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Jean — Molecular Biology & Genomics

build_ena_submission

Read-only

Turn a record into what ENA's Webin-CLI takes for an annotated sequence (-context sequence): an ENA flat file (.embl) and its manifest.

Input Schema

NameRequiredDescriptionDefault
studyNothe Webin Portal study accession (PRJEB… or ERP…). Webin-CLI refuses a set without one; left empty, the files are written and the reason reported.
_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.
genbankYesthe record to submit, as GenBank text. Its features, topology and DEFINITION are read from it.
_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.
mol_typeNothe source feature's mandatory /mol_type. `other DNA` is the INSDC value for a synthetic construct.other DNA
organismNothe scientific name of the source organism; ENA checks it against its taxonomy. `synthetic construct` is a real answer for a built vector.synthetic construct
topologyNocircular for a plasmid (the ID line; only then may a feature cross the origin). Left empty, the record's own topology is used. Values: (From the record), circular (Circular), linear (Linear). Advanced.
descriptionNothe DE line, what the sequence is. Left empty, each record's own DEFINITION is used; ENA refuses one shorter than 10 characters.
geo_loc_nameNowhere the sample came from, from the INSDC vocabulary, or a missing-value term.missing: lab stock
collection_dateNowhen the sample was collected, on the source feature. Optional, but must be INSDC-legal; a construct takes a missing-value term such as `missing: lab stock`.missing: lab stock

Output Schema

NameRequiredDescriptionDefault
filesYesthe flat file and its manifest, each with its `name` and `text`. Gzip the flat file before running Webin-CLI; the manifest already names the `.gz`
changesYesevery feature the writer refused, rewrote or left a qualifier off, each with ENA's reason
commandYesthe exact gzip and webin-cli invocation, with -validate
readingYeswhat the set is, generated from what was written
writtenYesfeatures written, source excluded
flatFileYesthe `.embl` alone, for reading or diffing
problemsYeswhy Webin-CLI will refuse the set as it stands: a short description, a short entry, no study, or a malformed date or locality. Empty means none of those, never that the validator will be silent

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior4/5

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

Annotations already declare readOnly/openWorld/destructive=false, so the safety profile is covered. The description adds real behavioural value beyond that: it discloses the two artifacts produced (an .embl flat file and its manifest) and the target consumer (Webin-CLI `-context sequence`). It stops short of saying where files land or what the return looks like, though an output schema exists.

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?

One sentence, front-loaded with the transformation and immediately followed by the concrete outputs and CLI context. No filler, nothing restated from the name.

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?

For a 10-parameter tool with nested objects, annotations and an output schema, the description covers what it produces and which submission context it serves, which is the essential framing. The heavier prerequisites (study accession required by Webin-CLI, taxonomy checks) are carried by the schema descriptions, so the remaining gap is minor.

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% across all 10 parameters (including the nested `_subject` and `_files` shapes, study accession, mol_type, topology), so the schema does the heavy lifting. The description adds no parameter-level meaning beyond the schema; baseline 3 applies.

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?

Specific verb+resource: it converts a record into an ENA flat file (`.embl`) plus a manifest, targeting Webin-CLI `-context sequence`. That names the output artifacts and the exact submission flavour, which cleanly separates it from siblings like build_genbank_submission and build_addgene_deposit.

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?

The mention of `-context sequence` implies the scenario (annotated sequence submission via Webin-CLI) rather than genome/other contexts, so usage is implied. But there is no explicit when-to-use/when-not-to-use guidance and no routing to build_genbank_submission for the GenBank alternative.

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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