Collection: build named bundle

Tool

Use Galaxy built-in __BUILD_LIST__.

The survey found two useful sub-cases:

• Manual-id output bundle: collect related outputs into a named result collection for organization or publishing.
• Identifier-id fan-in: assemble tool outputs into one collection for a downstream tool that expects collection input.

__MERGE_COLLECTION__ is the sibling operation when the inputs are already collections. Current corpus evidence does not justify a standalone merge pattern.

When to reach for it

Use __BUILD_LIST__ when you start with individual datasets or individual output connections and need a Galaxy list.

Use manual identifiers when element names should be human-authored result labels. Use inherited identifiers when downstream semantics already know those names.

Do not use this to concatenate file contents. Use tabular-concatenate-collection-to-table when the goal is one combined tabular dataset.

Parameters

The main knob is the element identifier source:

tool_id: __BUILD_LIST__
tool_state:
  elements:
    - src: { __class__: ConnectedValue }
      id_cond:
        id_select: manual
        identifier: bray_curtis_pcoa_results

• id_select: manual: human-authored names for output bundles.
• id_select: identifier: inherit source identifiers for downstream fan-in.
• id_select: idx: positional/default style; avoid when element identity matters.

Pitfalls

• Manual identifiers become collection element identifiers and may appear in output histories or reports.
• Manual bundles group outputs; they do not align rows, merge contents, or validate common keys.
• Use inherited identifiers only when source names are meaningful.
• Prefer __MERGE_COLLECTION__ only when inputs are already collections.

See also

• iwc-transformations-survey — Recipe K and candidate boundary.
• collection-flatten-after-fanout — collapse nested outputs before downstream pooling.
• tabular-concatenate-collection-to-table — row-bind a collection of tabulars after collection assembly.