bio-tools-router

name	bio-tools-router
description	Route bioinformatics intents to verified bio_tools operations, prioritizing PASS cases from bio_tools_test_matrix.json. Trigger on FASTA/FASTQ/SAM/BAM requests, assembly, alignment, annotation, taxonomy, phage, or workflow execution tasks.

Bio Tools Router

When to use

• Task includes FASTA/FASTQ/SAM/BAM/contigs input.
• User asks for sequence stats, alignment, gene prediction, phage checks, or workflow runner calls.

Routing rules

1. Prefer operations listed in references/verified_ops.md.
2. If operation choice is uncertain, call bio_tools(operation="help") for candidate tools first.
3. Prefer Tier-1 PASS operations before Tier-2 operations when both satisfy intent.
4. Only fall back to code_executor after at least one valid bio_tools attempt fails.

Input strategy

• Pass local absolute paths for input_file and path-like params.
• Keep output names relative where possible (e.g., aln.sam, stats.txt).

Reference

• Verified operation list: references/verified_ops.md