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Echo picklist export

export_echo_picklist
Read-onlyIdempotent

Generate a downloadable Beckman/Labcyte Echo acoustic-liquid-handler picklist CSV (columns: Source Plate Name, Source Plate Type, Source Well, Destination Plate Name, Destination Well, Transfer Volume, Name — the header row reproduced from PyEcho, a real open-source Echo-picklist generator) for the given PCR reactions, at the same well positions export_plate_layout assigns. Assumes a 5 uL Echo-scale PCR reaction (master mix 2500 nL, each primer 250 nL, template 250 nL, water 1750 nL) — a commonly used acoustic-dispensing miniaturization scale, not a universal standard; rescale the volumes for your own protocol. Source/Destination Plate Type uses a placeholder Echo plate-type code (384PP_AQ_BP) — replace with the exact type from your own Echo Plate Type Library. Each distinct template label gets its own well on the TemplateSource plate, row-major (A1, A2, … A24, then B1, …) across that 384-well source plate.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
reactionsYesOne entry per PCR reaction, up to 96 (a single 96-well plate).

TDQS

A4.6/5.0
Behavior5/5

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

Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, so the tool's safety profile is known. The description adds substantial behavioral context: the CSV columns, the plate type placeholder, the well-layout logic (row-major across a 384-well plate), and the assumption of a 5 uL reaction with explicit volume breakdowns. It also discloses that the plate type code is a placeholder, which is a non-obvious caveat. No contradictions exist.

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?

The description is dense but not wasteful. The first sentence captures the core purpose, and subsequent sentences provide important details (column names, volume assumptions, plate placeholder, well ordering). Every sentence adds value, though it is longer than strictly necessary and could be split into a summary plus caveats.

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

Completeness5/5

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

With no output schema, the description carries the burden of explaining the return value, and it does so thoroughly: it names the CSV columns, describes plate type placeholders, explains the source plate layout, and flags that the volume scale is not universal. It also references how positions relate to export_plate_layout, which gives richer context. The tool's assumptions and limitations are clearly stated.

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?

The schema covers 100% of the single parameter 'reactions' with nested object descriptions and a max of 96 entries. The description adds meaningful semantics beyond the schema by explaining how distinct template labels are assigned to unique wells and connecting the parameter to the output layout and volume assumptions. This goes beyond a baseline of 3.

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

Purpose5/5

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

The description begins with 'Generate a downloadable Beckman/Labcyte Echo acoustic-liquid-handler picklist CSV', which clearly states the action (generate), resource (picklist CSV), and target platform (Echo). It distinguishes from siblings like export_plate_layout and export_opentrons_protocol by specifying the exact output format and its association with Echo acoustic dispensing.

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?

The description gives clear context: it is for PCR reactions on an Echo acoustic liquid handler, and it aligns well positions with export_plate_layout. However, it does not explicitly mention when not to use it or name alternatives such as export_opentrons_protocol, so exclusions are absent. The context is strong, but the guidance could be more direct.

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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TDQS

A3.6/5.0
Disambiguation4/5

Most tools have highly specific purposes (e.g., crispr_grna_design vs base_editing_design vs prime_editing_design). However, there is some overlap in sequence analysis tools (characterize_sequence, sequence_report) and plasmid annotation tools (plasmid_annotate vs plasmid_deep_annotate) which could cause confusion.

Naming Consistency3/5

The naming pattern is largely consistent with snake_case verb_noun or noun_descriptor (e.g., primer_design, plasmid_annotate, fastq_trim). However, there are exceptions like 'batch', 'workflow', 'gc_content', and 'cloning_diagnose' which don't follow the verb_noun pattern consistently. Also, some names are phrases like 'golden_gate_from_parts'.

Tool Count2/5

With 101 tools, this server is extremely large and likely overwhelming for agents. Even for a comprehensive bioinformatics toolkit, this exceeds a manageable scope, risking agent confusion and inefficient tool selection. A more modular approach would be advisable.

Completeness4/5

The tool surface covers a wide range of bioinformatics workflows including sequence analysis, primer design, cloning, CRISPR, NGS, expression analysis, and data export. There are minor gaps such as lack of a dedicated protein structure prediction tool and limited off-target genome coverage, but overall the set is impressively complete for its domain.

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