jean — Molecular Biology & Genomics

draw_trace

Read-only

Draw a window of a Sanger read as an SVG figure: the four dye traces over their called bases, the per-base Phred bars and a base ruler. The same geometry the Chromatogram tab draws with, so the figure and the tab put every peak in the same place. Name the window around whatever you are asking about — a mutation site, a trim bound, an ambiguous call — because a whole 1,000-base read drawn at once shows nothing.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`from`	No	first base drawn, 1-based and inclusive. Clamped into the read.
`bases`	No	how many bases to draw. Keep it to a window you can read: past about 120 the peaks are narrower than the letters over them.
`width`	No	figure width. It SETS the per-base zoom for the window asked for, never crops it. In px.
`_files`	No	The 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.
`palette`	No	which ink each dye is drawn in. `print` is the default here because the figure travels outside the app and onto white; `cvd` is the color-vision-deficiency-safe set. Values: classic (Classic (ABI)), cvd (Color-blind safe), print (Print (on white)).	print
`quality`	No	print the per-base Phred bars. A file with no confidence (many SCFs) draws none whatever this says.
`_subject`	No	The 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.
`document`	No	which trace file to draw: its name (`read_F.ab1`) or its project file id. A file id is project-specific, so a template ships this unset.
`bases_row`	No	print the called bases between the ruler and the peaks. Advanced.
`trace_height`	No	height of the peak band, under the ruler, quality and base rows. In px. Advanced.

Output Schema

TableJSON Schema

Name	Required	Description
`svg`	Yes	the trace window as an SVG figure
`read`	Yes	the read drawn
`width`	Yes	figure width in px
`height`	Yes	figure height in px
`lastBase`	Yes	last base drawn, 1-based inclusive
`sequence`	Yes	the calls in the window drawn, so the picture and the string cannot disagree
`firstBase`	Yes	first base drawn, 1-based inclusive, AFTER clamping into the read
`hasQuality`	Yes	whether this file carries per-base confidence at all
`meanQuality`	Yes	mean Phred over the window drawn, or 0 when the file carries no confidence — read `hasQuality` beside it rather than reading 0 as bad calls

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.1/5.0

Behavior4/5

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

Annotations already cover the read-only, non-destructive safety profile. Beyond that, the description adds meaningful behavioral context: the figure uses the same geometry as the Chromatogram tab, and a file with no confidence draws no quality bars. These are real behavioral traits not captured by the annotations.

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?

Three sentences, front-loaded with the core action, then the geometry rationale, then the sizing advice. Each sentence carries weight, though the Chromatogram-tab sentence is partly flavor and could be trimmed.

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?

An output schema exists, so return-value explanation is not needed, and annotations cover the safety profile. Combined with fully documented parameters, the description is complete for an agent to call this rendering tool correctly; only explicit alternative-tool routing is absent.

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 already explains every parameter richly (from, bases, width, palette, quality, etc.), including the clamping and zoom behavior. The description adds no parameter-level detail beyond what the schema provides, so the baseline 3 is correct.

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 (draw) and resource (a window of a Sanger read as an SVG figure) and enumerates exactly what the figure contains: dye traces, Phred bars, and a base ruler. This clearly distinguishes it from siblings like draw_alignment, draw_gel, or draw_tree without the agent needing to open any schema.

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?

Gives explicit usage context: 'Name the window around whatever you are asking about — a mutation site, a trim bound, an ambiguous call' and warns that a whole read drawn at once shows nothing. It does not name a specific alternative tool to use instead, but the when-to-use framing (zoomed windows around a question) is clear and actionable.

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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