Tool to extract a tool list from galaxy.


usage: get-tool-list [-h] [-v] [-g GALAXY] [-u USER] [-p PASSWORD]
                     [-a API_KEY] -o OUTPUT [--include-tool-panel-id]
                     [--skip-tool-panel-name] [--skip-changeset-revision]
                     [--get-data-managers] [--get-all-tools]

Named Arguments

-o, --output-file

tool_list.yml output file

--include-tool-panel-id, --include_tool_panel_id

Include tool_panel_id in tool_list.yml ? Use this only if the tool panel id already exists. See

Default: False

--skip-tool-panel-name, --skip_tool_panel_name

Do not include tool_panel_name in tool_list.yml ?

Default: False

--skip-changeset-revision, --skip_changeset_revision

Do not include the changeset revision when generating the tool list.Use this if you would like to use the list to update all the tools inyour galaxy instance using shed-install.

Default: False

--get-data-managers, --get_data_managers

Include the data managers in the tool list. Requires admin login details

Default: False

--get-all-tools, --get_all_tools

Get all tools and revisions, not just those which are present on the web ui.Requires login details.

Default: False

General options

-v, --verbose

Increase output verbosity.

Default: False

Galaxy connection

-g, --galaxy

Target Galaxy instance URL/IP address

Default: “http://localhost:8080

-u, --user

Galaxy user email address

-p, --password

Password for the Galaxy user

-a, --api-key, --api_key

Galaxy admin user API key (required if not defined in the tools list file)