galaxy_run_tool: Generic run tool

In GalaxyR: 'Galaxy' API Implementation

Generic run tool

Description

galaxy_run_tool() is an S4 generic. With x as a character vector it is treated as a history ID; the specified tool is invoked in that history and the job ID is returned. With x as a Galaxy object, the history ID and URL are taken from the object and the object is updated with the job ID.

Usage

galaxy_run_tool(
  x,
  tool_id,
  inputs = NULL,
  dataset_id = NULL,
  galaxy_url = "https://usegalaxy.eu"
)

## S4 method for signature 'character'
galaxy_run_tool(
  x,
  tool_id,
  inputs = NULL,
  dataset_id = NULL,
  galaxy_url = "https://usegalaxy.eu"
)

## S4 method for signature 'Galaxy'
galaxy_run_tool(x, tool_id, inputs = NULL, dataset_id = NULL)

Arguments

x	A history ID (character) or a Galaxy object.
tool_id	Tool identifier to execute.
inputs	Named list of tool inputs.
dataset_id	ID of the input dataset (HDA).
galaxy_url	Base URL of the Galaxy instance, used by the character method.

Value

For the character method, a job ID; for the Galaxy method, the modified Galaxy object.

GalaxyR documentation built on July 6, 2026, 5:08 p.m.