gxformat2 skeleton with per-step TODOs from a paper summary and the paper-to-Galaxy design brief.
Directory Mold with only index.md frontmatter.
source-specific fields are coherent.
eval.md not written yet.
6 typed references; 0 resolver issues.
All on-demand references describe triggers.
Hypothesis references include verification.
Typed Mold references describe what casting consumes and when the generated skill should load each artifact.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
gxformat2 draft (see [[galaxy-workflow-draft-format]]): topology fully resolved (workflow inputs, outputs, step set, edges); tool_id / tool_state / tool_shed_repository and wrapper-determined port names may be TODO with free-text _plan_state / _plan_context / _plan_in / _plan_out per step for later implementation Molds.
Paper summary emitted by [[summarize-paper]]; consulted while emitting placeholder steps.
Combined Galaxy design brief from [[paper-summary-to-galaxy-design]] that pins interface and data-flow choices.
Structural diff guidance from [[compare-against-iwc-exemplar]] (run on the design brief); steers the skeleton toward IWC-aligned structure before per-step authoring.
Read the original paper artifact, the paper summary Markdown document, and the paper-to-Galaxy design brief. Emit a gxformat2 skeleton with workflow inputs, workflow outputs, placeholder steps, rough connections, and TODO slots for later implementation Molds.
The paper summary does not have a concrete schema yet; treat it as Markdown. Treat the prior-step index as the working context: paper source, paper summary, paper-to-Galaxy design brief, and any open questions carried forward.
Topology is this Mold’s job to settle. The output must be concrete gxformat2: workflow inputs with their final collection shapes and formats, workflow outputs, the step set, the producer→consumer edge graph, branches, and when: guards are all decided here. The upstream paper-to-Galaxy design brief guides those decisions, but if it hedges or leaves a topology choice open, this Mold makes the call from source evidence, IWC exemplars, and pattern pages — never emit a topology TODO. What is deferred to per-step authoring is strictly wrapper-tier: tool_id, tool_version, tool_shed_repository, tool_state, and the wrapper-determined port names that surface in in: / out: / outputSource. Capture deferred intent in the _plan_* family (_plan_state, _plan_context, _plan_in, _plan_out) so the per-step Mold has the source evidence and constraints it needs.
Defer thoughtfully. When research surfaces a Foundry pattern page that names the exact recipe — a galaxy-collection-patterns reshape, a conditional-run-optional-step gate, a galaxy-tabular-patterns filter — fill the step in as completely as the pattern allows: concrete tool_id, parameters, port names from the pattern’s worked example. Pattern pages encode resolved choices; emitting TODO over a covered recipe discards real evidence the per-step Mold cannot recover. Paper sources will rarely give you enough to fill a domain tool step concretely — defer those wrappers and parameters, but cite the originating paper section / figure / supplementary table in _plan_context and use _plan_state to record vague intent (“default settings”, “stranded reverse if mentioned, else unstranded”) so the per-step Mold knows the evidence ceiling.
Output shape is gxformat2 with wrapper-tier relaxations and _plan_state / _plan_context / _plan_in / _plan_out per tool step — see galaxy-workflow-draft-format. Refinement open work for those planning fields lives in refinement.md.