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

Configuration

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:

<fileSetConfig>
    <name>A short name for this aligner</name>
    <id>MY_FILESET_ID</id>
    <help>This message will appear on the web interface when users click on the question mark next to the aligner name.</help>
    <version>1.0</version>
    <files>
        <selector>
           <id>MY_ENTRY_NAME_1</id>
           <pattern>A SHELL PATTERN WITH WILDCARDS</pattern>
        </selector>
        <selector>
          <id>MY_ENTRY_NAME_2</id>
          <pattern>ANOTHER SHELL PATTERN WITH WILDCARDS</pattern>
        </selector>
   </files>
   <attributes>
        <attribute name="NAME_1"/>
        <attribute name="NAME_2"/>
        <attribute name="NAME_3"/>
   </attributes>
</fileSetConfig>

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