-workflow` as `starting-galaxy-workflow.gxwf.yml`. Format: `yaml`. The normalized concrete gxformat2 workflow this summary describes — passthrough when the input was already gxformat2, the `.ga`→gxformat2 conversion otherwise. The substrate apply-galaxy-workflow-changeset edits; distinct from the summary JSON, which is only context.

## Required Tools

- **`foundry`** (foundry). `npm install -g @galaxy-foundry/foundry`.
  Ephemeral run: `npx --package @galaxy-foundry/foundry foundry`.
  Check: `foundry --help`.
  Docs: https://github.com/galaxyproject/foundry/blob/main/packages/foundry/README.md
  Bundled reference: `references/cli/foundry.md`.
- **`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

## Load Upfront

- `references/cli/validate.json`: CLI command reference packaged as a sidecar. Validate the gxformat2 workflow before extraction and record diagnostics under documents.validation. Use when: before extracting structure from the workflow document.
- `references/cli/foundry.md`: CLI tool reference copied verbatim into the bundle. Schema-check summary-galaxy-workflow.json with `foundry validate-summary-galaxy-workflow` before returning it from the skill.
- `references/schemas/summary-galaxy-workflow.schema.json`: Schema file copied verbatim into the bundle. Validate the emitted Galaxy workflow summary JSON and provide downstream consumers the output contract.

## Load On Demand

- `references/cli/convert.json`: CLI command reference packaged as a sidecar. Convert a legacy `.ga` workflow to gxformat2 before summarizing, and record the conversion under documents.converted_path. Use when: the supplied workflow is native `.ga` rather than gxformat2.

## Validation

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

## Procedure

Read an existing Galaxy workflow and emit `summary-galaxy-workflow.json`. This skill is source-specific and target-agnostic: it records what the workflow *is* — inputs, outputs, steps, wiring, and existing tests — and leaves every modification decision to the downstream change-set and apply skills. It mirrors summarize-cwl on the Galaxy-as-source side.

gxformat2 is already a typed workflow graph, so do not infer structure — read it. The summary is an LLM-digestible index of the existing workflow that anchors the interview and the change-set; it is **context**, not the substrate edits apply to. The substrate the edits are applied against is the normalized gxformat2 workflow file, emitted here as `starting-galaxy-workflow.gxwf.yml` and consumed by apply-galaxy-workflow-changeset — not this JSON summary. Because this skill already normalizes `.ga` to gxformat2, it is the natural carrier for that substrate: a `.ga` input's converted form would otherwise have no declared home.

### Inputs

- A local workflow path or an HTTP(S) URL. Accept both gxformat2 (`.gxwf.yml` / `.gxfmt2.yml`) and legacy native `.ga`.
- Optional pin/version metadata supplied by the harness or user.
- Optional sibling tests file (`*-tests.yml`); if none is supplied or discoverable, emit `tests: []`.

### Procedure

1. **Normalize format.** If the input is native `.ga`, convert it to gxformat2 with convert (`--to format2`) and record the output path in `documents.converted_path`. If it is already gxformat2, leave `converted_path` null. Set `source.original_format` accordingly. All downstream extraction reads the gxformat2 form. Emit this normalized gxformat2 as the `starting-galaxy-workflow.gxwf.yml` output — the substrate apply-galaxy-workflow-changeset edits, so a `.ga` input's converted form has a real carrier rather than living only inside the summary.
2. **Validate.** Run gxwf validate on the gxformat2 workflow and record `command`, `status`, and `diagnostics` under `documents.validation`. If invalid, still emit source provenance and diagnostics; do not invent graph structure past what parses.
3. **Extract the interface.** Record `workflow_inputs` (class `data` / `collection` / `parameter`, `collection_type`, optionality, defaults, format restrictions) and `workflow_outputs` (each promoted `step/output` source), preserving gxformat2 labels verbatim — those labels are the anchors the change-set will address.
4. **Extract steps.** For each step record its class, `tool_id`, `tool_version`, pinned `tool_shed_repository`, verbatim `tool_state`, named input connections with their upstream sources, declared outputs, and any `when:` guard. Keep `tool_state` verbatim so a later change-set can address an individual parameter. Record each declared output under `out[]` as `{id, actions}`, preserving the gxformat2 post-job actions on that output (`hide`, `rename`, `add_tags`, `remove_tags`, `change_datatype`, `delete_intermediate`, …) verbatim in `actions` — `actions: null` when the output has none. A hidden output that is not promoted to a `workflow_outputs` entry is only visible through its `hide` action here, so dropping it would blind an expose-output change-set to the very anchor it edits.
5. **Build the graph.** Emit workflow-input → step, step → step, and step → workflow-output edges. Add `via` markers for shape-affecting features (map-over, batch, collection reduction).
6. **Record tests.** When a sibling tests file or embedded tests exist, record each case's name, job path, and expected outputs as the regression baseline. Do not fabricate expected outputs from tool names.
7. **Schema-check.** Validate the assembled object with `foundry validate-summary-galaxy-workflow summary-galaxy-workflow.json` before returning it.

### Caveats Baked Into The Procedure

- **Labels are load-bearing.** Preserve step and input labels exactly; the change-set anchors edits to them, and a relabel here would silently break that anchoring.
- **`tool_state` is preserved, not interpreted.** Record it verbatim. Deciding which parameter an interview wants changed is the change-set's job, not this skill's.
- **Post-job actions are preserved, not interpreted.** Record each output's gxformat2 actions verbatim under `out[].actions` (`hide`, `rename`, `add_tags`, …); whether to expose a hidden output or drop a rename is the change-set's decision, not this skill's. Flattening `out` to bare names would erase that anchor.
- **Existing tests are the regression baseline.** Capture them faithfully; the update pipeline judges the modified workflow against them.
- **Conversion is lossy-aware.** If `.ga` → gxformat2 conversion drops or rewrites anything, surface it in `warnings[]` rather than presenting a clean summary.

### Non-Goals

- **Modification.** Interviewing for changes, building a change-set, and applying edits belong to interview-to-galaxy-workflow-changeset and apply-galaxy-workflow-changeset.
- **Tool discovery or wrapper authoring.** `tool_id` / `tool_shed_repository` are recorded as-found; resolving newly introduced tools is the per-step Galaxy loop's job.
- **Runtime execution.** This skill summarizes structure; run-workflow-test owns execution.

## 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.