Jean by Melad Labs

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

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

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.

Changed2 schema fields changedOct 25, 2026
- addedOutput schema / properties / height / x-unit
```
Added value: +"px"
```
- addedOutput schema / properties / width / x-unit
```
Added value: +"px"
```
First observedOct 20, 2026

TDQS

A4.5/5.0

Behavior5/5

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

Annotations already declare readOnly, non-destructive, closed-world behavior, so the safety profile is covered. Beyond that, the description adds substantive context: the figure uses the same geometry as the Chromatogram tab, width sets zoom and never crops, `print` is the default palette because the figure travels outside the app, and confidence bars are omitted when the file has no quality data. These are exactly the behavioral traits an agent needs beyond the structured annotations.

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

Conciseness5/5

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

Three sentences, front-loaded with the core action and output format, followed by a useful geometry detail and a practical window-sizing directive. Every sentence earns its place with no filler or redundancy.

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?

An output schema exists, so the description need not explain return values. With annotations covering safety and schema covering all parameters, the description supplies the remaining context an agent needs: what is drawn, how window sizing works, and why to scope the view. Nothing essential is missing.

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%, so all ten parameters carry their own detailed docs (defaults, ranges, units, clamping semantics). The description does not add parameter-specific syntax or default information beyond the schema; its window advice indirectly relates to `from` and `bases` but does not name them. The baseline of 3 is appropriate when the schema does the heavy lifting.

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 states a specific verb (Draw), resource (a window of a Sanger read), and output format (SVG figure) in the first clause. It enumerates exactly what the figure contains — dye traces, Phred bars, base ruler — so an agent knows precisely what this tool produces. The resource is unambiguous against siblings like draw_alignment or draw_gel, which target different data.

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 usage context: name the window around a mutation site, trim bound, or ambiguous call, and explains why a whole read is useless. This tells the agent when the tool is appropriate. It stops short of naming explicit alternatives or exclusions (e.g., export_trace, trace_raw_signal), so it is strong context but not a full when/when-not guide.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All Jean by Melad Labs tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources

Need Help?