1.9.0pypi · galaxy-mcp · latest release
Observed 2026-08-21T23:18:48.861Z using mcpSecurity-inventory. Protocol 2025-06-18.
| Tool | Category | Risk |
|---|---|---|
cancel_workflow_invocationCancel a running workflow invocationInput schema{
"additionalProperties": false,
"properties": {
"invocation_id": {
"type": "string",
"description": "ID of the workflow invocation to cancel - a hexadecimal hash string"
}
},
"required": [
"invocation_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
connectConnect to Galaxy serverInput schema{
"additionalProperties": false,
"properties": {
"url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Galaxy server URL (optional, uses GALAXY_URL env var if not provided)"
},
"api_key": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Galaxy API key (optional, uses GALAXY_API_KEY env var if not provided)"
}
},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
create_historyCreate a new history to organize datasets and analyses.
A history is the primary workspace in Galaxy. Create a new history for each
distinct project or analysis to keep your work organized.
RECOMMENDED WORKFLOW:
1. Create a history with a descriptive name
2. Upload your input data: upload_file() or upload_file_from_url()
3. Run tools on the data: run_tool()
4. View results: get_history_contents()Input schema{
"additionalProperties": false,
"properties": {
"history_name": {
"type": "string",
"description": "Descriptive name for the history.\n Best practices:\n - Include project/sample name: \"RNA-seq Sample A\"\n - Include date if relevant: \"ChIP-seq 2024-01\"\n - Be specific: \"BWA alignment of patient_001\""
}
},
"required": [
"history_name"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
create_pageCreate a markdown page (Galaxy Notebook or Report).
Pass history_id to create a history-attached notebook (title auto-fills
from the history if omitted). Omit history_id to create a standalone
report -- reports REQUIRE both a title and a unique slug
(lowercase/digits/hyphens).
Content is Galaxy-flavored markdown. To embed a dataset, use a directive
with the ENCODED dataset id, e.g.
`history_dataset_display(history_dataset_id=f2db41e1fa331b3e)` or
`history_dataset_collection_display(history_dataset_collection_id=...)`.
Get encoded ids from get_history_contents / get_dataset_details.Input schema{
"additionalProperties": false,
"properties": {
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Encoded history id to attach the page to (notebook)."
},
"title": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Page title."
},
"content": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Initial markdown content."
},
"annotation": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optional annotation attached to the page."
},
"slug": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "URL slug (required for standalone reports)."
}
},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
create_user_toolCreate a user-defined tool in Galaxy from a YAML tool definition.
User-defined tools are lightweight, containerized tools that can be created
without admin privileges. They are stored in the database, scoped to the
creating user, and can be embedded in workflows (importing the workflow
automatically creates the tool for the importing user).Input schema{
"additionalProperties": false,
"properties": {
"representation": {
"additionalProperties": true,
"type": "object",
"description": "The tool definition as a dictionary matching the\nGalaxyUserTool schema. Required fields:\n- class: \"GalaxyUserTool\" (exactly this string)\n- id: tool identifier (lowercase, no spaces, 3-255 chars)\n- version: version string (e.g. \"0.1.0\")\n- name: display name shown in Galaxy tool menu\n- container: container image as a STRING (e.g. \"python:3.12-slim\"),\n NOT a dict -- this is a common mistake\n- shell_command: the command to execute, with $(inputs.name.path)\n for data inputs and $(inputs.name) for parameter inputs\n- inputs: list of input dicts, each with \"name\" and \"type\"\n (type can be: \"data\", \"integer\", \"float\", \"text\", \"boolean\")\n- outputs: list of output dicts, each with \"name\", \"type\": \"data\",\n \"format\" (e.g. \"tabular\", \"vcf\", \"bed\"), and \"from_work_dir\""
}
},
"required": [
"representation"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
delete_user_toolDeactivate a user-defined tool. Deactivated tools are not loaded into the toolbox.Input schema{
"additionalProperties": false,
"properties": {
"uuid": {
"type": "string",
"description": "The UUID of the tool to deactivate. Get this from list_user_tools()."
}
},
"required": [
"uuid"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
download_datasetDownload a dataset from Galaxy to the local filesystem or memoryInput schema{
"additionalProperties": false,
"properties": {
"dataset_id": {
"type": "string",
"description": "Galaxy dataset ID - a hexadecimal hash string identifying the dataset\n (e.g., 'f2db41e1fa331b3e', typically 16 characters)"
},
"file_path": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Local filesystem path where to save the downloaded file\n (e.g., '/path/to/data.txt', requires write access to filesystem)\n If not provided, downloads to memory instead"
},
"use_default_filename": {
"default": true,
"type": "boolean",
"description": "Deprecated - use file_path for specific locations\n (default: True, ignored when file_path not provided)"
},
"require_ok_state": {
"default": true,
"type": "boolean",
"description": "Only allow download if dataset processing state is 'ok'\n (default: True, set False to download datasets in other states)"
}
},
"required": [
"dataset_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_collection_detailsGet detailed information about a dataset collection and its members
Dataset collections group multiple datasets together (e.g., paired-end reads,
sample lists). This tool shows the collection structure and member datasets.Input schema{
"additionalProperties": false,
"properties": {
"collection_id": {
"type": "string",
"description": "Galaxy dataset collection ID - a hexadecimal hash string\n (e.g., 'a1b2c3d4e5f6g7h8', typically 16 characters)"
},
"max_elements": {
"default": 100,
"type": "integer",
"description": "Maximum number of collection elements to return (default: 100)\n Set lower for large collections to avoid overwhelming output"
}
},
"required": [
"collection_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_dataset_detailsGet detailed information about a specific dataset, optionally including a content previewInput schema{
"additionalProperties": false,
"properties": {
"dataset_id": {
"type": "string",
"description": "Galaxy dataset ID - a hexadecimal hash string identifying the dataset\n (e.g., 'f2db41e1fa331b3e', typically 16 characters)"
},
"include_preview": {
"default": true,
"type": "boolean",
"description": "Whether to include a preview of the dataset content showing first N lines\n (default: True, only works for datasets in 'ok' state)"
},
"preview_lines": {
"default": 10,
"type": "integer",
"description": "Number of lines to include in the content preview (default: 10)"
}
},
"required": [
"dataset_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_historiesGet list of user's histories with optional pagination and filtering.
Histories are Galaxy's primary organizational unit - each contains datasets,
collections, and records of analyses. Most operations require a history_id.
RECOMMENDED WORKFLOW:
1. Call get_histories() to see existing histories
2. Either use an existing history_id or create_history() for new work
3. Upload data or run tools in the selected historyInput schema{
"additionalProperties": false,
"properties": {
"limit": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Maximum histories to return. Default None returns all.\n Use with offset for pagination on large history lists."
},
"offset": {
"default": 0,
"type": "integer",
"description": "Skip this many histories (for pagination). Default 0."
},
"name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Filter by name pattern (case-sensitive partial match).\n Example: name=\"RNA\" matches \"RNA-seq analysis\", \"my RNA data\""
}
},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_history_contentsGet paginated contents (datasets and collections) from a specific history with ordering supportInput schema{
"additionalProperties": false,
"properties": {
"history_id": {
"type": "string",
"description": "Galaxy history ID - a hexadecimal hash string identifying the history\n (e.g., '1cd8e2f6b131e5aa', typically 16 characters)"
},
"limit": {
"default": 100,
"type": "integer",
"description": "Maximum number of items to return per page (default: 100, max recommended: 500)"
},
"offset": {
"default": 0,
"type": "integer",
"description": "Number of items to skip from the beginning (default: 0, for pagination)"
},
"deleted": {
"default": false,
"type": "boolean",
"description": "Include deleted datasets in results (default: False)"
},
"visible": {
"default": true,
"type": "boolean",
"description": "Include only visible datasets (default: True, set False to include hidden)"
},
"order": {
"default": "hid-asc",
"type": "string",
"description": "Sort order for results. Options include:\n - 'hid-asc': History ID ascending (default, oldest first)\n - 'hid-dsc': History ID descending (newest first)\n - 'create_time-dsc': Creation time descending (most recent first)\n - 'create_time-asc': Creation time ascending (oldest first)\n - 'update_time-dsc': Last updated descending (most recently modified first)\n - 'name-asc': Dataset name ascending (alphabetical)"
}
},
"required": [
"history_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_history_detailsGet history metadata and summary count ONLY - does not return actual datasets
This function provides quick access to history information without loading all datasets.
For the actual datasets/contents, use get_history_contents() which supports
pagination and ordering.Input schema{
"additionalProperties": false,
"properties": {
"history_id": {
"type": "string",
"description": "Galaxy history ID - a hexadecimal hash string identifying the history\n (e.g., '1cd8e2f6b131e5aa', typically 16 characters)"
}
},
"required": [
"history_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_invocationsView workflow invocations in GalaxyInput schema{
"additionalProperties": false,
"properties": {
"invocation_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Specific workflow invocation ID to view - a hexadecimal hash string\n (e.g., 'a1b2c3d4e5f6789a', typically 16 characters, optional)"
},
"workflow_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Filter invocations by workflow ID - a hexadecimal hash string\n (e.g., 'b2c3d4e5f6789abc', typically 16 characters, optional)"
},
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Filter invocations by history ID - a hexadecimal hash string\n (e.g., '1cd8e2f6b131e5aa', typically 16 characters, optional)"
},
"limit": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Maximum number of invocations to return (optional, default: no limit)"
},
"view": {
"default": "collection",
"type": "string",
"description": "Level of detail to return - 'element' for detailed or 'collection' for summary\n (default: 'collection')"
},
"step_details": {
"default": false,
"type": "boolean",
"description": "Include details on individual workflow steps\n (only applies when view is 'element', default: False)"
}
},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_iwc_workflow_detailsGet comprehensive details about a specific IWC workflow before importing.
Use this to examine a workflow's full documentation, inputs, and complexity
before deciding to import it into your Galaxy instance.
RECOMMENDED WORKFLOW:
1. Search workflows with search_iwc_workflows() or recommend_iwc_workflows()
2. Call this function with the trsID to get full details
3. Review the readme and inputs to ensure it fits your needs
4. Import with import_workflow_from_iwc(trs_id)Input schema{
"additionalProperties": false,
"properties": {
"trs_id": {
"type": "string",
"description": "The TRS (Tool Registry Service) ID from search results.\n Format: \"#workflow/github.com/iwc-workflows/<name>/<branch>\"\n Example: \"#workflow/github.com/iwc-workflows/rnaseq-pe/main\""
}
},
"required": [
"trs_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_iwc_workflowsFetch all workflows from the IWC (Interactive Workflow Composer)
Returns:
GalaxyResult with workflow manifest in data fieldInput schema{
"additionalProperties": false,
"properties": {},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_job_detailsGet detailed information about the job that created a specific datasetInput schema{
"additionalProperties": false,
"properties": {
"dataset_id": {
"type": "string",
"description": "Galaxy dataset ID - a hexadecimal hash string identifying the dataset\n (e.g., 'f2db41e1fa331b3e', typically 16 characters)"
},
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Galaxy history ID containing the dataset - optional for performance optimization\n (e.g., '1cd8e2f6b131e5aa', typically 16 characters)"
}
},
"required": [
"dataset_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_pageGet a page and the content of its latest revision.
Returns `content_editor`: the editable Galaxy-flavored markdown, with
ENCODED ids in directives (e.g. `history_dataset_id=f2db41e1fa331b3e`).
This is the form to edit and pass back to update_page.Input schema{
"additionalProperties": false,
"properties": {
"page_id": {
"type": "string",
"description": "Encoded id of the page (from list_pages / create_page)."
},
"include_rendered": {
"default": false,
"type": "boolean",
"description": "When True, also return `content` -- the\nembed-expanded render form (inlined dataset previews). Can be\nlarge; omit unless you need the rendered output."
}
},
"required": [
"page_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_page_revisionGet the content of a single page revision.
Returns the revision's `content`: the editable Galaxy-flavored markdown with
ENCODED ids in directives -- the form to diff against get_page or pass back
to update_page. Note: a revision exposes its editable markdown as `content`;
revisions have no separate `content_editor` field (unlike get_page).Input schema{
"additionalProperties": false,
"properties": {
"page_id": {
"type": "string",
"description": "Encoded id of the page."
},
"revision_id": {
"type": "string",
"description": "Encoded id of the revision (from list_page_revisions)."
}
},
"required": [
"page_id",
"revision_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_server_infoGet Galaxy server information including version, URL, and configuration details
Returns:
GalaxyResult with server information in data fieldInput schema{
"additionalProperties": false,
"properties": {},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_tool_citationsGet citation information for a specific toolInput schema{
"additionalProperties": false,
"properties": {
"tool_id": {
"type": "string",
"description": "ID of the tool"
}
},
"required": [
"tool_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_tool_detailsGet detailed information about a specific tool including its input parameters.
RECOMMENDED WORKFLOW:
1. First find tools using search_tools_by_name() or get_tool_panel()
2. Call this function with io_details=True to see all input parameters
3. Use the inputs schema to construct the inputs dict for run_tool()Input schema{
"additionalProperties": false,
"properties": {
"tool_id": {
"type": "string",
"description": "Galaxy tool identifier. Common formats:\n - Simple: \"fastqc\", \"bwa\", \"upload1\"\n - Toolshed: \"toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73\""
},
"io_details": {
"default": false,
"type": "boolean",
"description": "Set True to include detailed input/output parameter schemas.\n Essential for understanding how to call run_tool()."
}
},
"required": [
"tool_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_tool_input_templateReturn a ready-to-fill ``inputs`` skeleton for a tool, plus a compact schema.
Call this before run_tool when you are unsure how to shape ``inputs``. Replace
placeholders (e.g. ``<dataset_id>``) with real values. Repeats show one
instance (``name_0|...``); duplicate with ``name_1|...`` to add more. The
flattened-key convention is ``section|param``, ``cond|selector``,
``repeat_0|param``.Input schema{
"additionalProperties": false,
"properties": {
"tool_id": {
"type": "string"
}
},
"required": [
"tool_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_tool_panelGet the tool panel structure (toolbox)
Returns:
GalaxyResult with tool panel hierarchy in data fieldInput schema{
"additionalProperties": false,
"properties": {},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_tool_run_examplesReturn the exact XML test definitions (inputs, outputs, assertions, required files)
for a Galaxy tool so an LLM can study real, working run configurations.Input schema{
"additionalProperties": false,
"properties": {
"tool_id": {
"type": "string",
"description": "ID of the tool to inspect"
},
"tool_version": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optional version selector (use '*' for all versions)"
}
},
"required": [
"tool_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_userGet current user information
Returns:
GalaxyResult with current user details in data fieldInput schema{
"additionalProperties": false,
"properties": {},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_workflow_detailsGet detailed information about a specific workflowInput schema{
"additionalProperties": false,
"properties": {
"workflow_id": {
"type": "string",
"description": "ID of the workflow to get details for - a hexadecimal hash string"
},
"version": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Specific version of the workflow (optional, uses latest if not specified)"
}
},
"required": [
"workflow_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
get_workflow_input_templateReturn a ready-to-fill template plus a run guide for a workflow.
Call this before invoke_workflow. Each slot lists its label, expected source
(hda/hdca), accepted datatypes, collection type, and -- for parameters --
selectable `options` as [{label, value}]. On the `style=run` path these are
Galaxy-resolved: reference-genome dbkeys come from the server regardless of
history, and passing `history_id` additionally surfaces that history's
compatible datasets as candidates. The legacy .ga fallback carries only the
static restrictions baked into the workflow -- no server- or history-resolved
values -- see `guide.notes`. `guide` carries a short description and provenance.
Fill `inputs_template` (keyed by step_index) and invoke with
`inputs_by="step_index|step_uuid"`. Pass `verbose=True` for the full readme
and uncapped option lists. `warnings` flags legacy patterns.Input schema{
"additionalProperties": false,
"properties": {
"workflow_id": {
"type": "string"
},
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
},
"verbose": {
"default": false,
"type": "boolean"
}
},
"required": [
"workflow_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
import_workflow_from_iwcImport a workflow from IWC to the user's Galaxy instanceInput schema{
"additionalProperties": false,
"properties": {
"trs_id": {
"type": "string",
"description": "TRS ID of the workflow in the IWC manifest"
}
},
"required": [
"trs_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
invoke_workflowInvoke (run) a workflow with specified inputs and parametersInput schema{
"additionalProperties": false,
"properties": {
"workflow_id": {
"type": "string",
"description": "ID of the workflow to invoke - a hexadecimal hash string"
},
"inputs": {
"anyOf": [
{
"additionalProperties": true,
"type": "object"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Mapping of workflow inputs to datasets. Format:\n {'step_index': {'id': 'dataset_id', 'src': 'hda'}} where src can be:\n - 'hda' for HistoryDatasetAssociation\n - 'hdca' for HistoryDatasetCollectionAssociation\n - 'ldda' for LibraryDatasetDatasetAssociation\n - 'ld' for LibraryDataset"
},
"params": {
"anyOf": [
{
"additionalProperties": true,
"type": "object"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Tool parameter overrides as a nested dictionary"
},
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ID of history to store workflow outputs (optional)"
},
"history_name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Name for new history to create (ignored if history_id provided)"
},
"inputs_by": {
"default": "step_index",
"type": "string",
"description": "How to identify workflow inputs - 'step_index', 'step_uuid', 'name', or\n 'step_index|step_uuid' (recommended; matches get_workflow_input_template)"
},
"parameters_normalized": {
"default": false,
"type": "boolean",
"description": "Whether parameters are already in normalized format"
}
},
"required": [
"workflow_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
list_history_idsGet a simplified list of history IDs and names for easy reference
Returns:
GalaxyResult with list of {id, name} dictionaries in data fieldInput schema{
"additionalProperties": false,
"properties": {},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
list_page_revisionsList the revision history of a page.
Each revision carries an `edit_source` ("user", "agent", or "restore")
recording who made the edit.Input schema{
"additionalProperties": false,
"properties": {
"page_id": {
"type": "string",
"description": "Encoded id of the page."
},
"sort_desc": {
"default": false,
"type": "boolean",
"description": "Newest-first when True (default oldest-first)."
}
},
"required": [
"page_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
list_pagesList Galaxy pages (markdown documents) viewable by the user.
A page attached to a history is a "Galaxy Notebook"; a standalone page is
a "Report". Pass history_id to list only that history's notebooks.Input schema{
"additionalProperties": false,
"properties": {
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Encoded history id. When set, returns only notebooks\nattached to that history."
},
"search": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Freetext filter over title/content."
},
"limit": {
"default": 100,
"type": "integer",
"description": "Max pages to return (default 100)."
},
"offset": {
"default": 0,
"type": "integer",
"description": "Pagination offset."
},
"show_published": {
"default": false,
"type": "boolean",
"description": "Also include pages published by other users (default False)."
},
"show_shared": {
"default": false,
"type": "boolean",
"description": "Also include pages shared with the user (default False)."
}
},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
list_user_toolsList user-defined tools belonging to the current user.Input schema{
"additionalProperties": false,
"properties": {
"active": {
"default": true,
"type": "boolean",
"description": "If True (default), only show active tools. Set False to include deactivated tools."
}
},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
list_workflowsList workflows available in the Galaxy instanceInput schema{
"additionalProperties": false,
"properties": {
"workflow_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Specific workflow ID to get (optional) - a hexadecimal hash string"
},
"name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Filter workflows by name (optional)"
},
"published": {
"default": false,
"type": "boolean",
"description": "Include published workflows (default: False, shows only user workflows)"
}
},
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
recommend_iwc_workflowsSemantic search for IWC workflows based on natural language description.
Use this when you have a general analysis goal and want to find the best
matching workflows. Uses BM25 ranking to search across names, descriptions,
readmes, tags, and tool names.
RECOMMENDED WORKFLOW:
1. Describe your analysis goal in natural language
2. Review ranked recommendations with match explanations
3. Get details for promising workflows: get_iwc_workflow_details(trs_id)
4. Import the best match: import_workflow_from_iwc(trs_id)Input schema{
"additionalProperties": false,
"properties": {
"intent": {
"type": "string",
"description": "Natural language description of your analysis goal.\n Examples:\n - \"I have paired-end RNA-seq data and want differential expression\"\n - \"Assemble a bacterial genome from nanopore reads\"\n - \"Variant calling from whole exome sequencing data\"\n - \"Quality control for Illumina sequencing data\""
},
"limit": {
"default": 5,
"type": "integer",
"description": "Maximum number of recommendations to return (default: 5)"
}
},
"required": [
"intent"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
revert_page_revisionRoll a page back to an earlier revision.
Creates a NEW revision from the target revision's content, recorded with
edit_source="restore" (the history is append-only -- nothing is deleted).Input schema{
"additionalProperties": false,
"properties": {
"page_id": {
"type": "string",
"description": "Encoded id of the page."
},
"revision_id": {
"type": "string",
"description": "Encoded id of the revision to restore."
}
},
"required": [
"page_id",
"revision_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
run_toolRun a Galaxy tool on datasets in a history.
RECOMMENDED WORKFLOW:
1. Create or select a history: create_history() or get_histories()
2. Upload data: upload_file() or upload_file_from_url()
3. Get tool parameters: get_tool_details(tool_id, io_details=True)
4. Call this function with properly formatted inputs
5. Monitor job: get_job_details() or check history contentsInput schema{
"additionalProperties": false,
"properties": {
"history_id": {
"type": "string",
"description": "Galaxy history ID (16-char hex string like '1cd8e2f6b131e5aa').\n Get from create_history() or get_histories()."
},
"tool_id": {
"type": "string",
"description": "Tool identifier. Common formats:\n - Simple built-in: \"cat1\", \"Cut1\", \"upload1\"\n - Toolshed: \"toolshed.g2.bx.psu.edu/repos/iuc/fastqc/fastqc/0.73\""
},
"inputs": {
"additionalProperties": true,
"type": "object",
"description": "Tool input parameters. Dataset inputs use this format:\n {\"input_name\": {\"src\": \"hda\", \"id\": \"dataset_id\"}}"
}
},
"required": [
"history_id",
"tool_id",
"inputs"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
run_user_toolRun a user-defined tool via the standard Galaxy tools API.
Submits the UDT with POST /api/tools carrying the tool UUID. This
synchronous endpoint runs user-defined tools on every Galaxy that
supports them and needs no Celery -- unlike the newer POST /api/jobs
tool-request path, which is Celery-only and 500s for UDTs on 26.0.
It returns the job and output dataset handles immediately; the job
then runs asynchronously on the cluster (poll it for state).Input schema{
"additionalProperties": false,
"properties": {
"history_id": {
"type": "string",
"description": "Galaxy history ID where outputs will be placed."
},
"tool_uuid": {
"type": "string",
"description": "The UUID of the user-defined tool (from create_user_tool or list_user_tools)."
},
"inputs": {
"additionalProperties": true,
"type": "object",
"description": "Tool input parameters. Dataset inputs use:\n {\"input_name\": {\"src\": \"hda\", \"id\": \"dataset_id\"}}\n Scalar parameters use direct values:\n {\"param_name\": value}"
}
},
"required": [
"history_id",
"tool_uuid",
"inputs"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
search_iwc_workflowsSearch for workflows in the IWC (Intergalactic Workflow Commission) manifest.
IWC hosts curated, best-practice workflows for common bioinformatics analyses.
This function searches across workflow names, descriptions, tags, and readmes.
RECOMMENDED WORKFLOW:
1. Search for workflows matching your analysis need
2. Review the results - check step_count for complexity, readme_summary for details
3. Call get_iwc_workflow_details(trs_id) for full information
4. Import with import_workflow_from_iwc(trs_id)
5. Run with invoke_workflow()Input schema{
"additionalProperties": false,
"properties": {
"query": {
"type": "string",
"description": "Search query (case-insensitive). Matches against:\n - Workflow name (e.g., \"RNA-seq\")\n - Description/annotation\n - Tags (e.g., \"assembly\", \"transcriptomics\")"
}
},
"required": [
"query"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
search_tools_by_keywordsRecommend Galaxy tools based on a list of keywords.Input schema{
"additionalProperties": false,
"properties": {
"keywords": {
"items": {
"type": "string"
},
"type": "array",
"description": "A list of keywords or phrases describing what you're looking for,\ne.g., [\"csv\", \"rna\", \"alignment\", \"visualization\"]. The search will match tools\nwhose name, description, or accepted input formats contain any of these keywords."
}
},
"required": [
"keywords"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
search_tools_by_nameSearch Galaxy tools whose name, ID, or description contains the given query (substring match).
RECOMMENDED WORKFLOW:
1. Use this function to find tools by name/keyword
2. Review the returned tool IDs and names
3. Call get_tool_details(tool_id) for full input parameters
4. Call run_tool() with the correct inputsInput schema{
"additionalProperties": false,
"properties": {
"query": {
"type": "string",
"description": "Search query - matches against tool name, ID, or description.\n Examples: \"fastq\", \"alignment\", \"filter\", \"bwa\""
}
},
"required": [
"query"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
update_historyUpdate an existing Galaxy history's metadata.
Any combination of name, annotation, tags, deleted, and published can be updated
in a single call. Fields left as None are not modified.Input schema{
"additionalProperties": false,
"properties": {
"history_id": {
"type": "string",
"description": "The ID of the history to update. Obtain this from get_histories()\n or list_history_ids()."
},
"name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "New name for the history (optional)."
},
"annotation": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "New annotation/description text for the history (optional)."
},
"tags": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "New list of tags for the history (optional). Replaces any existing tags."
},
"deleted": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "If True, soft-delete the history; if False, restore a deleted history\n (optional)."
},
"published": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "If True, publish the history (make it public); if False, unpublish\n (optional)."
}
},
"required": [
"history_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
update_pageUpdate a page, creating a new revision when content changes.
Content is Galaxy-flavored markdown using ENCODED ids in directives
(e.g. `history_dataset_id=f2db41e1fa331b3e`) -- never raw integer ids or
HIDs. Get encoded ids from get_history_contents / get_dataset_details.
Edits made through this tool are recorded with edit_source="agent". This does
not change the page's content_format, so editing a page originally authored
as HTML with markdown content can mislabel it.Input schema{
"additionalProperties": false,
"properties": {
"page_id": {
"type": "string",
"description": "Encoded id of the page."
},
"content": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "New markdown content. Omit to leave content unchanged."
},
"title": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "New title. Omit to leave unchanged."
}
},
"required": [
"page_id"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
upload_fileUpload a local file to Galaxy for analysis.
Galaxy automatically detects the file type (FASTQ, BAM, BED, etc.) and
indexes the file appropriately. Large files are uploaded efficiently.
RECOMMENDED WORKFLOW:
1. Create a history: create_history("My Analysis")
2. Upload your data files with this function
3. Wait for upload to complete (check dataset state)
4. Run tools on the uploaded data: run_tool()Input schema{
"additionalProperties": false,
"properties": {
"path": {
"type": "string",
"description": "Local file path to upload. Supports common bioinformatics formats:\n - Sequences: .fastq, .fasta, .fa, .fq, .fastq.gz\n - Alignments: .bam, .sam, .cram\n - Annotations: .bed, .gff, .gtf, .vcf\n - Tabular: .csv, .tsv, .txt"
},
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Target history ID. If None, uses the most recent history.\n Recommend always specifying for clarity."
}
},
"required": [
"path"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
upload_file_from_urlUpload a file from a URL to GalaxyInput schema{
"additionalProperties": false,
"properties": {
"url": {
"type": "string",
"description": "URL of the file to upload (e.g., 'https://example.com/data.fasta')"
},
"history_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Galaxy history ID where to upload the file - optional, uses current history\n (e.g., '1cd8e2f6b131e5aa', typically 16 characters)"
},
"file_type": {
"default": "auto",
"type": "string",
"description": "Galaxy file format name (default: 'auto' for auto-detection)\n Common types: 'fasta', 'fastq', 'bam', 'vcf', 'bed', 'tabular', etc."
},
"dbkey": {
"default": "?",
"type": "string",
"description": "Database key/genome build (default: '?', e.g., 'hg38', 'mm10', 'dm6')"
},
"file_name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optional name for the uploaded file in Galaxy (inferred from URL if not provided)"
}
},
"required": [
"url"
],
"type": "object"
}Output schema{
"description": "Standardized response from Galaxy MCP tools.",
"properties": {
"data": {
"description": "Response data from Galaxy API"
},
"success": {
"default": true,
"description": "Whether the operation succeeded",
"type": "boolean"
},
"message": {
"description": "Human-readable status message",
"type": "string"
},
"count": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of items returned"
},
"pagination": {
"anyOf": [
{
"description": "Pagination metadata for list operations.",
"properties": {
"total_items": {
"description": "Total number of items available",
"type": "integer"
},
"returned_items": {
"description": "Number of items in this response",
"type": "integer"
},
"limit": {
"description": "Maximum items requested",
"type": "integer"
},
"offset": {
"description": "Number of items skipped",
"type": "integer"
},
"has_next": {
"description": "Whether more items are available",
"type": "boolean"
},
"has_previous": {
"description": "Whether previous items exist",
"type": "boolean"
},
"next_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for next page"
},
"previous_offset": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Offset for previous page"
},
"helper_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Human-readable pagination hint"
}
},
"required": [
"total_items",
"returned_items",
"limit",
"offset",
"has_next",
"has_previous"
],
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Pagination info for list operations"
}
},
"required": [
"data",
"message"
],
"type": "object"
} | — | — |
No completed comparison is available.
| Risk | Change | Subject |
|---|---|---|
| No material changes recorded. | ||
| Severity | Finding | Advisory |
|---|---|---|
| No confirmed vulnerability is published for this version. | ||
Artifact SHA-256: 06be7b303a6f9d5869d74ba8907ffdf55a1066ce873d29855fbdd83e52766576
Scanner: mcp-proof-engine 0.1.0.