Conditional: transform or pass through

Tool

Use a Galaxy when: gate on the optional transform branch, then use pick_value to collapse the optional transformed output and the original input/output back to one downstream value.

The observed shape is:

1. Derive or expose a boolean.
2. Connect that boolean as the gated step’s id: when input.
3. Set when: $(inputs.when) on every step in the optional transform branch.
4. Feed the transformed output and original value into pick_value.
5. Connect downstream steps only to the selected value.

When to reach for it

Use this when a workflow should optionally alter a dataset, collection, or report while preserving one stable downstream input slot.

This is not general mode routing. The pass-through side is not a peer algorithm; it is the same data before the optional cleanup, relabel, or rewrite. Reach for this when the user story is “apply the cleanup if requested or needed, otherwise keep the original.”

Use conditional-route-between-alternative-outputs instead when the branches are mutually exclusive peer routes: import mode A vs mode B, annotation mode 1 vs 2 vs 3, co-assembly vs individual assembly. In that route pattern, each branch independently produces a candidate output. Here, one branch is a transform of the other branch’s source.

Use conditional-run-optional-step when the optional branch has side outputs only and no downstream replacement value is needed.

Do not use this as collection failure cleanup. If mapped elements are empty or failed, use collection-cleanup-after-mapover-failure with __FILTER_EMPTY_DATASETS__ or __FILTER_FAILED_DATASETS__.

Operation Boundary

conditional-transform-or-pass-through is the “same value, optionally modified” pattern.

Keep it separate from route-with-pick_value for now because authors need to distinguish:

• Transform/pass-through: original value is valid downstream input; transformed value replaces it only when the branch runs.
• Route between alternatives: each branch is a different source, mode, or algorithm; there may be no privileged original.
• Optional side branch: downstream does not need a merged replacement value.
• Filter null outputs: not corpus-backed in IWC; __FILTER_NULL__ has zero observed hits in the conditionals survey.

If merged later, this should become a named subsection of conditional-route-between-alternative-outputs, not disappear; the authoring decision is common enough to teach explicitly.

Parameters

• when input on every optional transform step: connected from a workflow boolean, map_param_value, or another boolean-producing step.
• when: $(inputs.when) on each gated transform step.
• pick_value input order: put the transformed output before the original fallback so the transformed value wins when present.
• Original fallback: connect the unmodified value, or an upstream report/output equivalent, into the later pick_value candidate slot.

The exact transform tool is operation-specific. IWC examples use text replacement, line replacement, masking, concatenation, and suffixing tools; the pattern is the conditional merge shape, not those tools.

Idiomatic Shape

Conceptual gxformat2 shape:

- label: Optional transform
  tool_id: <transform-tool>
  in:
    - id: input
      source: original_input
    - id: when
      source: transform_boolean
  when: $(inputs.when)

- label: Use transformed value if present, otherwise original
  tool_id: pick_value
  in:
    - id: style_cond|pick_from
      source: Optional transform/output
    - id: style_cond|pick_from
      source: original_input

Read this as preserving a downstream contract: later steps consume one value regardless of whether the optional transform ran.

Pitfalls

• Put the transformed output before the original fallback in pick_value; otherwise the original may win even when the transform ran.
• Gate every step in a multi-step transform branch. A downstream transform step without the same when may run with missing inputs.
• Do not duplicate the whole downstream workflow after the optional transform. Merge once with pick_value, then continue with one path.
• Do not model pass-through as a fake transform step. The unmodified value should be connected directly as the fallback candidate.
• Do not cite __FILTER_NULL__ as the IWC idiom for this. The survey found zero __FILTER_NULL__ hits.

See Also

• iwc-conditionals-survey — Candidate D and boundary against Candidate B.
• galaxy-conditionals-patterns — conditionals MOC.
• conditional-route-between-alternative-outputs — sibling route-with-pick_value pattern for peer alternatives.
• conditional-run-optional-step — primitive when: branch without downstream merge.
• conditional-gate-on-nonempty-result — data-derived gate for downstream reporting/export.
• collection-cleanup-after-mapover-failure — collection-state cleanup, not a when + pass-through recipe.