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Tabular: cut and reorder columns

Use Cut1 with a comma-separated cN list to project — and reorder — columns. Listing out of order is the canonical reorder idiom.

draft patterntarget/galaxy
Revised
2026-05-03
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2
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  • IWC exemplar anchors

    2 abstract workflow anchors declared.

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    Pattern frontmatter matches the site contract.

Tabular: cut and reorder columns

Tool

Cut1 (Galaxy core; bundled, no toolshed owner). Display name “Cut columns from a table”. Source: $GALAXY/tools/filters/cutWrapper.xml.

When to reach for it

Project a tabular to a subset of columns, and/or reorder existing columns. By far the most-used tabular tool in the IWC corpus (127 step occurrences in the survey). Use Cut1 when the operation is purely “pick columns” — no computation, no row filtering, no aggregation.

For project + compute fused, see tabular-sql-query or tabular-compute-new-column.

Parameters

  • columnList: a single comma-separated string of cN references — e.g. c4,c6,c7. Range syntax c2-c5 is also accepted (per the tool’s tests). Order matters: the output column order is the list order, so listing columns out of input order reorders them. The IWC corpus uses long enumerations rather than ranges; either is valid.
  • delimiter: select enum from the wrapper. Values: T (Tab), Sp (Whitespace — collapses runs), Dt (Dot), C (Comma), D (Dash), U (Underscore), P (Pipe). Tab dominates the corpus; always set explicitly.
  • The connected input port is the tabular dataset.

Idiomatic shapes

Pure projection (preserve order, drop unwanted columns):

tool_id: Cut1
tool_state:
  columnList: c1,c2,c5
  delimiter: T

Projection + reorder in one step (note c20 placed after c26,c24,c25):

tool_id: Cut1
tool_state:
  columnList: c4,c6,c7,c13,c14,c15,c16,c17,c18,c19,c21,c22,c23,c26,c24,c25,c20
  delimiter: T

Anchored by the SARS-CoV-2 variation reporting IWC exemplar.

Pitfalls

  • No header awareness. The header row is cut and reordered identically to data rows. Usually what you want; flagging only because Filter1 / Grouping1 do take header_lines.
  • delimiter must match the input. Mismatched delimiter (e.g. delimiter: T on comma-separated input) treats each line as a single field — c1 echoes the whole row, c2… produce a . (the wrapper’s missing-column fill) per row. Silent.
  • Cut breaks Galaxy column metadata. The wrapper warns: re-cutting may invalidate column-assignment metadata (chrom/start/end for interval/BED). Re-establish via the dataset’s “edit attributes” if downstream tools need it.
  • Reorder-then-rename is not Cut1’s job. Renaming columns means rewriting the header row — handle that with tabular-compute-new-column or with a tp_replace_in_line pass.
  • Adding a constant column belongs to tabular-compute-new-column (column_maker/Add_a_column1), not Cut1 + Paste1. The latter is legacy.

Legacy alternative

None for Cut1 itself — it is the modern tool. The legacy idiom of “add a constant column with Paste1 then re-Cut1” survives but should be replaced by column_maker/Add_a_column1 (see tabular-compute-new-column).

See also

IWC exemplars2 anchors

IWC Exemplars

sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reportinghigh

Shows pure projection and reordering with long explicit column lists.

  • Long projection and reorder with c20 last
  • Sibling Cut1 steps with different column lists
genome_annotation/functional-annotation/functional-annotation-of-sequences/Functional_annotation_of_sequencesmedium

Shows a legacy Paste1 plus Cut1 chain that should usually be replaced by column_maker for new work.

Incoming References (9)

  • Parameter: compose runtime text parameterrelated pattern— Use compose_text_param to build connected text expressions from constants plus runtime scalar values.
  • Galaxy: tabular patternsrelated pattern— Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
  • Tabular: compute a new columnrelated pattern— Use column_maker (Add_a_column1) with strict error_handling to insert/replace a computed column. Per-expression-kind auto_col_types rule.
  • Tabular: concatenate collection to tablerelated pattern— Use collapse_dataset to row-bind a collection of tabulars into one table, with optional element IDs and header dedupe.
  • Tabular: split taxonomy stringrelated pattern— Use tp_awk_tool to split semicolon-delimited taxonomy strings into explicit rank columns with missing-rank handling.
  • Tabular: SQL queryrelated pattern— Use query_tabular when SQL semantics justify it: windows, joins, anti-joins, or fused project+compute over tabulars.
  • Iwc Parameter Derivation Surveyrelated pattern— Corpus survey of Galaxy workflow recipes that turn upstream data, metadata, or small files into runtime parameters.
  • Iwc Tabular Operations Surveyrelated note— Corpus survey of tabular tools and operations across IWC workflows; map for the operation pattern hierarchy on row/column data manipulation.
  • Nextflow-to-Galaxy channel shape mappingrelated note— Maps common Nextflow channel, tuple, and path shapes to Galaxy dataset and collection shapes.