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It is possible to create custom algorithmic blocks using scripts in the Workflow Designer.

To create an element either select Actions ‣ Create  Element with Script in the main menu.

The Create Element with Script dialog will appear:

Here you should set the name of the element, its description and input/output ports of the element. It is possible to create a port with several input/output slots.

There are 4 types of data for a slot available:

  • Multiple alignments
  • Sequence
  • Set of annotations
  • Files

You can also add an attribute. The following types are supported for attributes:

  • String
  • Number
  • Boolean

The element created is stored in a directory that can be set in the Application Settings dialog.

The element also becomes available in the Custom Elements with Scripts group on the Palette.

It is required to write a script for the element. Supported languages for the script are languages based on the ECMAScript (Javascript, QtScript).

To edit the script select the element on the Scene and either select Actions ‣ Edit script of the element in the main menu or use the Edit script of the element item in the context menu.

The Script editor dialog will appear:

As you can see there are predefined variables for the ports and the attributes in the script. The variables for the input slots begin with the “in_” prefix, variables for the output slots begin with the “out_” prefix. It is possible to load a script from a file (use the Used script field to do it).

For each supported data type UGENE provides a number of functions that can be used in the scripts.

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