A custom tool can be integrated into the UGENE GUI as a workflow element in the Workflow Designer - a UGENE component that allows joining tools into workflows.

As described in the "Custom Elements with External Tools" chapter of the Workflow Designer documentation, there are two options when one creates such workflow element:

The first option is intended for cases when a quick temporary integration of a tool into a workflow is enough.

The second option, although requires additional configuration steps, provides a more close integration with UGENE. It can be used by advanced UGENE users for providing a tool for their colleagues.

Below the preparatory configuration steps for the second option are described.

Create an XML configuration file for custom external tool

Create an XML file with the custom external tool description. The file should match the following XML schema:

<?xml version = "1.0" encoding = "UTF-8"?>
<xs:schema xmlns:xs = "http://www.w3.org/2001/XMLSchema">

<xs:element name = "ugeneExternalToolConfig">
            <xs:element name = "name" type = "xs:string" />
            <xs:element name = "id" type = "xs:string" />
            <xs:element name = "executableName" type = "xs:string" />
            <xs:element name = "executableFullPath" type = "xs:string" minOccurs ="0" />
            <xs:element name = "description" type = "xs:string" minOccurs ="0" />
            <xs:element name = "version" type = "xs:string" minOccurs ="0" />
            <xs:element name = "launcherId" type = "xs:string" minOccurs ="0" />
            <xs:element name = "dependencies" type = "xs:string" minOccurs ="0" />
        <xs:attribute name = "version" type = "xs:string" use="required" />



There XML elements have the following meaning:

See also the following examples:

Prepare a package with the XML configuration file, the tool executable and, optionally, other files

The easiest way to "pack" the custom external tool is to:

This "package" can be shared with other users, if required.

Import the tool into UGENE

To add the custom external tool one needs to import its XML configuration file in the "Custom tools" group on the "External Tools" page of the "Application Settings" dialog.