xtract-linux

name	xtract-linux
description	Use when calling the Linux-specific compiled `xtract.Linux` binary directly to extract tabular or XML output from structured XML records.
disable-model-invocation	true
user-invocable	true

xtract-linux

Linux platform binary for the EDirect xtract engine. It converts structured XML into tabular or generated XML output using record patterns, nested exploration scopes, conditional filters, and rich formatting controls.

Quick Start

• Command: xtract.Linux -pattern <record> -element <field>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xtract.Linux
• Version seen locally: 24.0

When To Use This Tool

• Extracting table rows directly from XML on Linux via the compiled xtract backend
• Debugging raw xtract behavior separately from the public wrapper
• Exploring XML structure before writing a larger Entrez Direct pipeline
• Using built-in compiled help as the canonical reference for xtract arguments

Common Patterns

# Basic extraction from a tiny XML sample
printf '<Root><Rec><Val>A</Val></Rec><Rec><Val>B</Val></Rec></Root>\n' | \
  xtract.Linux -pattern Rec -element Val

# Show direct binary help
xtract.Linux -help

# Read XML from a file instead of stdin
xtract.Linux -input records.xml -pattern Rec -element Val

Recommended Workflow

1. Start with xtract.Linux -help if you need the complete compiled argument taxonomy.
2. Identify the record boundary with -pattern.
3. Add -group, -block, -subset, or conditional operators only after the basic extraction works.
4. Prefer the public xtract wrapper if you need its front-end shortcuts into transmute or rchive.

Guardrails

• xtract.Linux -help and xtract.Linux -version both work here and report version 24.0.
• This is the compiled backend only; the public xtract wrapper intercepts some flags such as -format, -outline, -j2x, and -e2index before dispatch.
• In local testing, a minimal XML sample piped to xtract.Linux -pattern Rec -element Val emitted two lines: A and B.
• If you run it with no stdin and no -input, it expects XML input and will fail rather than acting like a metadata-only tool.