map_dartseq_to_reference

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of behavioral disclosure. It explains the alignment process, backend selection (auto/cli/mappy), and marker classification (unique, multi, unmapped). However, it does not mention error handling, performance expectations, or any side effects beyond writing a CSV. Additional details on RAM usage and failure modes would be beneficial.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured: a concise first sentence summarizing purpose, followed by details on alignment, output, and implementation. It is front-loaded and each part adds value. It could be slightly more concise (e.g., the backend explanation could be shorter), but it remains clear and efficient.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's complexity (6 parameters, no annotations, presence of output schema), the description is fairly complete. It covers the main workflow, output format, and integration with another tool. It lacks details on error conditions or input validation, but overall provides sufficient context for an agent to use correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so baseline is 3. The description adds meaningful context beyond the schema: it explains that reference_fasta can be a FASTA or .mmi index, backend 'auto' uses CLI if available, and min_mapq thresholds classification. For output_dir, it gives the default path. This adds value for an agent.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The tool's purpose is clearly stated: 'Guess genomic positions for DArTseq SNP markers by aligning their tag sequences.' It specifies the action (align/guess), the resource (DArTseq SNP markers), and the output. The description distinguishes from the sibling tool 'import_dartseq' by noting that the result can be passed to it, clarifying the mapping role.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explains when to use the tool: for mapping DArTseq markers to a reference genome, and that the output can feed into import_dartseq for genome-anchored import. It does not explicitly state when not to use or list alternatives, but the context is clear enough for an agent to decide. More explicit exclusions would improve this dimension.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.