VS Code screenshot capture kit

Verified staging for the VS Code extension figures (Fig 3, Fig S4–S7). Every diagnostic below was confirmed via gxwf validate against the same cache the extension uses, so what the editor renders is known-correct before you capture it.

Subject workflow

IWC “Taxonomy Profiling and Visualization with Krona” — 3 tool steps (kraken2 → krakentools_kreport2krona → taxonomy_krona_chart). Small enough that all three steps + their diagnostics fit one editor viewport. Source: iwc/workflows/microbiome/pathogen-identification/taxonomy-profiling-and-visualization-with-krona/.

Files in this kit

File	Purpose
`krona-demo.gxwf.yml`	Clean Format 2 — validates strict-clean. Baseline / before-shots.
`krona-demo-broken.gxwf.yml`	Format 2 with 3 planted errors in distinct steps (below). Main subject for Fig 3 / Fig S2.
`krona-demo-broken.ga`	Same 3 errors in native `.ga` (object `tool_state`). For Fig S4 native parity.
`krona-legacy.ga`	Clean workflow with string-encoded `tool_state` (legacy form). For Fig S5 quick fix.

Planted errors (verified)

Step	Edit	Class	What the editor shows
`kraken2` (step 2)	`min_base_quality: high` (was `0`)	type mismatch	Error on the value: `min_base_quality` expects a number, actual `"high"`
`kraken2` (step 2)	`use_name:` (was `use_names:`)	unknown parameter	Warning on the key: `Unknown tool parameter 'use_name'.` — editor/LSP-only; the `gxwf validate` CLI does NOT surface this, so the screenshot is the only evidence for this class
`taxonomy_krona_chart` (step 4)	`type_of_data_selector: txt` (was `text`)	illegal select	Error on the value listing legal options: must be one of `text`, `taxonomy`

CLI cross-check (default cache): gxwf validate krona-demo-broken.gxwf.yml --json → summary {ok:1, fail:2, skip:0} (the third, the unknown-param warning, is editor-only).

Prerequisite: warm cache (already done on this machine 2026-06-18)

The extension reads ~/.galaxy/tool_info_cache by default. The 3 Krona tools were added there via:

galaxy-tool-cache populate-workflow <Taxonomy-Profiling-...-Krona.ga>

On a fresh machine, re-run that once so the extension validates offline. (galaxyWorkflows.toolCache.directory is machine-scoped, so prefer populating the default cache over a workspace setting.)

Launch

From the extension checkout (galaxy-workflows-vscode, built — client/dist + server dists present):

code --extensionDevelopmentPath=. /tmp/gxwf_capture   # or this capture-kit folder

Diagnostics (squiggles + Problems panel) and the Tools: N cached status bar render automatically once the language server resolves — no interaction needed for those.

Per-figure capture checklist

Fig 3 — schema-aware editing (money shot). Open krona-demo-broken.gxwf.yml. Frame all three diagnostics, then stage the two transient popups in one composite (or three sub-panels):
- (a) hover the type_of_data_selector value → hover card shows the param label/help + legal options.
- (b) put the cursor on a new line inside the kraken2 state: block, press Ctrl+Space → completion popup of kraken2 parameter keys.
- (c) the red squiggle on min_base_quality: high with its error message visible.
Fig S4 — native .ga parity. Open krona-demo-broken.ga. Same three diagnostics on the native file; also show one object-tool_state step beside a hover, to make the “parity” point.
Fig S5 — legacy quick fix. Open krona-legacy.ga. The whole tool_state value carries a Hint; click the lightbulb → “Clean workflow (convert tool_state to object form)”. Capture before (hint) and after (object form with precise sub-diagnostics).
Fig S6 — conditional-aware completion. In krona-demo.gxwf.yml, use step 4 taxonomy_krona_chart type_of_data.type_of_data_selector (cases text / taxonomy). Set the selector to text, trigger completion inside type_of_data: → offers only input; set it to taxonomy → offers input and max_rank. The appearance of max_rank only in the taxonomy case is the case-aware-completion proof. Do not use kraken2’s single_paired conditional: every case exposes the same input_sequences key (only data arity differs), so the offered keys don’t change. Captured: web-shots/conditional-completion-{text,taxonomy}.png.
Fig S7 — cache lifecycle. Screenshot the Tools: N cached status bar; run Populate Tool Cache from the command palette; and (to show graceful degradation) open a workflow with one uncached tool to capture the Information vs Warning vs full-validation tiers. Cross-check N against galaxy-tool-cache list.

Automation notes

screencapture (macOS) is available; cliclick is not, osascript is. Non-interactive shots (diagnostics, Problems panel, status bar) can be screen-captured after launch. Transient popups (hover/completion/quick-fix menu) need either a human at the keyboard (≈5 quick captures) or fragile osascript keystroke automation.

In practice the transient-popup figures were captured headlessly via the browser extension host (vscode-test-web) driven by Playwright — completion dropdowns and the Insert Tool Step ToolShed QuickPick render in the workbench DOM and are scriptable there. The five curated results live in web-shots/ (inventory + provenance in ../MANIFEST.md, “Web-mode GUI captures”). Save additional captures as figures/fig3_vscode.png, figS4_native_parity.png, etc. (see ../MANIFEST.md).

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