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CovaSyn Chemistry Tools

covabio_parse_fasta

Parse FASTA text into named sequence entries. Handles multi-line sequences, multiple records, and raw sequence without a header (auto-named seq_1, seq_2, ...). Use to turn a pasted or downloaded FASTA into the input for covabio_batch_profile or any single-sequence tool.

Parameters:
  fasta_text: FASTA-formatted text (one or more records).

Returns: {entries: [{name, sequence}]}

Input Schema

NameRequiredDescriptionDefault
api_keyNo
fasta_textYes

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.9/5.0
Behavior3/5

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

No annotations are provided, so the description carries the full behavioral burden. It usefully discloses edge-case handling (multi-line sequences, multiple records, headerless input auto-named seq_1, seq_2), but never states that parsing is side-effect-free/non-mutating, says nothing about error behavior on malformed FASTA, and does not mention the api_key requirement.

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?

Front-loaded: parsing purpose and edge-case handling come first, then usage guidance. Tight overall, though the trailing 'Returns: {entries: ...}' line restates what the existing output schema already provides and is minor dead weight.

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 a simple text-parsing tool with an output schema present, the description covers purpose, edge cases, and downstream wiring well; return format need not be explained. The only real omission is the undocumented api_key parameter, which is a minor but real gap.

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 0%, so the description must compensate. It adequately defines fasta_text ('FASTA-formatted text (one or more records)') and its headerless behavior, but the second parameter (api_key) is never mentioned in either the schema or the description, leaving one of two parameters undocumented.

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?

States a specific verb+resource ('Parse FASTA text into named sequence entries') and immediately differentiates itself from the many analysis siblings by naming the downstream consumer (covabio_batch_profile / any single-sequence tool). An agent can tell this is the ingestion/preprocessing step, not an analysis step.

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?

Explicitly says when to use it: to turn pasted or downloaded FASTA into input for covabio_batch_profile or single-sequence tools. It does not name what to use instead when the input is already structured (e.g., vs. covabio_sequence_utils), so it stops short of full when-not guidance.

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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