| 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
printf '<Root><Rec><Val>A</Val></Rec><Rec><Val>B</Val></Rec></Root>\n' | \
xtract.Linux -pattern Rec -element Val
xtract.Linux -help
xtract.Linux -input records.xml -pattern Rec -element Val
Recommended Workflow
- Start with
xtract.Linux -help if you need the complete compiled argument taxonomy.
- Identify the record boundary with
-pattern.
- Add
-group, -block, -subset, or conditional operators only after the basic extraction works.
- 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.
