galaxyproject / galaxyproject/loom

Galaxy MCP: no tool to rename/update a dataset (no update_dataset)

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enhancement
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TypeScript
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Description

## What happened

After the agent produced a result dataset in Galaxy, the user asked to rename it. The agent could not: the Galaxy MCP server has no rename/update-dataset tool.

Agent transcript (abridged):
> I do not have a direct `galaxy_update_dataset` tool. ... The galaxy toolkit does not have a dedicated "rename dataset" tool, and the workaround I attempted is not permitted in this environment. However, you can rename it yourself in a few clicks in the Galaxy UI...

## Context (from activity tail)

- Agent called `galaxy_update_dataset` -> `Tool "galaxy_update_dataset" not found. Server "galaxy" has: galaxy_connect, galaxy_search_tools_by_name, ... (no update_dataset).`
- Agent then attempted a bash/jq workaround (heredoc piping into an upload tool call), which the exec-guard correctly denied: `bash: compound or redirected command (denied: low-capability model)`.
- Net result: the agent gave up and deferred to the Galaxy UI.

There is an `update_history` MCP tool but no equivalent for datasets.

## Expected vs actual

- Expected: the agent can rename (and ideally edit basic attributes -- name, info/annotation, datatype) of a dataset via an MCP tool.
- Actual: no such tool exists; the only path is the Galaxy web UI.

## Ask

Add a `galaxy_update_dataset` MCP tool (PUT `/api/histories/{hid}/contents/{id}`) supporting at minimum a `name` rename, ideally `annotation`/`info` and `datatype` as well.

## Sysinfo

app 0.3.1 - darwin/arm64 - electron 41.2.1 - node 24.14.1 - provider google / gemini-2.5-pro

Part of the Galaxy MCP capability-gap cluster: #226 (data libraries), #227 (save workflow), #228 (delete/purge datasets), #229 (paired collections).

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