galaxy_download_result: Generic for downloading files from a history

In GalaxyR: 'Galaxy' API Implementation

Generic for downloading files from a history

Description

galaxy_download_result() is an S4 generic. With x as a character vector of HDA output IDs, all corresponding datasets are downloaded into out_dir using their Galaxy names; duplicate names are disambiguated by appending ⁠_<i>⁠ before the extension. Existing files are not overwritten if overwrite = FALSE, and a warning is issued when a name is adjusted. With x as a Galaxy object its output_dataset_ids and galaxy_url are used; the object is returned invisibly after performing the downloads.

Usage

galaxy_download_result(
  x,
  out_dir = ".",
  galaxy_url = "https://usegalaxy.eu",
  overwrite = FALSE
)

## S4 method for signature 'character'
galaxy_download_result(
  x,
  out_dir = ".",
  galaxy_url = "https://usegalaxy.eu",
  overwrite = FALSE
)

## S4 method for signature 'Galaxy'
galaxy_download_result(x, out_dir = ".", overwrite = FALSE)

Arguments

x	A vector of HDA output IDs (character), or a Galaxy object.
out_dir	Directory in which to save the downloaded files.
galaxy_url	Base URL of the Galaxy instance, used by the character method.
overwrite	Logical; if FALSE (default), do not overwrite existing files but choose unique names instead.

Value

For the character method, a list of httr responses; for the Galaxy method, the (unchanged) Galaxy object invisibly.

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