Unipro UGENE Online User Manual v. 33
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  1. A minimalistic config: 

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>An imported custom tool</name>
    <binaryName>my_tool.py</binaryName>
</ugeneExternalToolConfig>

    This config describes only a tool name and a tool binary name. After the import the path will be empty, the tool won't have any dependencies, its version will be "unknown".

  2. A config without dependencies and a launcher:

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>RAxML</name>
    <path>raxmlHPC</path>
    <description>RAxML - Randomized Axelerated Maximum Likelihood</description>
    <version>8.2.12</version>
    <binaryName>raxmlHPC</binaryName>
</ugeneExternalToolConfig>

    This config describes an external tool with a description and a version. Path to the tool executable is relative: it is supposed that the executable is in the same folder as the config file.

  3. A config with a dependecy dependency and a launcher:

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>HISAT2</name>
    <path>d:\work\hisat2.1\hisat2</path>
    <description>HISAT2 is a fast and sensitive alignment program for 
mapping next-generation sequencing reads (both DNA and RNA) to a 
population of human genomes (as well as to a single reference genome).</description>
    <toolkitName>HISAT2</toolkitName>
    <version>2.1.0</version>
    <launcherId>PERL</launcherId>
    <dependencies>PERL</dependencies>
    <binaryName>hisat2</binaryName>
</ugeneExternalToolConfig>

    This config describes a tool that is supposed to be run by the Perl interpreter. There is no Perl by default on Windows, but the UGENE installer provides a possibility to install Perl. The tool can notify UGENE that it should be launched by Perl, so UGENE will add a path to Perl to the command that runs the tool.

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