source: trunk/src/plugins/core/core-plugins.xml @ 5770

<?xml version="1.0" encoding="UTF-8" ?>
<!--
  $Id: core-plugins.xml 5770 2011-09-29 11:27:33Z nicklas $

  Copyright (C) Nicklas Nordborg

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.

  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
-->
<extensions
  xmlns="http://base.thep.lu.se/extensions.xsd"
  id-base="net.sf.basedb.plugins."
  >
  <about>
    <version>3.0</version>
    <name>Core plug-in definitions</name>
    <description>
      This file contains information about all plug-ins
      that are shipped as part of the BASE core.
    </description>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>http://base.thep.lu.se/</url>
  </about>
  
  <plugin-definition id="Base1PluginExecuter">
    <about>
      <name>BASE 1 plug-in executor</name>
      <description>
        This plug-in simulates the plug-in runner from Base 1.2 
        to enable old plug-ins to be executed.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.Base1PluginExecuter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="BaseFileExporter">
    <about>
      <name>BASEfile exporter</name>
      <description>
        Exports bioassay set data to serial or matrix BASEfile format.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.BaseFileExporterPlugin</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="BfsExporter">
    <about>
      <name>BFS exporter</name>
      <description>
        Exports bioassay set data to BFS format.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.BfsExporterPlugin</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="FormulaFilter">
    <about>
      <name>Formula filter</name>
      <description>
        This plugin is used to filter a bioassay set, creating a new bioassay set with fewer spots in it.
        The filter is based on expressions entered by the user, which are parsed with the JEP package.
        Thus, the functionality of this plugin is very flexible.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.FormulaFilter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="HelpExporter">
    <about>
      <name>Help texts exporter</name>
      <description>
        This plugin is used to export a client applications help texts to a XML-file. The help 
        texts can later be imported by the corresponding import plugin.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.HelpExporter</plugin-class>
    <settings>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="HelpImporter">
    <about>
      <name>Help texts importer</name>
      <description>
        This plugin is used to import help texts from a XML-file to BASE.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.HelpImporter</plugin-class>
  </plugin-definition>
  
  <plugin-definition id="IntensityCalculator">
    <about>
      <name>Formula intensity calculator</name>
      <description>
        This plugin is used to calculate intensities from raw data creating an initial root bioassay set.
        The intensities are calculated using Formula objects registered for the experiment's raw data type.
        Thus, the functionality of this plugin can be extended by adding more formula objects to the database.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.IntensityCalculatorPlugin</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>
  
  <plugin-definition id="JepExtraValueCalculator">
    <about>
      <name>Formula extra value calculator</name>
      <description>
        This plugin is used to calculate extra values for a bioassay set using 
        formulas entered by the user.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.JepExtraValueCalculator</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>
  
  <plugin-definition id="JepIntensityTransformer">
    <about>
      <name>Formula intensity transformer</name>
      <description>
        This plugin is used to transform the intensities of a bioassayset using 
        formulas entered by the user.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.JepIntensityTransformer</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>
  
  <plugin-definition id="LowessNormalization">
    <about>
      <name>Normalization: Lowess</name>
      <description>
        This is an efficient java implementation by Johan Enell 
        of the LOWESS algorithm. It provides intensity-based normalization.
        The window size is the only smoothness parameter available 
        in this implementation. The higher it is, the smoother the 
        function will be. Tweaking the other two parameters allows 
        you to gain performance at the price of a small precision loss. 
        The default values are usually good.
        
        This plug-in supports the use of reporter lists for exclusion of 
        reporters in the LOWESS calculation. The option to select reporter 
        lists is visible for users with access to defined reporter lists.

        For more info on LOWESS:
        Cleveland WS, Devlin SJ: Locally weighted regression: an 
        approach to regression analysis by local fitting. J Am Stat 
        Assoc 1988, 83:596-610.
        Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: 
        Normalization for cDNA microarray data: a robust composite
        method addressing single and multiple slide systematic
        variation. Nucleic Acids Res 2002, 30:e15.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.LowessNormalization</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>
  
  <plugin-definition id="MedianRatioNormalization">
    <about>
      <name>Normalization: Median ratio</name>
      <description>
        This normalizer behaves differently depending on the array type.

        1-channel arrays: Intensities are changed in two different ways 
        depending on user selection.
        a) For absolute intensity data the intensities should be scaled 
        with the median intensity, Inew=Iold/Imedian, such that resulting 
        median is 1.
        b) For log intensity data the intensities should be subtracted with 
        the median intensity, log(Inew)=log(Iold)-log(Imedian), such that 
        resulting median is 0.

        2-channel arrays: Intensities are scaled such that their geometric 
        mean (sqrt(i1 * i2)) is kept constant but the median of their ratios 
        (i1/i2) is shifted to 1.

        All array types: The user can optionally exclude spots; all spots 
        with at least one intensity below a user selectable threshold are 
        removed. User selectable (low/high intensity) fractions of the 
        remaining spots are ignored in median calculation.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.MedianRatioNormalization</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="PlateFlatFileImporter">
    <about>
      <name>Plate importer</name>
      <description>
        This plugin is used to import plates from a simple flat file.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.PlateFlatFileImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="PlateMappingExporter">
    <about>
      <name>Plate mapping exporter</name>
      <description>
        This plugin is used to export plate mappings, which maps the 
        coordinates of one or more source plates to coordinates on 
        one or more destination plates. Use the "Plate mapping importer"
        to import the files produced by this plugin.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.PlateMappingExporter</plugin-class>
    <settings>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="PlateMappingImporter">
    <about>
      <name>Plate mapping importer</name>
      <description>
        This plugin is used to import plate mapping files created
        by the "Plate mapping exporter". The file maps the 
        coordinates of one or more source plates to coordinates 
        on one or more destination plates.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.PlateMappingImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="RawDataFlatFileImporter">
    <about>
      <name>Raw data importer</name>
      <description>
        This plugin is used to import raw data from a simple text file.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.RawDataFlatFileImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="ReporterFlatFileImporter">
    <about>
      <name>Reporter importer</name>
      <description>
        This plugin is used to import reporters from a simple flat file.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.ReporterFlatFileImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="ReporterMapFlatFileImporter">
    <about>
      <name>Reporter map importer</name>
      <description>
        This plugin is used to import features to an ArrayDesign from a simple flat file.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.ReporterMapFlatFileImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="SpotImageCreator">
    <about>
      <name>Spot images creator</name>
      <description>
        Converts a full-size scanned image into smaller preview jpg images for each individual spot.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.SpotImageCreator</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="ZipFileUnpacker">
    <about>
      <name>ZIP file unpacker</name>
      <description>
        This plugin unpacks a zip file on the BASE file system. 
        It supports zip and jar files.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.ZipFileUnpacker</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="TarFileUnpacker">
    <about>
      <name>TAR file unpacker</name>
      <description>
        This plugin unpacks a tar file on the BASE file system. 
        It also supports TAR files compressed with the GZIP and
        BZIP algorithms.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.TarFileUnpacker</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="PluginConfigurationExporter">
    <about>
      <name>Plugin configuration exporter</name>
      <description>
        This plugin is used to export selected plugin configurations 
        to an XML-file. The plugin configurations can later be imported 
        by the "Plugin configuration importer".
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.PluginConfigurationExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="PluginConfigurationImporter">
    <about>
      <name>Plugin configuration importer</name>
      <description>
        This plugin is used to import configuration for a BASE plugin from 
        an XML-file created by the "Plugin configuration exporter".
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.PluginConfigurationImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="PrintMapFlatFileImporter">
    <about>
      <name>Print map importer</name>
      <description>
        This plugin is used to import arraydesign from a print map.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.PrintMapFlatFileImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="CdfFileReporterImporter">
    <about>
      <name>Affymetrix CDF probeset importer</name>
      <description>
        This plug-in is used to import probesets from an Affymetrix 
        CDF file as reporters. It can be used in import mode from the 
        reporter list view and from the array design view and in 
        verification mode from the array design view. The plug-in can 
        only set the name and ID of the reporters, since the CDF file 
        doesn't contains any annotation information. Probesets already 
        in BASE will not be affected by the import.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.CdfFileReporterImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="PackedFileExporter">
    <about>
      <name>Packed file exporter</name>
      <description>
        This plugin is used to pack one or more files/directories 
        into a single file. Items should be selected before starting 
        the plug-in and they must all be located in the same parent 
        directory. The compressed file can be downloaded immediately 
        or stored in the BASE file system. The user can choose to have 
        the selected files and directories removed after they've been 
        packed.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.PackedFileExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="AnnotationFlatFileImporter">
    <about>
      <name>Annotation importer</name>
      <description>
        This plugin is used to import annotations to any annotatable items.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.AnnotationFlatFileImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="IlluminaRawDataImporter">
    <about>
      <name>Illumina raw data importer</name>
      <description>
        This plugin is used to import raw data from Illumina data files. 
        The plug-in can be executed from the list of raw bioassays and 
        will then only create new raw bioassays, or from within an experiment, 
        in which case the imported data will also be associated with 
        the experiment.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.IlluminaRawDataImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="GalExporter">
    <about>
      <name>GAL exporter</name>
      <description>
        This plugin exports the features of an array design to a 
        GAL file. The plugin only works for array designs that 
        has features in the database and is disabled for other
        array designs.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.GalExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="ManualTransformCreator">
    <about>
      <name>Manual transform</name>
      <description>
        This plug-in allows a user to manually register an external 
        analysis procedure that has happened outside of BASE and to 
        register the parameters used and the output files that was 
        generated. Before this plug-in can be used a configuration 
        that represents the external tool must be created. The 
        configuration will be used to register possible parameters 
        and output files.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.ManualTransformCreator</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="ManualDerivedBioAssayCreator">
    <about>
      <name>Manual derived bioassay creator</name>
      <description>
        This plug-in allows a user to manually register an external 
        analysis procedure that has happened outside of BASE and to 
        register the parameters used and the output files that was 
        generated. Before this plug-in can be used a configuration 
        that represents the external tool must be created. The 
        configuration will be used to register possible parameters 
        and output files.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.ManualDerivedBioAssayCreator</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="BioSourceImporter">
    <about>
      <name>Biosource importer</name>
      <description>
        Imports and updates biosources in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.BioSourceImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>
  
  <plugin-definition id="BioPlateImporter">
    <about>
      <name>Bioplate importer</name>
      <description>
        Imports and updates bioplates in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.BioPlateImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="SampleImporter">
    <about>
      <name>Sample importer</name>
      <description>
        Imports and updates samples in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.SampleImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="ExtractImporter">
    <about>
      <name>Extract importer</name>
      <description>
        Imports and updates extracts in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.ExtractImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <!-- Used for backwards compatibility with older server installations -->
  <plugin-definition id="LabeledExtractImporter">
    <about>
      <name>Labeled extract importer (deprecated)</name>
      <description>
        Imports and updates labeled extracts in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.LabeledExtractImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="deprecated">1</property>
    </settings>
  </plugin-definition>

  <!-- Used for backwards compatibility with older server installations -->
  <plugin-definition id="HybridizationImporter">
    <about>
      <name>Hybridization importer (deprecated)</name>
      <description>
        Imports and updates hybridizations in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.HybridizationImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="deprecated">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="PhysicalBioAssayImporter">
    <about>
      <name>Physical bioassay importer</name>
      <description>
        Imports and updates physical bioassays in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>
  
  <!-- Used for backwards compatibility with older server installations -->
  <plugin-definition id="ScanImporter">
    <about>
      <name>Scan importer (deprecated)</name>
      <description>
        Imports and updates scans in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.ScanImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="deprecated">1</property>
    </settings>
  </plugin-definition>
  
  <plugin-definition id="DerivedBioAssayImporter">
    <about>
      <name>Derived bioassay importer</name>
      <description>
        Imports and updates derived bioassays in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>
  
  <plugin-definition id="RawBioAssayImporter">
    <about>
      <name>Raw bioassay importer</name>
      <description>
        Imports and updates raw bioassays in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.RawBioAssayImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="ArrayDesignImporter">
    <about>
      <name>Array design importer</name>
      <description>
        Imports and updates array designs in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayDesignImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="ArrayBatchImporter">
    <about>
      <name>Array batch importer</name>
      <description>
        Imports and updates array batches in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayBatchImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="ArraySlideImporter">
    <about>
      <name>Array slide importer</name>
      <description>
        Imports and updates array slides in a batch.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.batchimport.ArraySlideImporter</plugin-class>
  </plugin-definition>

  <plugin-definition id="ExternalProgramExecutor">
    <about>
      <name>External program executor</name>
      <description>
        This plug-in is used to export data from BASE to an external
        program, run the program, and import the result back into BASE.
        The export and import format is set by the user but must be a 
        format supported by the external program. The export also handles
        the parameters needed to run the external program.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.executor.ExternalProgramExecutor</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="BfsExporterSupport">
    <about>
      <name>BFS exporter for the ExternalProgramExecutor</name>
      <description>
        Support plug-in for the external program executor that
        exports data to the external program in BFS format. This 
        plug-in can't be used as a standalone plug-in.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.executor.BfsExporterSupport</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="BfsImporterSupport">
    <about>
      <name>BFS importer for the ExternalProgramExecutor</name>
      <description>
        Support plug-in for the external program executor that 
        imports BFS formatted data from the external program to 
        BASE. This plug-in can't be used as a standalone plug-in.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.executor.BfsImporterSupport</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="BaseFileExporterSupport">
    <about>
      <name>BASEFile exporter for the ExternalProgramExecutor</name>
      <description>
        Support plug-in for the external program executor that 
        exports data to the external program in BASEFile format. 
        This plug-in can't be used as a standalone plug-in.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.executor.BaseFileExporterSupport</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="BaseFileImporterSupport">
    <about>
      <name>BASEfile importer for the ExternalProgramExecutor</name>
      <description>
        Support plug-in for the external program executor that
        imports BASEfile formatted data from the external program 
        to BASE. This plug-in can't be used as a standalone plug-in.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.executor.BaseFileImporterSupport</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="FileOnlyImporterSupport">
    <about>
      <name>File-only importer for the ExternalProgramExecutor</name>
      <description>
        Support plug-in for the external program executor that 
        uploads all created files to BASE and attaches them to 
        a child bioassay set. This plug-in can't be used as a 
        standalone plug-in.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.executor.FileOnlyImporterSupport</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="GtfReporterImporter">
    <about>
      <name>GTF reporter importer</name>
      <description>
        Creates reporters and reporter lists from GTF (Gene transfer format) 
        files. The default configuration uses the transcript_id+seqname value
        as the reporter id and name, and gene_id as "symbol". This can
        be changed by user configurations. For example, to use the gene_id 
        instead or to add prefixes to the id values. The importer
        builds on the regular reporter importer and performs on-the-fly
        transformation of GTF attributes to a completely column-based format.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.gtf.GtfReporterImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="GtfReporterMapImporter">
    <about>
      <name>GTF reporter map importer</name>
      <description>
        Maps reporters to array design features from GTF files. The default
        implementation use the transcript_id as both the feature id and
        reporter id, but this can be changed by user configuration. For
        example, to use the gene_id instead or to add prefixes to the id
        values. The importer build on the regular reporter map importer
        and perform on-the-fly transformation of GTF attributes to a
        completely column-based format.
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.gtf.GtfReporterMapImporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
    </settings>
  </plugin-definition>

  <!-- 
  <plugin-definition id="">
    <about>
      <name></name>
      <description>
      </description>
    </about>
    <plugin-class>net.sf.basedb.plugins.</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
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</extensions>