Collection: harmonize by sortlist from identifiers

Tool

Use Galaxy built-in __SORTLIST__ with sort_type: file, driven by an identifier list from collection_element_identifiers.

This is the corpus-attested harmonization recipe. __HARMONIZELISTS__ exists in the collection-tools catalog, but the survey found zero corpus uptake.

When to reach for it

Use this when two sibling collections must line up by element identifier before downstream map-over, zip-like pairing, or parallel per-sample processing.

The usual shape is: extract identifiers from the reference collection, feed that identifier file into __SORTLIST__, and sort the sibling collection with sort_type: file.

This is a reorder, not a filter. The identifier file has to name every element exactly once or the job fails, so it cannot be used to subset. Use sync-collections-by-identifier when membership is what needs changing.

This page is about order harmonization. Use sync-collections-by-identifier when membership alone is the issue and regex-relabel-via-tabular when labels need cleanup.

Parameters

Identifier extraction has no meaningful knobs. sort_type is a conditional whose select is also named sort_type, and sort_file lives inside it:

tool_id: __SORTLIST__
tool_state:
  input: { __class__: ConnectedValue }
  sort_type:
    sort_type: file
    sort_file: { __class__: ConnectedValue }

Connect the identifier file through sort_type|sort_file. It must be the identifiers of the collection whose order should be copied.

Pitfalls

• This cannot drop elements, it fails instead. SortTool requires the file’s line count to equal the element count, and every line to name an element that exists — otherwise the job errors. A sort file that has drifted out of sync stops the workflow rather than quietly shrinking the collection.
• The reference collection defines truth. If the identifier file comes from the wrong sibling, downstream pairing silently follows the wrong axis.
• Extract identifiers after upstream relabel, filter, or flatten operations, not before.
• Mention __HARMONIZELISTS__ only as the absent catalog alternative; do not recommend it from corpus evidence.

See also

• iwc-transformations-survey — Recipe I, decision table, and Q7 on sort-as-filter.
• sync-collections-by-identifier — membership sync without explicit order harmonization.
• collection-flatten-after-fanout — one-step collection-shape cleanup after map-over.