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Jean — Molecular Biology & Genomics

rank_strategies

Read-only

Compare EVERY assembly chemistry this engine has against one set of parts, and say what each one costs and risks.

Input Schema

NameRequiredDescriptionDefault
partsNothe parts to assemble, in order — order is meaningful for Type-IIS. Wire records in, or name project documents.
_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.
enzymeNoType-IIS enzyme for the chemistries that use one. `auto` is DnaCauldron's own default: it picks the enzyme from the sites the parts carry.auto
_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.
order_byNowhich criterion to order the feasible strategies by. Every criterion is reported for every strategy whichever one you pick. Values: steps (Steps (lower is better)), junctions (Junctions (lower is better)), primers (Primers (lower is better)), overhangFidelity (Overhang fidelity (higher is better)), weakestJunctionTm (Weakest junction Tm (higher is better)), framesBroken (Frames broken (lower is better)), diagnosticCutters (Diagnostic cutters (higher is better)), cost (Cost (lower is better)).junctions
digest_enzymesNothe enzymes a verification digest may use. Left unset the run uses your active enzyme collection; with neither, the diagnostic-digest criterion is reported as unavailable rather than guessed, because a digest is only meaningful against enzymes you have.

Output Schema

NameRequiredDescriptionDefault
bestYesthe chemistry at the top of the order you asked for — a position in that order, not a verdict. Null when no chemistry built these parts
rankedYesevery feasible strategy in order, each with every criterion and the reason for any it could not score
refusedYesthe chemistries that produced nothing, each with the refusal it gave. Never dropped: 'this cannot be built that way, and here is why' is half the answer
criteriaYesthe criteria themselves: what each one means and which direction is better
feasibleYeshow many chemistries produced a construct from these parts
notScoredYescriteria NO strategy could score, with the reason — so an empty column says why it is empty

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 establish readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds that output covers cost and risk per strategy, which is useful context beyond the annotations, but it leaves 'risks' undefined and never says whether infeasible strategies are omitted or included with a failure note.

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?

A single front-loaded sentence that leads with the exhaustive comparison and ends with what the caller gets back. It is tight and waste-free, though the terseness is also why behavioral detail is missing.

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

Completeness3/5

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 not be explained here, and the schema fully covers inputs. For a tool that ranks every available assembly chemistry, however, one sentence leaves the notion of cost and risk undefined and gives no hint about feasibility filtering or result ordering behavior.

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 every parameter, including the order_by enum values and the digest_enzymes fallback behavior, is already documented in the schema. The description adds no parameter-level meaning, so the baseline 3 applies.

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?

States a specific action with scope: 'Compare EVERY assembly chemistry this engine has against one set of parts' — verb, resource, and the exhaustive scope are all explicit. It is distinguishable from assembly-executing siblings like golden_gate_assemble or gibson_assemble, though it never names those siblings to sharpen the contrast.

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 explicit when-to-use or when-not-to-use guidance, and no alternative is named. The implied workflow — survey all chemistries before committing to one — must be inferred from the word 'Compare' rather than stated, and nothing says whether this should precede or replace a tool like assembly_plan_simulate.

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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