Collection: regex relabel via tabular

Tool

Use a tabular mapping source, optionally transform it with tp_find_and_replace, then relabel the collection with __RELABEL_FROM_FILE__.

Corpus-shaped chain:

1. collection_element_identifiers or another mapping source emits identifiers as data.
2. tp_find_and_replace rewrites identifier text.
3. __RELABEL_FROM_FILE__ applies the modified labels to the target collection.

When to reach for it

Use this when the collection structure is right but element identifiers are wrong, noisy, or need a simple regex/string transformation.

Good fits include tool output that lost original sample names, identifiers that need prefix/suffix cleanup, and paired/unpaired outputs that need the same manifest-derived names.

Do not use this when relabeling is coupled to a structural reshape. Use relabel-via-rules-and-find-replace for the influenza-style restructure, extract identifiers, regex-relabel, restructure again shape.

This page is about label rewrite. Use sync-collections-by-identifier for membership sync and harmonize-by-sortlist-from-identifiers for order harmonization.

Parameters

collection_element_identifiers emits one identifier per line and no header.

For tp_find_and_replace, set regex mode deliberately. For no-header identifier lists, do not skip the first line.

For __RELABEL_FROM_FILE__, choose line-based labels only when row order matches collection order. Use tabular old-to-new mapping when order is uncertain.

Idiomatic shape

# collection_element_identifiers(input collection)
# -> optional tp_find_and_replace
# -> __RELABEL_FROM_FILE__(target collection, labels=modified identifiers)

Regex cleanup before relabel:

tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3
tool_state:
  infile: { __class__: ConnectedValue }
  find_pattern: "^(.*)\\.fastq(\\.gz)?$"
  replace_pattern: "\\1"
  is_regex: true
  skip_first_line: false

Pitfalls

• Line-based relabeling assumes mapping rows match collection element order.
• collection_element_identifiers has no header; skipping the first line drops a real identifier.
• Relabeling does not reorder or filter. Use a filter or sort pattern when membership or order changes.
• Keep regex cleanup narrow enough that distinct elements do not collapse to the same identifier.

See also

• iwc-transformations-survey — Recipe G and candidate boundary.
• relabel-via-rules-and-find-replace — use when relabeling is fused with Apply Rules structural fan-out.
• sync-collections-by-identifier — use when identifiers filter or relabel sibling collections without regex cleanup.