gxwf-layout

gxwf-layout computes node positions for a Galaxy workflow (Format 2 .gxwf.yml or native .ga) and merges {left, top} position records back into the document, replacing the degenerate diagonal layout Galaxy applies when positions are absent. For Format 2 YAML the original comments, key order, and quoting are preserved; only position records are added or updated.

It gives hand-authored and machine-generated workflows sensible, stable coordinates without opening them in the Galaxy workflow editor.

Cyclic workflows are invalid in Galaxy and are rejected with an error rather than laid out.

Strategies

topological (default)

Strict layering: column is the longest path from any input, row is declaration order within the column. Dependency-free and identical to gxwf-viz –layout topological (a cross-language layout shared with the TypeScript port). Legible but applies no crossing reduction, so wide workflows can show more edge crossings.

layered

Sugiyama-style layered layout: the same longest-path layering plus a barycenter crossing-reduction pass that reorders rows to align each node with its neighbors. Fewer edge crossings on wide/real workflows. The exact coordinates are not a cross-language contract; both strategies satisfy the same structural properties (every edge points rightward, roots are leftmost, no overlapping nodes).

Comparing the strategies

Both strategies assign the same columns; layered only reorders the rows within each column to pull connected nodes into line. On dense, real-world graphs this removes most edge crossings. The figures below lay out the amr_gene_detection IWC workflow (13 nodes, 28 edges, 4 layers) both ways – positions stripped, recomputed by each strategy, and rendered with gxwf-viz –layout preset (which honors the baked positions). Layered cuts the crossings from 13 to 2:

gxwf-layout --strategy topological – 13 edge crossings.

gxwf-layout --strategy layered – 2 edge crossings.

Both layouts satisfy the same structural properties (every edge points rightward, roots are leftmost, no overlapping nodes); the workflow ships as the real-amr-gene-detection.ga example fixture.

Subworkflows

By default gxwf-layout recurses into subworkflows defined within the same file, giving each its own coordinate space:

• Format 2 steps with an embedded run: GalaxyWorkflow block

• native steps carrying an inline subworkflow: block

• every workflow in a $graph multi-workflow document

Subworkflows referenced by file path, URL, or $graph #id are not followed – at each level such a step is treated as a single node, matching the Cytoscape builder. Pass --no-recursive to lay out only the top-level document.

This script computes node positions for a Galaxy workflow (Format 2 .gxwf.yml or native .ga) and merges them back into the document, replacing the degenerate diagonal layout applied when positions are absent.

For Format 2 YAML the original file’s comments and formatting are preserved; only position records are added or updated. Steps/inputs with an explicit position are left untouched unless –overwrite is given; a “position: auto” marker is always replaced.

usage: gxwf-layout [-h] [--strategy {topological,layered}] [--overwrite]
                   [--no-recursive]
                   INPUT [OUTPUT]

Positional Arguments

INPUT

input workflow path (.ga/.gxwf.yml)

OUTPUT

output path (defaults to updating INPUT in place)

Named Arguments

--strategy

Possible choices: topological, layered

layout strategy (default: topological). ‘topological’ is the dependency-free, cross-language layering; ‘layered’ adds barycenter crossing reduction for fewer edge crossings on wide workflows.

Default: 'topological'

--overwrite

overwrite existing explicit positions (default: only fill missing / ‘auto’)

Default: False

--no-recursive

do not lay out embedded in-file subworkflows (default: recurse into Format2 ‘run:’ blocks, native ‘subworkflow:’ blocks, and $graph entries)

Default: True