tools

This section is auto-generated from the help text for the arrow command tools.

get_tool_panel command

Usage:

parsec tools get_tool_panel [OPTIONS]

Help

Get a list of available tool elements in Galaxy’s configured toolbox.

Options:

-h, --help  Show this message and exit.

get_tools command

Usage:

parsec tools get_tools [OPTIONS]

Help

Get all tools or filter the specific one(s) via the provided name or tool_id. Provide only one argument, name or tool_id, but not both.

Options:

--tool_id TEXT  id of the requested tool
--name TEXT     name of the requested tool(s)
--trackster     if True, only tools that are compatible with Trackster are
                returned
-h, --help      Show this message and exit.

install_dependencies command

Usage:

parsec tools install_dependencies [OPTIONS] TOOL_ID

Help

Install dependencies for a given tool via a resolver. This works only for Conda currently. This functionality is available since Galaxy release_16.10 and is available only to Galaxy admins.

Options:

-h, --help  Show this message and exit.

paste_content command

Usage:

parsec tools paste_content [OPTIONS] CONTENT HISTORY_ID

Help

Upload a string to a new dataset in the history specified by history_id.

Options:

-h, --help  Show this message and exit.

put_url command

Usage:

parsec tools put_url [OPTIONS] CONTENT HISTORY_ID

Help

Upload a string to a new dataset in the history specified by history_id.

Options:

-h, --help  Show this message and exit.

run_tool command

Usage:

parsec tools run_tool [OPTIONS] HISTORY_ID TOOL_ID TOOL_INPUTS

Help

Runs tool specified by tool_id in history indicated by history_id with inputs from dict tool_inputs.

Options:

-h, --help  Show this message and exit.

show_tool command

Usage:

parsec tools show_tool [OPTIONS] TOOL_ID

Help

Get details of a given tool.

Options:

--io_details    if True, get also input and output details
--link_details  if True, get also link details
-h, --help      Show this message and exit.

upload_file command

Usage:

parsec tools upload_file [OPTIONS] PATH HISTORY_ID

Help

Upload the file specified by path to the history specified by history_id.

Options:

--dbkey TEXT      (optional) genome dbkey
--file_name TEXT  (optional) name of the new history dataset
--file_type TEXT  Galaxy datatype for the new dataset, default is auto
--space_to_tab    whether to convert spaces to tabs. Default is False.
                  Applicable only if to_posix_lines is True
--to_posix_lines  if True, convert universal line endings to POSIX line
                  endings. Default is True. Set to False if you upload a gzip,
                  bz2 or zip archive containing a binary file
-h, --help        Show this message and exit.

upload_from_ftp command

Usage:

parsec tools upload_from_ftp [OPTIONS] PATH HISTORY_ID

Help

Upload the file specified by path from the user’s FTP directory to the history specified by history_id.

Options:

-h, --help  Show this message and exit.