galaxy_upload_ftp: Generic upload ftp

In GalaxyR: 'Galaxy' API Implementation

Generic upload ftp

Description

galaxy_upload_ftp() is an S4 generic. With no x supplied it uploads a local file via FTP and registers it in the specified history, returning the encoded dataset ID. When called with a Galaxy object it uses the object's history_id and galaxy_url and updates the object with the new input_dataset_id.

Usage

galaxy_upload_ftp(
  x,
  input_file,
  galaxy_ftp = "ftp.usegalaxy.eu",
  galaxy_url = "https://usegalaxy.eu",
  ...
)

## S4 method for signature 'character'
galaxy_upload_ftp(
  x,
  input_file,
  galaxy_ftp = "ftp.usegalaxy.eu",
  galaxy_url = "https://usegalaxy.eu",
  ...
)

## S4 method for signature 'Galaxy'
galaxy_upload_ftp(
  x,
  input_file,
  galaxy_ftp = "ftp.usegalaxy.eu",
  galaxy_url = "https://usegalaxy.eu",
  ...
)

Arguments

x	A Galaxy object, or a history_id to use the default method.
input_file	Path to the local file to upload.
galaxy_ftp	FTP server address of the Galaxy instance.
galaxy_url	Base URL of the Galaxy instance, used by the default method. If GALAXY_URL is set it takes precedence.
...	not in use

Details

A valid API key (GALAXY_API_KEY) and FTP credentials (GALAXY_USERNAME, GALAXY_PASSWORD) must be available in the environment.

Value

For the default method, a character scalar dataset ID. For the Galaxy method, the modified Galaxy object.

Examples

galaxy_ftp <- "ftp.usegalaxy.eu"
input_file <- tempfile(fileext = ".txt")
writeLines("Example", input_file)
hid <- galaxy_initialize("test upload")
did <- galaxy_upload_ftp(input_file, hid, galaxy_ftp)
g <- galaxy()
g <- galaxy_initialize(g)
g <- galaxy_upload_ftp(g, input_file, galaxy_ftp = galaxy_ftp)

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