source: plugins/base2/net.sf.basedb.illumina/trunk/META-INF/extensions.xml @ 1386

Last change on this file since 1386 was 1386, checked in by Nicklas Nordborg, 10 years ago

Fixes #311: Updates required for BASE 3 support

BGX and SNP manifest file validation seems to be working. Updated readme and installation instructions.

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File size: 11.1 KB
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1<?xml version="1.0" encoding="UTF-8" ?>
2<!--
3  $Id: extensions.xml 1386 2011-09-06 06:59:39Z nicklas $
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>1.7-dev</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    <description>
34      This package contains plug-ins and extensions for the Illumina platform.
35    </description>
36    <min-base-version>3.0.0</min-base-version>
37  </about>
38  <plugin-definition id="Installer">
39    <about>
40      <name>Illumina plug-in package installer</name>
41      <description>
42        This plug-in will install required platforms, data files types, etc. that
43        are required to use the Illumina plug-ins. Start the installation by selecting this
44        plug-in from the list at Administrate -> Plugins -> Definitions. Then click on the
45        'Run plugin' button.
46      </description>     
47    </about>   
48    <plugin-class>net.sf.basedb.illumina.install.Install</plugin-class>
49  </plugin-definition>
50  <plugin-definition id="ExpressionBackgroundCorrection">
51    <about>
52      <name>Illumina expression background correction</name>
53      <description>   
54        This plug-in will remove a per-slide global background from all
55        spots. The background is calculated from a set of negative control
56        spots on the array.
57        Each assay is treated separately, i.e., no samples are combined
58        together. All calculations are made on the current bioassay data
59        implying that this plug-in should be used early in analysis and before
60        background spots are removed.
61        A spot is considered to be a negative control spot if it has an
62        ''Control group name'' exactly matching the string ''negative''.
63        There is one parameter to set that specifies how background
64        intensities should be calculated. Allowed values are median or mean,
65        i.e. the background is either the median or the mean of the negative
66        control spots on the array.
67        The expression of the background probes is optionally saved to a
68        file. The default is not to save the expression matrix but this can be
69        changed during job configuration.   
70      </description>     
71    </about>   
72    <plugin-class>net.sf.basedb.illumina.plugins.BackgroundCorrection</plugin-class>
73  </plugin-definition>
74  <plugin-definition id="BeadSummaryImporter">
75    <about>
76      <name>Illumina Bead Summary importer</name>
77      <description>
78        Raw data importer for Illumina bead summary files. This plug-in can import data from one
79        or more related bead summary files that are part of the same array but different stripes.
80      </description>     
81    </about>   
82    <plugin-class>net.sf.basedb.illumina.plugins.BeadSummaryImporter</plugin-class>
83  </plugin-definition>
84  <plugin-definition id="BgxFeatureImporter">
85    <about>
86      <name>Illumina BGX feature importer</name>
87      <description>
88        Plugin that imports features from a Illumina BGX-file.
89        Both compressed(gzip) and uncompressed files are supported.
90        None of the mappings for the [Controls] section are configurable.
91        These are set like follows:
92        Identify features by->FEATURE_IDReporter ID->\\Probe_Id\\Feature ID->\\Array_Address_Id\\
93        Reg exp for data header is preconfigured to 'Probe_Id\\tArray_Address_Id.*'
94      </description>
95    </about>
96    <plugin-class>net.sf.basedb.illumina.plugins.BgxFeatureImporter</plugin-class>
97  </plugin-definition>
98  <plugin-definition id="BgxReporterImporter">
99    <about>
100      <name>Illumina BGX reporter importer</name>
101      <description>
102        Imports reporter annotation from Illumina BGX files. This importer is
103        based on the regular reporter importer and has the same features and functions.
104        It supports both compressed and uncompressed BGX files. File format configurations
105        made for this plug-in applies to the [Probes] section only. Column mappings for the
106        [Controls] section can't be configured. Some controls appear more than one time
107        in the [Controls] section. If the they have different values for the any of the
108        Reporter_Group_Name, Reporter_Group_Id and/or Reporter_Composite_Map columns the values
109        are merged with a ; as separator.
110      </description>
111    </about>   
112    <plugin-class>net.sf.basedb.illumina.plugins.BgxReporterImporter</plugin-class>
113  </plugin-definition> 
114  <plugin-definition id="DetectionPvalueCalculation">
115    <about>
116      <name>Illumina detection P-value calculation</name>
117      <description>
118        This plug-in implements BeadStudio like detection P-value calculations
119        for Illumina expression data.
120        The plug-in will _always_ base the detection P-value calculation on
121        raw data values, i.e., the mean raw intensity for the different
122        signals. By default the calculations are based on negative controls
123        available in the root bioassay set for the current analysis
124        branch. The user may change this to only use negative controls in the
125        current bioassay set.
126        The detection P-value plug-in does not filter the assays, it provides
127        the detection P-values usable in a filter step after running this
128        plug-in.
129        Parameters
130        - The plug-in requires input of array type since detection P-value are
131        calculated differently depending on array type.
132        - Users may select to use negative controls in the current bioassay set
133        only. The default behaviour is to use all negative controls in the
134        root bioassay set for the current bioassay set.
135        - A cut off parameter is available to exclude outliers within
136        the negative controls. The `cutoff` defines the acceptable negative
137        control signal range
138        $median-MAD*cutoff &lt; I &lt; median+MAD*cutoff$
139        where $MAD$ is the median absolute deviation.
140        Implementation details
141        Each assay is treated separately, i.e., no samples are combined
142        together. All calculations are made on the raw bead-type level data,
143        i.e., on the average expression value for each bead type and raw data
144        is always used irrespective when in analysis the detection P-value is
145        calculated.
146        Pvalue calculation for whole genome arrays:
147        For all signals $i$ calculate the detection P-value as
148        $Pvalue = 1-R/N$ where $R$ is the rank of the signal $i$ relative to the
149        negative controls and $N$ is the number of negative controls.
150        Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL,
151        and Focused Arrays):
152        For all signals $i$ calculate the detection P-value as
153        $Pvalue = 1/2 - 1/2 * erf( [i-AvgControl]/StdControl/sqrt(2) )$ where
154        $AvgControl$ is the average intensity of the negative controls,
155        $StdControl$ is the standard deviation of the the negative controls,
156        and $erf$ is the error function
157        (http://mathworld.wolfram.com/Erf.html). The error function is used
158        for arguments within the range (-4,4). To save CPU cycles, the function
159        value for arguments outside this range is set to -1 and 1,
160        respectively.
161        More details about this plug-in is found at the URL
162         Please send feedback to the email-address
163      </description>
164    </about>   
165    <plugin-class>net.sf.basedb.illumina.plugins.DetectionPValue</plugin-class>
166  </plugin-definition>
167  <plugin-definition id="SnpRootBioAssaysetCreator">
168    <about>
169      <name>Illumina SNP root bioassayset creator</name>
170      <description>
171        Creates a root bioassay set from Illumina SNP data. This plug-in works
172        only if all raw bioassays has the same array design and SNP split data files
173        are present. The root bioassayset is created by copying values from the data files
174        as follows:
175         * Channel 1 = GType (AA = 1.0, AB = 0.0, BB = -1.0, NC = null)
176         * Channel 2 = Log R Ratio
177         * Channel 3 = B Allele Freq
178      </description>
179    </about>
180    <plugin-class>net.sf.basedb.illumina.plugins.SnpIntensityCalculator</plugin-class>
181  </plugin-definition>
182  <plugin-definition id="SnpRawDataImporter">
183    <about>
184      <name>Illumina SNP raw data importer</name>
185      <description>
186        This plug-in is used to import raw data for Illumina SNP from a tab separated text file. The plug-in can be
187        executed both from the list of raw bioassays and from within an experiment. In the
188        last case the imported data will be associated with the experiment
189      </description>
190    </about> 
191    <plugin-class>net.sf.basedb.illumina.plugins.SnpRawDataImporter</plugin-class>
192  </plugin-definition>
193  <plugin-definition id="SnpReporterImporter">
194    <about>
195      <name>Illumina SNP reporter importer</name>
196      <description>
197        Imports reporters from SNP manifest files. This importer works exactly
198        as the regular reporter importer and has the same features.
199      </description>
200    </about>
201    <plugin-class>net.sf.basedb.illumina.plugins.SnpReporterImporter</plugin-class>
202  </plugin-definition>
203  <extension 
204    id="net.sf.basedb.illumina.extensions.overviewplots.illuminaPlots" 
205    extends="net.sf.basedb.clients.web.bioassayset.overviewplots"
206    >
207    <index>20</index>
208    <about>
209      <name>Illumina overview plot</name>
210      <description>Generates overview plot for Illumina expression data.</description>
211    </about>
212    <action-factory>
213      <factory-class>net.sf.basedb.illumina.extensions.plot.PlotFactory</factory-class>
214      <parameters>
215        <width>800</width>
216        <height>600</height>       
217      </parameters>
218    </action-factory>
219  </extension>
220  <extension 
221    id="net.sf.basedb.illumina.extensions.bgxvalidator"
222    extends="net.sf.basedb.core.filehandler.validator"
223    >
224    <about>
225      <name>BGX file validator</name>
226      <description>
227        Validator and metadata extractor implementation for Illumina BGX files.
228        It will parse the start of the file until the [Probes] section is found
229        and then extract the number of probes + controls and set that as the
230        number of features on the array design.
231      </description>
232    </about>
233    <index>1</index>
234    <action-factory>
235      <factory-class>net.sf.basedb.illumina.filehandler.BgxValidationFactory</factory-class>
236    </action-factory>
237  </extension>
238  <extension 
239    id="net.sf.basedb.illumina.extensions.snpvalidator"
240    extends="net.sf.basedb.core.filehandler.validator"
241    >
242    <about>
243      <name>SNP manifest validator</name>
244      <description>
245        Validator and metadata extractor implementation for Illumina SNP manifest files.
246        It will parse the start of the file until the [Assay] section is found
247        and then extract the SNP Count value and set that as the number of features
248        on the array design.
249      </description>
250    </about>
251    <index>1</index>
252    <action-factory>
253      <factory-class>net.sf.basedb.illumina.filehandler.SnpCvsValidationFactory</factory-class>
254    </action-factory>
255  </extension>
256 
257</extensions>
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