Unipro UGENE Online User Manual v. 33
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  • name - the external tool name as it should be displayed in the UGENE GUI. This XML element is mandatory.
  • id - the external tool unique identifier. This XML element is mandatory. It can contains only latin letters, digits and symbols '_', '-'.
  • executableName - the name of the tool executable file (with the file extension, if it is present). This XML element is mandatory.
  • executableFullPath - a full path to the external tool executable. This XML element is optional. If the "executableFullPath" value is not specified, UGENE searches for a file with the specified "executableName" name in the same folder as the XML config file and sets the tool path accordingly. One can also specify either an absolute path to a file or a path, relative to the XML config. The path is displayed near the tool in the "Application Settings" dialog. It can be also manually set up by a user.
  • description - a detailed description of the external tool. This XML element is optional.
  • version - a version of the tool executable. This XML element is optional.

  • launcherId - if the tool is supposed to be run with some script interpreter or it is a java application, then this element should contain an appropriate ID. Currently, UGENE supports the following launchers IDs: PYTHON2, PERL, RSCRIPT, JAVA. If the launcher is specified, it would be added to the launch command explicitly whenever you try to launch the external tool. The path to the launcher will be taken from the "Application Settings" (see the corresponding tools in the "Supported tools" group). If the element is not specified or it is empty, no additional launcher will be added to the command that will run the tool. This XML element is optional.

  • dependencies - a comma-separated list of other external tool IDs the new tool is dependent from. If the dependency is not satisfied, then the dependent tool is marked as "not valid" in UGENE. This XML element is optional.

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  • A minimalistic config: 

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

    This config describes only the tool name, the tool ID and the tool executable file path. If the XML config is imported from the same folder as the python script, the path will be set to the python script. The tool won't have any dependencies, its version will be "unknown".

  •  

    A config without dependencies and a launcher:

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>RAxML</name>
    <id>RAXML</id>
    <executableName>raxmlHPC</executableName>
    <executableFullPath>./my_folder/raxmlHPC</executableFullPath>
    <description>RAxML - Randomized Axelerated Maximum Likelihood</description>
    <version>8.2.12</version>
</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 folder structure is the following:

    Code Block
    my_config.xml
my_folder/
   raxmlHPC

  • A config with a dependency and a launcher:

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>HISAT2</name>
    <id>HISAT2</id>
    <executableName>hisat2</executableName>
    <executableFullPath>d:\work\hisat2.1\hisat2<executableFullPath>
    <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>
</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. The XML config also specifies an absolute full path to the executable file.

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