galaxy_list_files: List all files (datasets) in a Galaxy history
In GalaxyR: 'Galaxy' API Implementation

galaxy_list_files

R Documentation

List all files (datasets) in a Galaxy history

Description

galaxy_list_files() is an S4 generic. With x as a character scalar, it is treated as a Galaxy history ID and returns a data frame of history datasets (files). With x as a Galaxy object, the history ID and URL are taken from the object.

Usage

galaxy_list_files(
  x,
  include_deleted = FALSE,
  include_hidden = FALSE,
  galaxy_url = "https://usegalaxy.eu",
  limit = 500L
)

## S4 method for signature 'character'
galaxy_list_files(
  x,
  include_deleted = FALSE,
  include_hidden = FALSE,
  galaxy_url = "https://usegalaxy.eu",
  limit = 500L
)

## S4 method for signature 'Galaxy'
galaxy_list_files(
  x,
  include_deleted = FALSE,
  include_hidden = FALSE,
  limit = 500L
)

Arguments

`x`	A history ID (`character`) or a `Galaxy` object.
`include_deleted`	Logical; if `TRUE`, include deleted datasets. Default: `FALSE`.
`include_hidden`	Logical; if `TRUE`, include hidden datasets. Default: `FALSE`.
`galaxy_url`	Character. Base URL of the Galaxy instance, used by the character method. If `GALAXY_URL` is set, it takes precedence.
`limit`	Integer page size for API pagination. Default: `500L`.

Details

The function queries ⁠/api/histories/{history_id}/contents⁠ using pagination and returns one row per history content item, restricted to datasets (history_content_type == "dataset" when available).

Value

A data.frame with one row per dataset and columns:

id: Encoded dataset ID.
name: Dataset name.
history_id: Encoded history ID.
history_content_type: Usually "dataset".
type: Galaxy item type (if provided by server).
state: Dataset state (e.g. "ok", "running", "error").
deleted: Logical deletion flag.
hidden: Logical hidden flag.
file_ext: Datatype extension (if available).
file_size: Dataset size in bytes (if available).
create_time: Creation timestamp (if available).
update_time: Update timestamp (if available).

If no datasets are found, an empty data frame with these columns is returned.

Examples


# Character method (history_id)
hid <- galaxy_initialize("List files example")
files_df <- galaxy_list_files(hid)
head(files_df)

# Galaxy-object method
g <- galaxy(history_name = "List files example")
g <- galaxy_initialize(g)
files_df2 <- galaxy_list_files(g)
head(files_df2)

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