source: plugins/base2/net.sf.basedb.illumina/trunk/META-INF/extensions.xml @ 1385

<?xml version="1.0" encoding="UTF-8" ?>
<!-- 
  $Id: extensions.xml 1385 2011-09-02 13:39:29Z martin $

  Copyright (C) 2009 Martin Svensson

  This file is part of FTP extension for BASE.
  Available at http://baseplugins.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
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  but WITHOUT ANY WARRANTY; without even the implied warranty of
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-->

<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
  <about>
    <name>Illumina extensions</name>
    <version>1.7pre</version>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina</url>  
    <minbaserversion>3.0</minbaserversion>  
  </about>
  <plugin-definition id="Installer">
    <about>
      <name>Illumina plug-in package installer</name>
      <description>
        This plug-in will install required platforms, data files types, etc. that
        are required to use the Illumina plug-ins. Start the installation by selecting this 
        plug-in from the list at Administrate -> Plugins -> Definitions. Then click on the 
        'Run plugin' button.
      </description>      
    </about>    
    <plugin-class>net.sf.basedb.illumina.install.Install</plugin-class>
  </plugin-definition>
  <plugin-definition id="ExpressionBackgroundCorrection">
    <about>
      <name>Illumina expression background correction</name>
      <description>   
        This plug-in will remove a per-slide global background from all 
        spots. The background is calculated from a set of negative control 
        spots on the array.\n\n
        Each assay is treated separately, i.e., no samples are combined 
        together. All calculations are made on the current bioassay data 
        implying that this plug-in should be used early in analysis and before 
        background spots are removed.\n\n
        A spot is considered to be a negative control spot if it has an 
        ''Control group name'' exactly matching the string ''negative''.\n\n
        There is one parameter to set that specifies how background 
        intensities should be calculated. Allowed values are median or mean, 
        i.e. the background is either the median or the mean of the negative 
        control spots on the array.\n\n
        The expression of the background probes is optionally saved to a 
        file. The default is not to save the expression matrix but this can be 
        changed during job configuration.   
      </description>      
    </about>    
    <plugin-class>net.sf.basedb.illumina.plugins.BackgroundCorrection</plugin-class>
  </plugin-definition>
  <plugin-definition id="BeadSummaryImporter">
    <about>
      <name>Illumina Bead Summary importer</name>
      <description>
        Raw data importer for Illumina bead summary files. This plug-in can import data from one 
        or more related bead summary files that are part of the same array but different stripes.
      </description>      
    </about>    
    <plugin-class>net.sf.basedb.illumina.plugins.BeadSummaryImporter</plugin-class>
  </plugin-definition>
  <plugin-definition id="BgxFeatureImporter">
    <about>
      <name>Illumina BGX feature importer</name>
      <description>
        Plugin that imports features from a Illumina BGX-file. 
        Both compressed(gzip) and uncompressed files are supported. 
        None of the mappings for the [Controls] section are configurable. 
        These are set like follows:\n
        Identify features by->FEATURE_ID\nReporter ID->\\Probe_Id\\\nFeature ID->\\Array_Address_Id\\\n
        Reg exp for data header is preconfigured to 'Probe_Id\\tArray_Address_Id.*'
      </description>
    </about>
    <plugin-class>net.sf.basedb.illumina.plugins.BgxFeatureImporter</plugin-class>
  </plugin-definition>
  <plugin-definition id="BgxReporterImporter">
    <about>
      <name>Illumina BGX reporter importer</name>
      <description>
        Imports reporter annotation from Illumina BGX files. This importer is 
        based on the regular reporter importer and has the same features and functions. 
        It supports both compressed and uncompressed BGX files. File format configurations 
        made for this plug-in applies to the [Probes] section only. Column mappings for the 
        [Controls] section can't be configured. Some controls appear more than one time 
        in the [Controls] section. If the they have different values for the any of the 
        Reporter_Group_Name, Reporter_Group_Id and/or Reporter_Composite_Map columns the values 
        are merged with a ; as separator.
      </description>
    </about>    
    <plugin-class>net.sf.basedb.illumina.plugins.BgxReporterImporter</plugin-class>
  </plugin-definition>  
  <plugin-definition id="DetectionPvalueCalculation">
    <about>
      <name>Illumina detection P-value calculation</name>
      <description>
        This plug-in implements BeadStudio like detection P-value calculations 
        for Illumina expression data.\n\n
        The plug-in will _always_ base the detection P-value calculation on 
        raw data values, i.e., the mean raw intensity for the different 
        signals. By default the calculations are based on negative controls 
        available in the root bioassay set for the current analysis 
        branch. The user may change this to only use negative controls in the 
        current bioassay set.\n\n
        The detection P-value plug-in does not filter the assays, it provides 
        the detection P-values usable in a filter step after running this 
        plug-in.\n\n
        Parameters\n
        - The plug-in requires input of array type since detection P-value are 
        calculated differently depending on array type.\n
        - Users may select to use negative controls in the current bioassay set 
        only. The default behaviour is to use all negative controls in the 
        root bioassay set for the current bioassay set.\n
        - A cut off parameter is available to exclude outliers within 
        the negative controls. The `cutoff` defines the acceptable negative 
        control signal range 
        $median-MAD*cutoff &lt; I &lt; median+MAD*cutoff$ 
        where $MAD$ is the median absolute deviation.\n\n
        Implementation details\n\n
        Each assay is treated separately, i.e., no samples are combined 
        together. All calculations are made on the raw bead-type level data, 
        i.e., on the average expression value for each bead type and raw data 
        is always used irrespective when in analysis the detection P-value is 
        calculated.\n\n
        Pvalue calculation for whole genome arrays:\n
        For all signals $i$ calculate the detection P-value as 
        $Pvalue = 1-R/N$ where $R$ is the rank of the signal $i$ relative to the 
        negative controls and $N$ is the number of negative controls.\n\n
        Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL, 
        and Focused Arrays):\n
        For all signals $i$ calculate the detection P-value as 
        $Pvalue = 1/2 - 1/2 * erf( [i-AvgControl]/StdControl/sqrt(2) )$ where 
        $AvgControl$ is the average intensity of the negative controls, 
        $StdControl$ is the standard deviation of the the negative controls, 
        and $erf$ is the error function 
        (http://mathworld.wolfram.com/Erf.html). The error function is used 
        for arguments within the range (-4,4). To save CPU cycles, the function 
        value for arguments outside this range is set to -1 and 1, 
        respectively.\n\n
        More details about this plug-in is found at the URL
        \n\n Please send feedback to the email-address
      </description>
    </about>    
    <plugin-class>net.sf.basedb.illumina.plugins.DetectionPValue</plugin-class>
  </plugin-definition>
  <plugin-definition id="SnpRootBioAssaysetCreator">
    <about>
      <name>Illumina SNP root bioassayset creator</name>
      <description>
        Creates a root bioassay set from Illumina SNP data. This plug-in works 
        only if all raw bioassays has the same array design and SNP split data files 
        are present. The root bioassayset is created by copying values from the data files 
        as follows:\n
         * Channel 1 = GType (AA = 1.0, AB = 0.0, BB = -1.0, NC = null\n
         * Channel 2 = Log R Ratio\n
         * Channel 3 = B Allele Freq
      </description>
    </about>
    <plugin-class>net.sf.basedb.illumina.plugins.SnpIntensityCalculator</plugin-class>
  </plugin-definition>
  <plugin-definition id="SnpRawDataImporter">
    <about>
      <name>Illumina SNP raw data importer</name>
      <description>
        This plug-in is used to import raw data for Illumina SNP from a tab separated text file. The plug-in can be 
        executed both from the list of raw bioassays and from within an experiment. In the 
        last case the imported data will be associated with the experiment
      </description>
    </about>  
    <plugin-class>net.sf.basedb.illumina.plugins.SnpRawDataImporter</plugin-class>
  </plugin-definition>
  <plugin-definition id="SnpReporterImporter">
    <about>
      <name>Illumina SNP reporter importer</name>
      <description>
        Imports reporters from SNP manifest files. This importer works exactly 
        as the regular reporter importer and has the same features.
      </description>
    </about>
    <plugin-class>net.sf.basedb.illumina.plugins.SnpReporterImporter</plugin-class>
  </plugin-definition>
  <extension 
    id="net.sf.basedb.illumina.extensions.overviewplots.illuminaPlots" 
    extends="net.sf.basedb.clients.web.bioassayset.overviewplots"
    >
    <index>20</index>
    <about>
      <name>Illumina overview plot</name>
      <description>Generates overview plot for Illumina expression data.</description>
    </about>
    <action-factory>
      <factory-class>net.sf.basedb.illumina.extensions.plot.PlotFactory</factory-class>
      <parameters>
        <width>800</width>
        <height>600</height>        
      </parameters>
    </action-factory>
  </extension>
</extensions>