Figure asset MANIFEST

Capture/generation procedures and source provenance for every figure asset. Mirrors the role of galaxy-notebooks/figures/MANIFEST.md but, because this is a tooling paper, most entries are reproducible commands rather than Galaxy object IDs. Re-running the commands here regenerates the asset; that reproducibility is itself part of the paper’s argument.

Environment (verified 2026-06-18)

• gxwf and galaxy-tool-cache CLIs: @galaxy-tool-util/cli 1.7.2 (homebrew global, used for the captures here); behavior verified identical on 1.8.0 (npm latest at capture date). Note: gxwf --version misreports 1.0.0 regardless of the installed version — a stale hardcoded string; read the real version from the package’s package.json. Record the actual version per capture, not the --version output.
• IWC corpus checkout: ~/projects/repositories/iwc (122 .ga workflows under workflows/).
• gxwf-web (browser editor) checkout: ~/projects/repositories/gxwf-web.
• galaxy-tool-util-ts monorepo checkout: ~/projects/repositories/galaxy-tool-util-ts.
• Anchor workflow for the worked example: iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga (“COVID-19: variation analysis on ARTIC PE data”, 33 steps, 25 tool steps). Collection-heavy (paired collection input → map-over) so it exercises connection validation; a smaller workflow may be substituted for the typeset listing if 33 steps is too long.

Warm the tool cache (prerequisite for state/connection/roundtrip assets)

WF=~/projects/repositories/iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga
C=/tmp/gxwf_si/cache
galaxy-tool-cache populate-workflow "$WF" --cache-dir "$C"   # ~25 tools, network (ToolShed TRS)
galaxy-tool-cache list --cache-dir "$C"

Main figures

fig1_stack — Format 2 / gxwf stack diagram

• Type: generated diagram (no capture). Author figures/fig1_stack.mmd (Mermaid) or TikZ; nodes: ToolShed (TRS) → tool cache → validation core (@galaxy-tool-util/core) → {CLI gxwf, VS Code galaxy-workflows-vscode, browser gxwf-ui, IWC CI}. Render → figures/fig1_stack.png.

fig2_layers — validation depth layers

• Type: generated diagram. Three stacked bands (structural / per-step state / per-connection). Author figures/fig2_layers.mmd or TikZ → figures/fig2_layers.png.

fig3_vscode — schema-aware editing in VS Code

• Type: GUI screenshot. Launch galaxy-workflows-vscode (F5 from the extension checkout, or install the marketplace build) with C as the configured cache. Open the worked-example Format 2 file. Stage one frame showing simultaneously: an invalid select value (red squiggle + message listing legal options), a state:-key completion popup, and a hover card with tool-XML help. Pick a tool with clean XML docs (e.g. fastp or bwa_mem). Save → figures/fig3_vscode.png. Resolution ≥ 1600 wide.

fig4_corpus — IWC corpus validate + round-trip results

• Type: generated chart, gated on the corpus measurement run (same data as the manuscript [NUMBER] placeholders).

# Cache all corpus tools first (large, network-heavy):
for wf in $(find ~/projects/repositories/iwc/workflows -name '*.ga'); do
  galaxy-tool-cache populate-workflow "$wf" --cache-dir "$C"; done
gxwf validate-tree ~/projects/repositories/iwc/workflows --strict --cache-dir "$C" --json > captures/corpus-validate.json
gxwf roundtrip-tree ~/projects/repositories/iwc/workflows --cache-dir "$C" --json > captures/corpus-roundtrip.json

• Chart the category counts → figures/fig4_corpus.png. The Axis-4 categorical finding (modal diagnostic class, a named tool whose version bump introduced drift) comes from the same two JSON files.

Supporting figures

figS1_encoding — native vs Format 2 for one step

gxwf convert "$WF" --to format2 --stateful --cache-dir "$C" --output captures/pe-artic.gxwf.yml

• Excerpt one step’s native tool_state (from $WF) beside the same step’s state: block (from the converted file). Typeset two-column.

figS2_depth — planted errors and real diagnostics (= “Listing 1”)

• Real capture proven 2026-06-18. Procedure used:

cp captures/pe-artic.gxwf.yml captures/pe-artic-broken.gxwf.yml
# plant (for the final figure, put each in a SEPARATE step so errors don't cascade):
#   illegal select:  single_paired_selector: paired_collection -> paired_coll
#   misspelled key:  disable_adapter_trimming -> disable_adaptor_trimming
#   type mismatch:   overrepresentation_analysis: false -> maybe
gxwf validate captures/pe-artic-broken.gxwf.yml --cache-dir "$C" --json > captures/validate-broken.json

• Real diagnostic text (illegal select): single_paired.single_paired_selector: Expected "paired_collection", actual "paired_coll" (+ the "single" union alternative). Structured form lives in results[].errors[] with per-step status: fail|ok.
• Caveat learned: an invalid conditional selector value cascades — the per-branch sub-errors collapse into one parent-object mismatch. To show distinct, legible categories, plant each error in a different step, and add a separate stale-__current_case__/removed-parameter step (warning class) and a bad-collection-connection step (see figS3).

figS3_connections — collection / map-over validation

gxwf validate "$WF" --cache-dir "$C" --connections          # clean baseline: 46 ok, 0 invalid, 0 skip
gxwf mermaid "$WF" --annotate-connections --cache-dir "$C" figures/figS3_mapover.mmd
# panel (b): build one invalid variant (list:paired output -> paired input, no flatten) and run --connections

• Render the annotated .mmd (map-over depth + reduction edges) for panel (a); capture the rejection diagnostic for panel (b).

figS4_native_parity, figS5_legacy_quickfix, figS6_conditional_completion, figS7_cache — VS Code GUI screenshots

• All four are interactive captures from galaxy-workflows-vscode. See fig3 launch notes.
  • figS4: same diagnostics/hover/completion on a .ga file; show both an object-tool_state step and a legacy string-encoded step.
  • figS5: open a .ga with string-encoded tool_state; screenshot the Hint + “Clean workflow (convert tool_state to object form)” quick fix; then the object-form after applying.
  • figS6: completion popup that changes with the selected conditional case (capture two frames, two selector values).
  • figS7: run Populate Tool Cache; screenshot the Tools: N cached status bar and the three diagnostic tiers (uncached Information, failed Warning, cached full validation). Cross-check N against galaxy-tool-cache list --cache-dir "$C".

figS8_browser — gxwf-ui browser editor

• Run the gxwf-web dev server (cd ~/projects/repositories/gxwf-web && <pnpm dev>; confirm the exact script), warm the IndexedDB cache in-page, paste the worked-example Format 2, capture a diagnostic + completion + the Cytoscape diagram. Playwright-capturable (MCP browser tools available).

figS9_conversion — bidirectional conversion + roundtrip

gxwf roundtrip "$WF" --cache-dir "$C" --brief     # panel (b): 23/25 ok, 54 benign, 0 real

• Panel (a) is the VS Code previewConvertToFormat2/previewConvertToNative diff view (GUI screenshot).

figS10_toolsearch — tool ID search

• Real capture proven 2026-06-18.

gxwf tool-search bwa --max-results 8 > captures/tool-search-bwa.txt
gxwf tool-versions iuc/bwa_mem2/bwa_mem2_idx
gxwf tool-revisions devteam/bwa/bwa --latest

• Typeset the tool-search table directly (scored owner/repo, tool_id, name, description).
• GUI variant of the same capability: web-shots/toolshed-search-dropdown.png (the Insert Tool Step command’s ToolShed-search QuickPick). See “Web-mode GUI captures” below.

Web-mode GUI captures (capture-kit/web-shots/)

Curated screenshots from the browser extension host (vscode-test-web), captured 2026-06-19 against the web_tool_resolution_fixes build (galaxy-workflows-vscode, @galaxy-tool-util/* 1.8.2) at a fixed 1280×800 viewport, light theme. ToolShed was reached through a local CORS proxy configured via the workspace setting galaxyWorkflows.toolShed.url (settable per-workspace after the machine→window scope fix). Earlier exploratory/uncached frames were removed.

Conditional choice for S6: kraken2’s single_paired conditional is not usable here — every case exposes the same input_sequences key (only the data arity differs), so the offered keys don’t visibly change. taxonomy_krona_chart’s type_of_data conditional is the right subject: the taxonomy case adds max_rank (a select 0–21) that the text case lacks, making the case-dependent key set visible in the completion list.

Fixture note: capture-kit/krona-legacy.ga was corrected on 2026-06-19 — it carried 5 stray step-level connected_paths: {} fields (in-memory-only derived data that @galaxy-tool-util strips on serialize and the native schema rejects), which produced 5 “Property connected_paths is not allowed” errors inconsistent with its documented “clean except legacy encoding” purpose. Removed via jq while preserving the string-encoded tool_state, so the file now shows only the legacy-encoding Hint/quick-fix.

Working captures

Live under /tmp/gxwf_si/captures/ during authoring (not committed): tool-search-bwa.txt, connections-ok.txt, validate-broken.txt, plus pe-artic.gxwf.yml / pe-artic-broken.gxwf.yml. Promote the curated subset into si/ (see supporting-information.md) once the worked example is finalized.