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

Last change on this file since 1385 was 1385, checked in by Martin Svensson, 10 years ago

References #311 The Illumina plugin package can now be build with base3-jars and install in BASE3.0

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1<?xml version="1.0" encoding="UTF-8" ?>
2<!--
3  $Id: extensions.xml 1385 2011-09-02 13:39:29Z martin $
4
5  Copyright (C) 2009 Martin Svensson
6
7  This file is part of FTP extension for BASE.
8  Available at http://baseplugins.thep.lu.se/
9
10  BASE is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License
12  as published by the Free Software Foundation; either version 3
13  of the License, or (at your option) any later version.
14
15  BASE is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18  GNU General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with this program; if not, write to the Free Software
22  Foundation, Inc., 59 Temple Place - Suite 330,
23  Boston, MA  02111-1307, USA.
24-->
25
26<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
27  <about>
28    <name>Illumina extensions</name>
29    <version>1.7pre</version>
30    <copyright>BASE development team</copyright>
31    <email>basedb-users@lists.sourceforge.net</email>
32    <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina</url> 
33    <minbaserversion>3.0</minbaserversion> 
34  </about>
35  <plugin-definition id="Installer">
36    <about>
37      <name>Illumina plug-in package installer</name>
38      <description>
39        This plug-in will install required platforms, data files types, etc. that
40        are required to use the Illumina plug-ins. Start the installation by selecting this
41        plug-in from the list at Administrate -> Plugins -> Definitions. Then click on the
42        'Run plugin' button.
43      </description>     
44    </about>   
45    <plugin-class>net.sf.basedb.illumina.install.Install</plugin-class>
46  </plugin-definition>
47  <plugin-definition id="ExpressionBackgroundCorrection">
48    <about>
49      <name>Illumina expression background correction</name>
50      <description>   
51        This plug-in will remove a per-slide global background from all
52        spots. The background is calculated from a set of negative control
53        spots on the array.\n\n
54        Each assay is treated separately, i.e., no samples are combined
55        together. All calculations are made on the current bioassay data
56        implying that this plug-in should be used early in analysis and before
57        background spots are removed.\n\n
58        A spot is considered to be a negative control spot if it has an
59        ''Control group name'' exactly matching the string ''negative''.\n\n
60        There is one parameter to set that specifies how background
61        intensities should be calculated. Allowed values are median or mean,
62        i.e. the background is either the median or the mean of the negative
63        control spots on the array.\n\n
64        The expression of the background probes is optionally saved to a
65        file. The default is not to save the expression matrix but this can be
66        changed during job configuration.   
67      </description>     
68    </about>   
69    <plugin-class>net.sf.basedb.illumina.plugins.BackgroundCorrection</plugin-class>
70  </plugin-definition>
71  <plugin-definition id="BeadSummaryImporter">
72    <about>
73      <name>Illumina Bead Summary importer</name>
74      <description>
75        Raw data importer for Illumina bead summary files. This plug-in can import data from one
76        or more related bead summary files that are part of the same array but different stripes.
77      </description>     
78    </about>   
79    <plugin-class>net.sf.basedb.illumina.plugins.BeadSummaryImporter</plugin-class>
80  </plugin-definition>
81  <plugin-definition id="BgxFeatureImporter">
82    <about>
83      <name>Illumina BGX feature importer</name>
84      <description>
85        Plugin that imports features from a Illumina BGX-file.
86        Both compressed(gzip) and uncompressed files are supported.
87        None of the mappings for the [Controls] section are configurable.
88        These are set like follows:\n
89        Identify features by->FEATURE_ID\nReporter ID->\\Probe_Id\\\nFeature ID->\\Array_Address_Id\\\n
90        Reg exp for data header is preconfigured to 'Probe_Id\\tArray_Address_Id.*'
91      </description>
92    </about>
93    <plugin-class>net.sf.basedb.illumina.plugins.BgxFeatureImporter</plugin-class>
94  </plugin-definition>
95  <plugin-definition id="BgxReporterImporter">
96    <about>
97      <name>Illumina BGX reporter importer</name>
98      <description>
99        Imports reporter annotation from Illumina BGX files. This importer is
100        based on the regular reporter importer and has the same features and functions.
101        It supports both compressed and uncompressed BGX files. File format configurations
102        made for this plug-in applies to the [Probes] section only. Column mappings for the
103        [Controls] section can't be configured. Some controls appear more than one time
104        in the [Controls] section. If the they have different values for the any of the
105        Reporter_Group_Name, Reporter_Group_Id and/or Reporter_Composite_Map columns the values
106        are merged with a ; as separator.
107      </description>
108    </about>   
109    <plugin-class>net.sf.basedb.illumina.plugins.BgxReporterImporter</plugin-class>
110  </plugin-definition> 
111  <plugin-definition id="DetectionPvalueCalculation">
112    <about>
113      <name>Illumina detection P-value calculation</name>
114      <description>
115        This plug-in implements BeadStudio like detection P-value calculations
116        for Illumina expression data.\n\n
117        The plug-in will _always_ base the detection P-value calculation on
118        raw data values, i.e., the mean raw intensity for the different
119        signals. By default the calculations are based on negative controls
120        available in the root bioassay set for the current analysis
121        branch. The user may change this to only use negative controls in the
122        current bioassay set.\n\n
123        The detection P-value plug-in does not filter the assays, it provides
124        the detection P-values usable in a filter step after running this
125        plug-in.\n\n
126        Parameters\n
127        - The plug-in requires input of array type since detection P-value are
128        calculated differently depending on array type.\n
129        - Users may select to use negative controls in the current bioassay set
130        only. The default behaviour is to use all negative controls in the
131        root bioassay set for the current bioassay set.\n
132        - A cut off parameter is available to exclude outliers within
133        the negative controls. The `cutoff` defines the acceptable negative
134        control signal range
135        $median-MAD*cutoff &lt; I &lt; median+MAD*cutoff$
136        where $MAD$ is the median absolute deviation.\n\n
137        Implementation details\n\n
138        Each assay is treated separately, i.e., no samples are combined
139        together. All calculations are made on the raw bead-type level data,
140        i.e., on the average expression value for each bead type and raw data
141        is always used irrespective when in analysis the detection P-value is
142        calculated.\n\n
143        Pvalue calculation for whole genome arrays:\n
144        For all signals $i$ calculate the detection P-value as
145        $Pvalue = 1-R/N$ where $R$ is the rank of the signal $i$ relative to the
146        negative controls and $N$ is the number of negative controls.\n\n
147        Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL,
148        and Focused Arrays):\n
149        For all signals $i$ calculate the detection P-value as
150        $Pvalue = 1/2 - 1/2 * erf( [i-AvgControl]/StdControl/sqrt(2) )$ where
151        $AvgControl$ is the average intensity of the negative controls,
152        $StdControl$ is the standard deviation of the the negative controls,
153        and $erf$ is the error function
154        (http://mathworld.wolfram.com/Erf.html). The error function is used
155        for arguments within the range (-4,4). To save CPU cycles, the function
156        value for arguments outside this range is set to -1 and 1,
157        respectively.\n\n
158        More details about this plug-in is found at the URL
159        \n\n Please send feedback to the email-address
160      </description>
161    </about>   
162    <plugin-class>net.sf.basedb.illumina.plugins.DetectionPValue</plugin-class>
163  </plugin-definition>
164  <plugin-definition id="SnpRootBioAssaysetCreator">
165    <about>
166      <name>Illumina SNP root bioassayset creator</name>
167      <description>
168        Creates a root bioassay set from Illumina SNP data. This plug-in works
169        only if all raw bioassays has the same array design and SNP split data files
170        are present. The root bioassayset is created by copying values from the data files
171        as follows:\n
172         * Channel 1 = GType (AA = 1.0, AB = 0.0, BB = -1.0, NC = null\n
173         * Channel 2 = Log R Ratio\n
174         * Channel 3 = B Allele Freq
175      </description>
176    </about>
177    <plugin-class>net.sf.basedb.illumina.plugins.SnpIntensityCalculator</plugin-class>
178  </plugin-definition>
179  <plugin-definition id="SnpRawDataImporter">
180    <about>
181      <name>Illumina SNP raw data importer</name>
182      <description>
183        This plug-in is used to import raw data for Illumina SNP from a tab separated text file. The plug-in can be
184        executed both from the list of raw bioassays and from within an experiment. In the
185        last case the imported data will be associated with the experiment
186      </description>
187    </about> 
188    <plugin-class>net.sf.basedb.illumina.plugins.SnpRawDataImporter</plugin-class>
189  </plugin-definition>
190  <plugin-definition id="SnpReporterImporter">
191    <about>
192      <name>Illumina SNP reporter importer</name>
193      <description>
194        Imports reporters from SNP manifest files. This importer works exactly
195        as the regular reporter importer and has the same features.
196      </description>
197    </about>
198    <plugin-class>net.sf.basedb.illumina.plugins.SnpReporterImporter</plugin-class>
199  </plugin-definition>
200  <extension 
201    id="net.sf.basedb.illumina.extensions.overviewplots.illuminaPlots" 
202    extends="net.sf.basedb.clients.web.bioassayset.overviewplots"
203    >
204    <index>20</index>
205    <about>
206      <name>Illumina overview plot</name>
207      <description>Generates overview plot for Illumina expression data.</description>
208    </about>
209    <action-factory>
210      <factory-class>net.sf.basedb.illumina.extensions.plot.PlotFactory</factory-class>
211      <parameters>
212        <width>800</width>
213        <height>600</height>       
214      </parameters>
215    </action-factory>
216  </extension>
217</extensions>
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