Figure 1: A Workflow is a set of Nodes and Connections
Workflow – a complex scenario or pipeline of operations on some data (see Figure 1). User specifies only inputs. The output of one operation is automatically fed to downstream operations. A workflow can be represented as a Directed Acyclic Graph (DAG). Another synonym is Workspace.
WM – workflow module. The operation that is seen by a software as one command and is displayed to the user as a rectangle. It can be also called as Node or operator.
Each WM has several or zero Input and Output Ports. Input Ports are drawn as small rectangles on the left hand side of a Node and Output Ports – on the right hand side.
WM’s are connected with Connections that are displayed as lines in the GUI. Each Input Port can have one and only one Connection. Each Output Port can have any or zero number of Connections.
Consequently, a Workflow is a set of Nodes and Connections. It is stored as a text file in AP format (see Sect.7). This file can be edited manually or graphically with the Graphical scenario builder (see Sect.6.2).
In the following sections the left click denotes an event when the user presses and releases the left button of a mouse. middle click corresponds to the middle button and right click corresponds to the right button. If there are only two buttons on the mouse, the event of pressing the middle one is usually emulated by the simultaneous pressing of both left and right buttons. The emulation is done on the system level and thus is outside the scope of this manual. The shift+middle click denotes an event that happens when the user presses and releases the middle button of a mouse while holding the shift key pressed. The ctrl+middle click denotes an event that happens when the user presses and releases the middle button of a mouse while holding the ctrl key pressed.
On Mac OS X with the mouse pointer that has only one button left click, right click and middle click is emulated by pressing the modifier key on the keyboard and the mouse button simultaneously. As a result, the left click corresponds to the event when the user presses and releases the mouse button while holding the modifier key pressed and the ctrl+middle click event denotes an event that happens when the user presses and releases the middle button of a mouse while holding the modifier and the ctrl keys pressed. Consult the manual for your OS installation for the correct key combinations.