@galaxy-tool-util/tool-xml

XML tool-source layer for Galaxy tools. Holds the XML-specific parsing weight (an XML parser dependency) out of the browser-safe @galaxy-tool-util/schema package.

Currently ships a port of Galaxy's macro expander, lib/galaxy/util/xml_macros.py: the XML-only, pre-parse transform that expands <macros> — <token> substitution (including nested tokens and cycle detection), <xml>/<macro> templates via <expand>, <import> of external macro files, named/unnamed yield, and macro token parameters — mutating an XmlElement tree in place.

import { loadTool, canonicalize } from "@galaxy-tool-util/tool-xml";

const expanded = loadTool("tool.xml"); // reads + expands macros

parseXmlToTree(text) parses XML into a mutable XmlElement tree; expandMacros(root, importResolver) expands it (filesystem-agnostic); loadTool(path) is the filesystem-backed convenience that resolves <import> paths relative to the tool file. canonicalize(el) reduces a tree to a whitespace-normalized shape for structural comparison.

Behavior is verified against golden macro-expansion fixtures synced from Galaxy (test/fixtures/macro-expansion/cases/), compared structurally rather than byte-for-byte so the port need not reproduce Galaxy's XML serializer.

On top of the expander, XmlToolSource ports the parse accessors from Galaxy's galaxy.tool_util.parser.xml.XmlToolSource that don't need the input-parameter tree — the tool metadata (id, version, name, description, profile, license, edam operations/topics, xrefs, citations, help, command) and the <outputs> tree (parseOutputs() → the ToolOutput union: data / collection / expression outputs, with discover_datasets):

import { loadXmlToolSource } from "@galaxy-tool-util/tool-xml";

const src = loadXmlToolSource("tool.xml");
src.parseId(); // "cat1"
src.parseCitations(); // [{ type: "doi", content: "..." }]
src.parseOutputs(); // [{ type: "data", name: "out1", format: "bam", ... }]

Extraction is raw — the model-level validation Galaxy's pydantic models run when the ParsedTool is assembled is not applied yet. parseCitations passes doi:-prefixed or malformed citations through rather than normalizing/dropping them (DOI/BibTeX shape checks, profile-gated skips), and parseOutputs does not enforce the collection-structure invariants (e.g. both type and type_source set) that Galaxy raises on.

Assembling these (plus inputs, behind the InputSource seam) into a full ParsedTool, with that validation, is the remaining work; see the repository's tool-parsing issue.