Tool reference
The remote BioNodulo server at https://bionodulo.com/api/mcp exposes the cloud tools below. Each request is authorized for the connected account and selected team. A team override is accepted only when that user belongs to the team. The server requires one of three OAuth scopes for each tool:
bionodulo:readallows the listed account, catalog, workflow, run, billing, and file reads.bionodulo:writeallows changes to saved workflows and cloud files.bionodulo:runallows starting and cancelling cloud runs.
An AI client may request these scopes during sign-in or ask you to reconnect when a tool needs an additional scope. A default login may grant read access only. A tool call also checks your account and team permissions. Run operations can consume credits; submit_run requires confirmation of the team, workflow, and credit use.
Read tools (bionodulo:read)
| Tool | What it does |
|---|---|
open_bionodulo | Open the authorized cloud workbench in a host that supports MCP Apps. In a client without embedded UI, use the regular tools; get_workflow can provide an editor link. It does not access the local desktop app. |
get_account_info | Show the connected account and team. |
get_credit_balance | Show plan, credit balance, and AI quota. |
list_workflows | List saved workflows accessible to the team. |
get_workflow | Read one saved workflow definition and an editor link. |
list_runs | List the team’s recent cloud runs. |
get_run_status | Read a cloud run’s current status. Queued or running does not mean completed. |
get_run_events | Read paginated durable events for a run. |
get_run_outputs | Read verified output artifacts and temporary download links. |
estimate_run_cost | Get the compute credit rate for a resource profile; this does not predict total runtime. |
list_files | List cloud uploads and run outputs accessible to the team. |
search_node_types | Search the live built-in node catalog. |
get_node_info | Read a node’s actual input, output, and parameter schema. |
validate_workflow | Check a graph against the shared editor’s validation rules. This does not run it or prove local tools are installed. |
import_workflow | Translate supported Nextflow, Snakemake, CWL, or Galaxy text into a BioNodulo draft. It does not execute or save the source; review portability warnings and validate the result. |
export_workflow | Export a graph as Nextflow, Snakemake, CWL, Galaxy, JSON, RIS, BibTeX, or CSV. Review the portability report; export does not prove another engine can run it. |
Write tools (bionodulo:write)
| Tool | What it does |
|---|---|
create_workflow | Save a new workflow draft; it does not start compute. Requires a client request ID to prevent duplicate drafts after retries. |
update_workflow | Change selected fields of a saved workflow. |
delete_workflow | Permanently delete a saved workflow. |
get_upload_url | Request a temporary storage URL for a declared file. This does not upload the bytes. |
complete_upload | Verify bytes sent to an upload URL and mark the file available. |
delete_file | Permanently delete a selected cloud file. |
Run tools (bionodulo:run)
| Tool | What it does |
|---|---|
submit_run | Submit a saved workflow for cloud execution. Requires explicit authorization of credit use; the result is a submitted run, not a completed one. |
cancel_run | Request cancellation of a queued or running run. It cannot undo charges already incurred. |
Local desktop tools
These belong to the separate local bionodulo-mcp connector, which runs on the same computer as the BioNodulo desktop app. They are not exposed by the remote /api/mcp endpoint: desktop_status, desktop_list_node_types, desktop_get_node_info, desktop_list_templates, desktop_validate_workflow, desktop_submit_run, desktop_get_run, desktop_get_run_logs, desktop_get_queue, desktop_get_history, and desktop_get_system_stats.
The repository’s older Python MCP package also has additional cloud tools, resources, and prompts. Its capabilities and operator configuration are separate from this remote server’s OAuth tool list. See the source README for developer details.