FileSets plugins are defined in the plugins root/plugins/filesets directory.


The FileSet configuration is an XML file named config.xml that must follow these rules:

  1. the root element is named fileSetConfig
  2. the XML document is valid against the XML Schema at plugins root/plugins/schemas

The file config.xml contains the following:

    <name>A short name for this aligner</name>
    <help>This message will appear on the web interface when users click on the question mark next to the aligner name.</help>
           <pattern>A SHELL PATTERN WITH WILDCARDS</pattern>
          <pattern>ANOTHER SHELL PATTERN WITH WILDCARDS</pattern>
        <attribute name="NAME_1"/>
        <attribute name="NAME_2"/>
        <attribute name="NAME_3"/>

The first part of the configuration reports the metadata common to all the plugins types.

Next, there are two main containers of information:

  • files or directories: define the patterns that files belonging to the FileSet must match. For example, a Goby Alignment defines 3 file selectors with the following patterns: *.entries, *.index, *.header
  • attributes: these are a set of arbitrary key-value pairs that can be associated to a FileSet instance generated from this configuration. For example, Organism=Homo Sapiens, Basename=A NAME