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Jean by Melad Labs

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check_color_balance

Read-only

Will the sequencer SEE these indexes? Per-cycle channel occupancy for a set of index sequences under an instrument's own SBS chemistry, checked against Illumina's rules (no dark cycle, both channels preferred, no GG in the first two cycles), each violation citing the vendor article it comes from — and the same set scored across EVERY chemistry generation at once, because XLEAP moved the dual-color base from A to C and a set balanced on a NovaSeq 6000 is not balanced on a NovaSeq X.

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.
barcodesYesthe index sequences to score, one per sample.
instrumentNothe instrument whose chemistry the set is judged under, and whose index-2 orientation applies.NovaSeq X / X Plus

Output Schema

NameRequiredDescriptionDefault
okYeswhether the set clears every rule for this chemistry
tierYesIllumina's own grading of this set on this instrument: `ideal`, `acceptable` or `unacceptable`
cyclesYesper-cycle channel occupancy — the census the tier is computed from
violationsYeseach rule broken, the cycles it was broken at, and the vendor article it comes from
channelPlotYesthe fraction of the pool producing signal in each channel at each index cycle; the series are named after the channels, and their colors are not the dyes
acrossChemistriesYesthe SAME set scored under every chemistry generation, so a set that passes here and fails on another instrument says so before the run

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • changedOutput schema / properties / channelPlot / description
      Previous value: -"the fraction of the pool producing signal in each channel at each index cycle; the series are named after the channels, and their colours are not the dyes"New value: +"the fraction of the pool producing signal in each channel at each index cycle; the series are named after the channels, and their colors are not the dyes"
  2. Changed2 schema fields changed
    • addedOutput schema / properties / channelPlot
      Added value: +{
+  "description": "the fraction of the pool producing signal in each channel at each index cycle; the series are named after the channels, and their colours are not the dyes",
+  "properties": {
+    "mark": {
+      "enum": [
+        "line",
+        "bar",
+        "point"
+      ],
+      "type": "string"
+    },
+    "rules": {
+      "items": {
+        "properties": {
+          "label": {
+            "type": "string"
+          },
+          "y": {
+            "type": "number"
+          }
+        },
+        "required": [
+          "y",
+          "label"
+        ],
+        "type": "object"
+      },
+      "type": "array"
+    },
+    "series": {
+      "items": {
+        "properties": {
+          "name": {
+            "type": "string"
+          },
+          "y": {
+            "items": {
+              "type": [
+                "number",
+                "null"
+              ]
+            },
+            "type": "array"
+          }
+        },
+        "required": [
+          "name",
+          "y"
+        ],
+        "type": "object"
+      },
+      "type": "array"
+    },
+    "title": {
+      "type": "string"
+    },
+    "x": {
+      "items": {
+        "type": "number"
+      },
+      "type": "array"
+    },
+    "xLabel": {
+      "type": "string"
+    },
+    "yLabel": {
+      "type": "string"
+    }
+  },
+  "required": [
+    "x",
+    "series",
+    "xLabel",
+    "yLabel"
+  ],
+  "type": [
+    "object",
+    "null"
+  ]
+}
    • changedOutput schema / required
      Previous value: -[
-  "tier",
-  "ok",
-  "violations",
-  "cycles",
-  "acrossChemistries"
-]New value: +[
+  "tier",
+  "ok",
+  "violations",
+  "cycles",
+  "channelPlot",
+  "acrossChemistries"
+]
  3. First observed

TDQS

A4/5.0
Behavior4/5

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

Annotations already establish read-only, non-destructive, closed-world behavior, but the description adds substantive behavior beyond them: the exact rules checked, per-violation vendor citations, and simultaneous scoring across all chemistry generations. It leaves some ambiguity about how the single instrument parameter relates to that all-generation scoring.

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 dense but front-loaded, and the rationale for cross-chemistry scoring earns its place. The rhetorical opening and one-sentence em-dash structure are slightly less scannable than a direct statement, but there is little waste.

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?

For a complex, multi-rule, multi-chemistry checker with an output schema and full schema descriptions, the definition supplies enough domain context to invoke it correctly. Return-value detail is correctly left to the output schema.

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 coverage is 100%, so the schema already documents barcodes, the instrument enum and default, and the generic subject/file parameters. The description reinforces that sequences are judged under the instrument's chemistry and index-2 orientation, but it adds no syntax or value constraints beyond what the schema provides, so the baseline 3 is appropriate.

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 computation—per-cycle channel occupancy for index sequences—and names the rule set and cross-chemistry scoring. It distinguishes this from a generic barcode audit by tying the judgment to the selected instrument's SBS chemistry and index-2 orientation.

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?

It gives a clear context: validating index sets against Illumina chemistry rules and comparing across chemistry generations. However, it never says when to choose it over siblings such as check_index_pool or audit_barcodes, and it provides no exclusions or prerequisites.

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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