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jean — Molecular Biology & Genomics

plan_next_tools

Read-only

What can run next, and what each next step would add. Give it a tool whose run just finished (or the output types in hand) and it returns the tools whose own declared inputs those outputs fill, each with the parameter the wire lands on, the question that tool answers, its limits, what grades it, whether it is seeded, asynchronous, writing or leaving the machine, and which of the data files it reads the run in hand already read — so a step that would re-read the same table can be told from one that brings independent evidence. Ask for a target_type and it returns the shortest chains of tools that reach it. The hand-offs are the workflow builder's own port graph, so a step it names is a wire the builder would draw.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
afterNothe tool whose run just finished — its declared outputs are what is in hand. Leave unset and give `output_types` instead.
_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.
max_stepsNolongest chain to consider when a `target_type` is given.
read_onlyNokeep only steps that write nothing.
target_typeNooptional: the output type you want to reach. Returns the shortest chains of tools that get there.
output_typesNothe port types in hand, when no single tool produced them (`sequence`, `record`, `bands`, `sites`, `protocol`, `matrix`, `series`).
independent_onlyNokeep only steps that read none of the data files the finished run read, so each adds its own evidence.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYeshow many tools can consume these outputs by their declared types
pathsYesthe shortest chains of tools reaching `target_type`, when one was asked for
toolsYesthe candidates, in catalog order: the parameter each wire lands on, the question that tool answers, its limits, what grades it, and what it reads
messageYeswhat was walked, in words
outputsYesthe types the walk started from
untypedYestools declaring an untyped parameter the builder would let this be wired into — a wire the graph cannot vouch for

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.9/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, establishing this as a safe read/planning call. The description adds real context beyond that: returned steps are tagged with seeded/asynchronous status, whether they write or leave the machine, what grades them, and which already-read data files they re-read. It does not cover latency or whether prior run context is required, keeping it from a 5.

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

Conciseness3/5

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

The purpose is front-loaded in the opening clause and there is no filler about generic benefits. The middle sentence, however, is an overlong clause packing a list of return attributes and the data-file-overlap concept into one breath, which harms scanability. Useful content, but structure could be tightened.

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?

For an 8-parameter, nested-schema, closed-world planning tool with an output schema, the description covers both invocation modes and the nature of the returned graph edges. Since an output schema exists, it need not detail return shapes, and its coverage of the input modes is adequate. Error handling and session prerequisites are unaddressed, so not a 5.

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

Parameters4/5

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

Schema coverage is 100%, so the baseline is 3. The description still adds mode-level meaning the schema cannot: `after` vs `output_types` as the mutually-exclusive hand-in, and `target_type` triggering shortest-chain search. It lightly implies `max_steps` bounds chain search but adds no detail on `read_only`/`independent_only` beyond the schema text.

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 names a specific function: given a just-finished tool (or output types), it returns candidate next tools whose declared inputs those outputs fill, and with `target_type` it returns shortest tool chains. This is clearly a workflow-graph traversal/planning tool, distinguishable from `run_workflow` or `validate_workflow`. It stops short of explicitly naming sibling alternatives such as `rank_next_tests`, so it does not reach 5.

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

Usage Guidelines4/5

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

It gives concrete entry conditions: 'Give it a tool whose run just finished (or the output types in hand)' and 'Ask for a `target_type` and it returns the shortest chains'. That cleanly describes the two invocation modes. It never states when not to use it or which sibling to prefer for adjacent needs, so 4 rather than 5.

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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