galaxy_upload_https: Generic upload file with https

In GalaxyR: 'Galaxy' API Implementation

Generic upload file with https

Description

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

Usage

galaxy_upload_https(
  x,
  input_file,
  wait = FALSE,
  wait_timeout = 600,
  galaxy_url = "https://usegalaxy.eu",
  file_type = "auto",
  dbkey = "?",
  ...
)

## S4 method for signature 'character'
galaxy_upload_https(
  x,
  input_file,
  wait = FALSE,
  wait_timeout = 600,
  galaxy_url = "https://usegalaxy.eu",
  file_type = "auto",
  dbkey = "?",
  ...
)

## S4 method for signature 'Galaxy'
galaxy_upload_https(
  x,
  input_file,
  wait = FALSE,
  wait_timeout = 600,
  galaxy_url = "https://usegalaxy.eu",
  file_type = "auto",
  dbkey = "?",
  ...
)

Arguments

x	A Galaxy object, or a history_id to use the default method.
input_file	Path to the local file to upload.
wait	Logical. Whether to wait for Galaxy to finish processing.
wait_timeout	Time in seconds until wait times out with an error.
galaxy_url	Base URL of the Galaxy instance, used by the default method. If GALAXY_URL is set it takes precedence.
file_type	Galaxy datatype identifier (e.g. "auto", "fastq", "bam").
dbkey	Reference genome identifier (e.g. "?" or "hg38").
...	not in use

Details

This uses Galaxy's built‑in upload1 tool and performs a multipart form POST. Large files may still require FTP depending on server configuration. A valid API key (GALAXY_API_KEY) 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

hid <- galaxy_initialize("test upload")
test_file <- tempfile(fileext = ".txt")
writeLines("This is an example test file.", test_file)
file_id <- galaxy_upload_https(hid, test_file)
g <- galaxy()
g <- galaxy_initialize(g)
g <- galaxy_upload_https(g, test_file)

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