Jean — Molecular Biology & Genomics

export_map_svg

Read-only

Render the open record's map to a publication SVG string, circular or linear — the same figure the Export panel draws, with the same knobs and the same defaults.

Input Schema

Name	Required	Description	Default
`end`	No	linear only: last base of the window to draw (1-based, inclusive); left unset, the record's last base. In bp. Only applies when layout is linear.
`font`	No	figure font — one of the three stacks that survive an SVG-to-PDF conversion without substitution.	sans
`size`	No	square canvas edge, before a legend strip is added below it. In px.
`start`	No	linear only: first base of the window to draw (1-based); left unset, the record's first base. In bp. Only applies when layout is linear.
`title`	No	figure title; left empty, the record's own name is used.
`_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.
`layout`	No	circular: the ring; linear: the record unrolled into rows, features in lanes under a ruler and sites above it.	circular
`legend`	No	add a colour key on its own strip below the map.
`enzymes`	No	enzymes whose cut sites fill the site ring — resolved against the bundled cut catalog (REBASE spellings; smaller than the REBASE dossier the editor shows). Left unset, the run uses your active enzyme collection; with none active the ring is drawn empty rather than silently filled.
`_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.
`show_bases`	No	linear only: draw both strands' bases over the ruler; rows wrap to keep each base readable. Only applies when layout is linear.
`show_sites`	No	draw the outer restriction-site ring.
`show_labels`	No	draw each feature's name beside its arc.
`transparent`	No	omit the backing rect, so the figure drops onto any ground.
`collapse_duplicate_labels`	No	fold leader labels that would repeat a name into one row, as `misc_binding ×13` — the same rule the interactive map uses. Off reproduces the upstream renderer's figure exactly, one leader per feature.

Output Schema

Name	Required	Description
`svg`	Yes	publication SVG string
`rows`	Yes	rows a linear map wrapped into; 0 for the circular layout
`sites`	Yes	cut sites drawn (the outer ring, or the ticks above a linear map's ruler)
`width`	Yes	rendered width in px
`height`	Yes	rendered height in px — taller than the width when a legend strip was added

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"
```

Changed7 schema fields changedOct 24, 2026

addedInput schema / properties / end

Added value: +{
+  "description": "linear only: last base of the window to draw (1-based, inclusive); left unset, the record's last base. In bp. Only applies when layout is linear.",
+  "minimum": 1,
+  "type": "number"
+}

addedInput schema / properties / layout

Added value: +{
+  "default": "circular",
+  "description": "circular: the ring; linear: the record unrolled into rows, features in lanes under a ruler and sites above it.",
+  "enum": [
+    "circular",
+    "linear"
+  ],
+  "type": "string"
+}

addedInput schema / properties / show_bases

Added value: +{
+  "default": false,
+  "description": "linear only: draw both strands' bases over the ruler; rows wrap to keep each base readable. Only applies when layout is linear.",
+  "type": "boolean"
+}

addedInput schema / properties / start

Added value: +{
+  "description": "linear only: first base of the window to draw (1-based); left unset, the record's first base. In bp. Only applies when layout is linear.",
+  "minimum": 1,
+  "type": "number"
+}

addedOutput schema / properties / rows

Added value: +{
+  "description": "rows a linear map wrapped into; 0 for the circular layout",
+  "type": "number"
+}

changedOutput schema / properties / sites / description

Previous value: -"cut sites drawn in the outer ring"New value: +"cut sites drawn (the outer ring, or the ticks above a linear map's ruler)"

changedOutput schema / required

Previous value: -[
-  "svg",
-  "width",
-  "height",
-  "sites"
-]New value: +[
+  "svg",
+  "width",
+  "height",
+  "sites",
+  "rows"
+]

First observedOct 20, 2026

TDQS

B3.4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description usefully adds that the result is an SVG *string* and that it mirrors the Export panel's knobs and defaults, but says nothing about whether anything is written to disk or how large the string can get.

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?

A single dense sentence with the action and output front-loaded; no filler. The trailing clause about the Export panel is slightly vague but earns its place by pinning down expectations.

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?

With 15 parameters, a nested _subject object, full schema coverage and an output schema, the description does the minimum: purpose, output type, and default-alignment with the Export panel. It leaves the record-input and project (_files) mechanics entirely to the schema, which is defensible but thin for a tool of this complexity.

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 every one of the 15 parameters is already documented in structured form. The description only alludes to the layout choice ('circular or linear') via the 'same knobs' framing and adds no format or default detail beyond the schema — baseline 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?

States a specific verb and resource — 'Render the open record's map' — plus the output medium ('publication SVG string') and the two layouts. It is clearly distinct from drawing tools like draw_alignment or export_tree, though no sibling is named explicitly.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Implies usage by saying 'the open record's map' (so a record must be open) and anchors expectations to the Export panel, but never says when to pick this over other export/draw tools or what preconditions apply. Usage must be inferred.

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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