Tbl2xml

tbl2xml

Quick Start

• Command: tbl2xml < table.tsv > table.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/tbl2xml
• Full reference: See references/help.md for complete options and usage

When To Use This Tool

• Turn table-like text into XML so it can be processed with XML-side tools.
• Bridge text-table intermediate files into the XML-centric parts of an EDirect workflow.
• Normalize tabular annotations before downstream extraction or archiving.

Common Patterns

# 1) Convert a tabular text file into XML
tbl2xml < table.tsv > table.xml

# 2) Convert and inspect the first emitted XML blocks
tbl2xml < table.tsv | sed -n '1,40p'

Recommended Workflow

1. Make sure the upstream table really matches the format expected by your workflow.
2. Feed it to tbl2xml through stdin redirection or a pipe.
3. Inspect a small sample before converting an entire dataset.
4. Use the resulting XML with downstream xtract or reporting steps after that smoke test passes.

Guardrails

• This wrapper simply runs transmute -t2x, so transmute must be on PATH.
• The installed wrapper does not provide a real --help / --version interface.
• In this environment, a trivial tabular smoke test produced no output rather than a schema error, so validate on representative data first.
• Prefer stdin/pipes over undocumented positional-file behavior.