Swift Enabled Galaxy Workflows
-------------------------------

This section documents running Swift enabled workflows in Galaxy environment.

Galaxy is a workflow portal environment through which users can compose
workflows via galaxy-tools chained together via inputs and outputs. See Galaxy
home page to know more about Galaxy user environment.

Writing Swift-enabled Galaxy Tool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Following is a template to write Swift-enabled Galaxy tools. It contains a
single self contained script.

Following is an example Galaxy-tool generated with the above mentioned template
script.

It has capability to process a dataset that resides outside of Galaxy, and to
create a new dataset that resides outside of Galaxy. Each dataset could be a
list of one or more external references such as GridFTP URIs or authenticated
GO transfers.

The tool can invoke other (non-swift) Galaxy tools as app() functions within
the embedded Swift script.

Generic Swift Galaxy Tool
~~~~~~~~~~~~~~~~~~~~~~~~~~
A Generic Swift Galaxy Tool which allows users to add arbitrary Swift scripts,
input data and designated outputs. This tool can be used as a hosted
'try-swift' capability. User can push in new Swift workflows as tools. User can
set config related values using web forms: drop-downs or checkboxes for various
throttle levels, site options, tc elements, etc. Reuse existing Galaxy tools to
upload scripts and/or input data.

A Special Swift Galaxy Tool: The foreach-tool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The for-each can enable many workflows with parallel iteration ("foreach") to
be composed in Galaxy.

Convert Galaxy Workflows to Swift
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A tool that converts existing Galaxy workflow representation to Swift script.