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trace_raw_signal

Read-only

The UNPROCESSED signal of a Sanger trace: how many scans the instrument recorded, where each channel's baseline sits, the peak raw value, and how many scans analysis discarded off the front as dye front.

Input 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.
documentNowhich trace file to read: its name (`read_F.ab1`) or its project file id. A file id is project-specific, so a template ships this unset.

Output Schema

NameRequiredDescriptionDefault
baselineYesper-channel median raw sample (A/C/G/T) — the offset analysis subtracts
rawScansYesscans the instrument recorded, on its own time base
peakRawValueYesthe largest raw sample across all four channels
baselineSpreadYeshighest channel baseline minus lowest. A large spread is one dye channel sitting high, which analysis removes and a raw view shows
droppedFromFrontYesscans analysis discarded off the front (dye front and primer peak). Gate on it: an unusually long discard is a run that took a long time to resolve

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.4/5.0
Behavior4/5

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

The annotations already establish that this is a safe read-only operation with no mutation. Beyond that, the description adds useful behavioral context about what raw signal is exposed, including discarded front scans as dye front, though it does not discuss trace availability errors or prerequisites.

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 definition is a single front-loaded sentence that avoids filler. It is somewhat run-on because it packs four output metrics into one clause, but every phrase provides relevant signal.

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?

The rich input schema, output schema, and annotations cover most calling details, so the description need not explain parameter formats or return structure. However, it leaves the tool weakly situated among many trace siblings and gives no selection context beyond the word 'UNPROCESSED'.

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%, and the schema documents _files, _subject, and document in detail. The description adds no parameter-specific meaning such as accepted document identifiers or file-id behavior, so the baseline of 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?

The description states a specific resource, the unprocessed signal of a Sanger trace, and enumerates the raw metrics returned: scan count, channel baselines, peak raw value, and discarded dye-front scans. This distinguishes it from processed-basecalling siblings, but it is phrased as output content rather than an explicit action and does not name a sibling alternative.

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 guidance, no when-not guidance, and no named alternative among the many trace-related tools. An agent can infer that this is for inspecting raw signal before processing, but that inference is not stated.

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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