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jean — Molecular Biology & Genomics

list_sgrna_scaffolds

Read-only

Every sgRNA scaffold this workbench has sourced, with the nucleases each covers and the publication it comes from. A scaffold not listed here is one we do not have — the list is what we ship, not what exists.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYeshow many scaffolds are shipped
scaffoldsYeseach scaffold: id, name, sequence, length, which side of the spacer it sits, the nucleases it covers, its citation and accessions

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so safety and closed-world behavior are covered. The description adds a genuine nuance — the list is a curated shipping catalog, not an exhaustive registry of what exists — but says nothing about pagination, filtering, or response shape beyond that.

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

Conciseness4/5

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

Two short sentences, front-loaded with the payload and followed by the scope caveat. The second sentence is slightly editorial but earns its place by preventing the agent from assuming an unlisted scaffold exists elsewhere.

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

Completeness4/5

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

An output schema exists, so return values need no explanation, and the description already names the salient fields (nucleases, publication). For a zero-required-parameter catalog tool this is nearly complete; the only gap is not explaining the presence of the _subject/_files record parameters.

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

Parameters3/5

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

Schema description coverage is 100%, so the baseline is 3. However, the description never addresses the two parameters (_files, _subject), and since both are optional record-selection inputs on a pure listing tool, an agent could reasonably wonder whether filtering is expected; the description's 'every sgRNA scaffold' phrasing only implicitly signals no filtering.

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

Purpose4/5

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

The description states exactly what the tool returns: every sgRNA scaffold the workbench has sourced, annotated with the nucleases each covers and its source publication. That is specific enough to distinguish it from sibling design/scoring tools like crispr_design_guides or screen_guides, though it never uses an explicit verb and relies on the name/title for the 'list' action.

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

Usage Guidelines2/5

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

There is no statement of when to call this versus alternatives, and no prerequisite or sequencing guidance (e.g. 'call before crispr_design_guides to see supported scaffolds'). The second sentence clarifies the corpus contents but is about data completeness, not usage context.

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

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