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<?xml version="1.0" encoding="UTF-8" ?> |
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<!-- |
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$Id$ |
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|
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Copyright (C) Nicklas Nordborg |
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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<extensions |
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xmlns="http://base.thep.lu.se/extensions.xsd" |
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id-base="net.sf.basedb.plugins." |
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> |
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<about> |
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<version>3.0</version> |
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<name>Core plug-in definitions</name> |
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<description> |
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This file contains information about all plug-ins |
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that are shipped as part of the BASE core. |
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</description> |
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<copyright>BASE development team</copyright> |
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<email>basedb-users@lists.sourceforge.net</email> |
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<url>https://base.thep.lu.se/</url> |
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</about> |
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|
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<plugin-definition id="Base1PluginExecuter"> |
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<about> |
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<name>BASE 1 plug-in executor</name> |
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<description> |
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This plug-in simulates the plug-in runner from Base 1.2 |
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to enable old plug-ins to be executed. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.Base1PluginExecuter</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="BaseFileExporter"> |
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<about> |
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<name>BASEfile exporter</name> |
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<description> |
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Exports bioassay set data to serial or matrix BASEfile format. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.BaseFileExporterPlugin</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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<property name="immediate-execution">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="BfsExporter"> |
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<about> |
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<name>BFS exporter</name> |
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<description> |
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Exports bioassay set data to BFS format. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.BfsExporterPlugin</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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<property name="immediate-execution">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="FormulaFilter"> |
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<about> |
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<name>Formula filter</name> |
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<description> |
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This plugin is used to filter a bioassay set, creating a new bioassay set with fewer spots in it. |
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The filter is based on expressions entered by the user, which are parsed with the JEP package. |
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Thus, the functionality of this plugin is very flexible. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.FormulaFilter</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="HelpExporter"> |
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<about> |
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<name>Help texts exporter</name> |
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<description> |
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This plugin is used to export a client applications help texts to a XML-file. The help |
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texts can later be imported by the corresponding import plugin. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.HelpExporter</plugin-class> |
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<settings> |
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<property name="immediate-execution">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="HelpImporter"> |
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<about> |
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<name>Help texts importer</name> |
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<description> |
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This plugin is used to import help texts from a XML-file to BASE. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.HelpImporter</plugin-class> |
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</plugin-definition> |
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|
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<plugin-definition id="IntensityCalculator"> |
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<about> |
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<name>Formula intensity calculator</name> |
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<description> |
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This plugin is used to calculate intensities from raw data creating an initial root bioassay set. |
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The intensities are calculated using Formula objects registered for the experiment's raw data type. |
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Thus, the functionality of this plugin can be extended by adding more formula objects to the database. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.IntensityCalculatorPlugin</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="JepExtraValueCalculator"> |
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<about> |
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<name>Formula extra value calculator</name> |
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<description> |
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This plugin is used to calculate extra values for a bioassay set using |
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formulas entered by the user. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.JepExtraValueCalculator</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="JepIntensityTransformer"> |
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<about> |
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<name>Formula intensity transformer</name> |
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<description> |
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This plugin is used to transform the intensities of a bioassayset using |
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formulas entered by the user. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.JepIntensityTransformer</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="LowessNormalization"> |
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<about> |
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<name>Normalization: Lowess</name> |
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<description> |
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This is an efficient java implementation by Johan Enell |
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of the LOWESS algorithm. It provides intensity-based normalization. |
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The window size is the only smoothness parameter available |
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in this implementation. The higher it is, the smoother the |
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function will be. Tweaking the other two parameters allows |
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you to gain performance at the price of a small precision loss. |
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The default values are usually good. |
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|
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This plug-in supports the use of reporter lists for exclusion of |
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reporters in the LOWESS calculation. The option to select reporter |
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lists is visible for users with access to defined reporter lists. |
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|
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For more info on LOWESS: |
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Cleveland WS, Devlin SJ: Locally weighted regression: an |
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approach to regression analysis by local fitting. J Am Stat |
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Assoc 1988, 83:596-610. |
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Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: |
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Normalization for cDNA microarray data: a robust composite |
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method addressing single and multiple slide systematic |
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variation. Nucleic Acids Res 2002, 30:e15. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.LowessNormalization</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="MedianRatioNormalization"> |
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<about> |
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<name>Normalization: Median ratio</name> |
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<description> |
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This normalizer behaves differently depending on the array type. |
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|
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1-channel arrays: Intensities are changed in two different ways |
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depending on source data. |
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a) For absolute intensity data the intensities are scaled |
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with the median intensity, Inew=Iold/Imedian, such that resulting |
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median is 1. |
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b) For log intensity data the intensities are subtracted with |
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the median intensity, log(Inew)=log(Iold)-log(Imedian), such that |
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resulting median is 0. |
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|
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2-channel arrays: Intensities are scaled such that their geometric |
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mean (sqrt(i1 * i2)) is kept constant but the median of their ratios |
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(i1/i2) is shifted to 1. |
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|
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All array types: The user can optionally exclude spots; all spots |
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with at least one intensity below a user selectable threshold are |
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removed. User selectable (low/high intensity) fractions of the |
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remaining spots are ignored in median calculation. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.MedianRatioNormalization</plugin-class> |
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<settings> |
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<property name="everyone-use">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="PlateFlatFileImporter"> |
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<about> |
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<name>Plate importer</name> |
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<description> |
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This plugin is used to import plates from a simple flat file. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.PlateFlatFileImporter</plugin-class> |
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</plugin-definition> |
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|
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<plugin-definition id="PlateMappingExporter"> |
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<about> |
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<name>Plate mapping exporter</name> |
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<description> |
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This plugin is used to export plate mappings, which maps the |
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coordinates of one or more source plates to coordinates on |
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one or more destination plates. Use the "Plate mapping importer" |
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to import the files produced by this plugin. |
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</description> |
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</about> |
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<plugin-class>net.sf.basedb.plugins.PlateMappingExporter</plugin-class> |
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<settings> |
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<property name="immediate-execution">1</property> |
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</settings> |
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</plugin-definition> |
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|
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<plugin-definition id="PlateMappingImporter"> |
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<about> |
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<name>Plate mapping importer</name> |
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<description> |
| 5612 |
18 Apr 11 |
nicklas |
256 |
This plugin is used to import plate mapping files created |
| 5612 |
18 Apr 11 |
nicklas |
257 |
by the "Plate mapping exporter". The file maps the |
| 5612 |
18 Apr 11 |
nicklas |
258 |
coordinates of one or more source plates to coordinates |
| 5612 |
18 Apr 11 |
nicklas |
259 |
on one or more destination plates. |
| 5612 |
18 Apr 11 |
nicklas |
260 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
261 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
262 |
<plugin-class>net.sf.basedb.plugins.PlateMappingImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
263 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
264 |
|
| 5612 |
18 Apr 11 |
nicklas |
265 |
<plugin-definition id="RawDataFlatFileImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
266 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
267 |
<name>Raw data importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
268 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
269 |
This plugin is used to import raw data from a simple text file. |
| 5612 |
18 Apr 11 |
nicklas |
270 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
271 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
272 |
<plugin-class>net.sf.basedb.plugins.RawDataFlatFileImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
273 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
274 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
275 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
276 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
277 |
|
| 5612 |
18 Apr 11 |
nicklas |
278 |
<plugin-definition id="ReporterFlatFileImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
279 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
280 |
<name>Reporter importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
281 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
282 |
This plugin is used to import reporters from a simple flat file. |
| 5612 |
18 Apr 11 |
nicklas |
283 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
284 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
285 |
<plugin-class>net.sf.basedb.plugins.ReporterFlatFileImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
286 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
287 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
288 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
289 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
290 |
|
| 5612 |
18 Apr 11 |
nicklas |
291 |
<plugin-definition id="ReporterMapFlatFileImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
292 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
293 |
<name>Reporter map importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
294 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
295 |
This plugin is used to import features to an ArrayDesign from a simple flat file. |
| 5612 |
18 Apr 11 |
nicklas |
296 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
297 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
298 |
<plugin-class>net.sf.basedb.plugins.ReporterMapFlatFileImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
299 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
300 |
|
| 5612 |
18 Apr 11 |
nicklas |
301 |
<plugin-definition id="ZipFileUnpacker"> |
| 5612 |
18 Apr 11 |
nicklas |
302 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
303 |
<name>ZIP file unpacker</name> |
| 5612 |
18 Apr 11 |
nicklas |
304 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
305 |
This plugin unpacks a zip file on the BASE file system. |
| 5612 |
18 Apr 11 |
nicklas |
306 |
It supports zip and jar files. |
| 5612 |
18 Apr 11 |
nicklas |
307 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
308 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
309 |
<plugin-class>net.sf.basedb.plugins.ZipFileUnpacker</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
310 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
311 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
312 |
<property name="immediate-execution">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
313 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
314 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
315 |
|
| 5612 |
18 Apr 11 |
nicklas |
316 |
<plugin-definition id="TarFileUnpacker"> |
| 5612 |
18 Apr 11 |
nicklas |
317 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
318 |
<name>TAR file unpacker</name> |
| 5612 |
18 Apr 11 |
nicklas |
319 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
320 |
This plugin unpacks a tar file on the BASE file system. |
| 5612 |
18 Apr 11 |
nicklas |
321 |
It also supports TAR files compressed with the GZIP and |
| 5612 |
18 Apr 11 |
nicklas |
322 |
BZIP algorithms. |
| 5612 |
18 Apr 11 |
nicklas |
323 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
324 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
325 |
<plugin-class>net.sf.basedb.plugins.TarFileUnpacker</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
326 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
327 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
328 |
<property name="immediate-execution">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
329 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
330 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
331 |
|
| 6049 |
18 Apr 12 |
nicklas |
332 |
<plugin-definition id="GzipFileUnpacker"> |
| 6049 |
18 Apr 12 |
nicklas |
333 |
<about> |
| 6049 |
18 Apr 12 |
nicklas |
334 |
<name>GZip file unpacker</name> |
| 6049 |
18 Apr 12 |
nicklas |
335 |
<description> |
| 6049 |
18 Apr 12 |
nicklas |
336 |
This plugin unpacks gzip compressed files to the BASE file system. |
| 6049 |
18 Apr 12 |
nicklas |
337 |
</description> |
| 6049 |
18 Apr 12 |
nicklas |
338 |
</about> |
| 6049 |
18 Apr 12 |
nicklas |
339 |
<plugin-class>net.sf.basedb.plugins.GzipFileUnpacker</plugin-class> |
| 6049 |
18 Apr 12 |
nicklas |
340 |
<settings> |
| 6049 |
18 Apr 12 |
nicklas |
341 |
<property name="everyone-use">1</property> |
| 6049 |
18 Apr 12 |
nicklas |
342 |
<property name="immediate-execution">1</property> |
| 6049 |
18 Apr 12 |
nicklas |
343 |
</settings> |
| 6049 |
18 Apr 12 |
nicklas |
344 |
</plugin-definition> |
| 6049 |
18 Apr 12 |
nicklas |
345 |
|
| 6049 |
18 Apr 12 |
nicklas |
346 |
<plugin-definition id="Bzip2FileUnpacker"> |
| 6049 |
18 Apr 12 |
nicklas |
347 |
<about> |
| 6049 |
18 Apr 12 |
nicklas |
348 |
<name>BZip2 file unpacker</name> |
| 6049 |
18 Apr 12 |
nicklas |
349 |
<description> |
| 6049 |
18 Apr 12 |
nicklas |
350 |
This plugin unpacks BZip2 compressed files to the BASE file system. |
| 6049 |
18 Apr 12 |
nicklas |
351 |
</description> |
| 6049 |
18 Apr 12 |
nicklas |
352 |
</about> |
| 6049 |
18 Apr 12 |
nicklas |
353 |
<plugin-class>net.sf.basedb.plugins.Bzip2FileUnpacker</plugin-class> |
| 6049 |
18 Apr 12 |
nicklas |
354 |
<settings> |
| 6049 |
18 Apr 12 |
nicklas |
355 |
<property name="everyone-use">1</property> |
| 6049 |
18 Apr 12 |
nicklas |
356 |
<property name="immediate-execution">1</property> |
| 6049 |
18 Apr 12 |
nicklas |
357 |
</settings> |
| 6049 |
18 Apr 12 |
nicklas |
358 |
</plugin-definition> |
| 6049 |
18 Apr 12 |
nicklas |
359 |
|
| 6049 |
18 Apr 12 |
nicklas |
360 |
|
| 5612 |
18 Apr 11 |
nicklas |
361 |
<plugin-definition id="PluginConfigurationExporter"> |
| 5612 |
18 Apr 11 |
nicklas |
362 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
363 |
<name>Plugin configuration exporter</name> |
| 5612 |
18 Apr 11 |
nicklas |
364 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
365 |
This plugin is used to export selected plugin configurations |
| 5612 |
18 Apr 11 |
nicklas |
366 |
to an XML-file. The plugin configurations can later be imported |
| 5612 |
18 Apr 11 |
nicklas |
367 |
by the "Plugin configuration importer". |
| 5612 |
18 Apr 11 |
nicklas |
368 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
369 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
370 |
<plugin-class>net.sf.basedb.plugins.PluginConfigurationExporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
371 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
372 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
373 |
<property name="immediate-execution">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
374 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
375 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
376 |
|
| 5612 |
18 Apr 11 |
nicklas |
377 |
<plugin-definition id="PluginConfigurationImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
378 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
379 |
<name>Plugin configuration importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
380 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
381 |
This plugin is used to import configuration for a BASE plugin from |
| 5612 |
18 Apr 11 |
nicklas |
382 |
an XML-file created by the "Plugin configuration exporter". |
| 5612 |
18 Apr 11 |
nicklas |
383 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
384 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
385 |
<plugin-class>net.sf.basedb.plugins.PluginConfigurationImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
386 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
387 |
|
| 5637 |
20 May 11 |
nicklas |
388 |
<plugin-definition id="PrintMapFlatFileImporter"> |
| 5637 |
20 May 11 |
nicklas |
389 |
<about> |
| 5637 |
20 May 11 |
nicklas |
390 |
<name>Print map importer</name> |
| 5637 |
20 May 11 |
nicklas |
391 |
<description> |
| 5637 |
20 May 11 |
nicklas |
392 |
This plugin is used to import arraydesign from a print map. |
| 5637 |
20 May 11 |
nicklas |
393 |
</description> |
| 5637 |
20 May 11 |
nicklas |
394 |
</about> |
| 5637 |
20 May 11 |
nicklas |
395 |
<plugin-class>net.sf.basedb.plugins.PrintMapFlatFileImporter</plugin-class> |
| 5637 |
20 May 11 |
nicklas |
396 |
</plugin-definition> |
| 5637 |
20 May 11 |
nicklas |
397 |
|
| 5612 |
18 Apr 11 |
nicklas |
398 |
<plugin-definition id="CdfFileReporterImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
399 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
400 |
<name>Affymetrix CDF probeset importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
401 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
402 |
This plug-in is used to import probesets from an Affymetrix |
| 5612 |
18 Apr 11 |
nicklas |
403 |
CDF file as reporters. It can be used in import mode from the |
| 5612 |
18 Apr 11 |
nicklas |
404 |
reporter list view and from the array design view and in |
| 5612 |
18 Apr 11 |
nicklas |
405 |
verification mode from the array design view. The plug-in can |
| 5612 |
18 Apr 11 |
nicklas |
406 |
only set the name and ID of the reporters, since the CDF file |
| 5612 |
18 Apr 11 |
nicklas |
407 |
doesn't contains any annotation information. Probesets already |
| 5612 |
18 Apr 11 |
nicklas |
408 |
in BASE will not be affected by the import. |
| 5612 |
18 Apr 11 |
nicklas |
409 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
410 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
411 |
<plugin-class>net.sf.basedb.plugins.CdfFileReporterImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
412 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
413 |
|
| 5612 |
18 Apr 11 |
nicklas |
414 |
<plugin-definition id="PackedFileExporter"> |
| 5612 |
18 Apr 11 |
nicklas |
415 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
416 |
<name>Packed file exporter</name> |
| 5612 |
18 Apr 11 |
nicklas |
417 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
418 |
This plugin is used to pack one or more files/directories |
| 5612 |
18 Apr 11 |
nicklas |
419 |
into a single file. Items should be selected before starting |
| 5612 |
18 Apr 11 |
nicklas |
420 |
the plug-in and they must all be located in the same parent |
| 5612 |
18 Apr 11 |
nicklas |
421 |
directory. The compressed file can be downloaded immediately |
| 5612 |
18 Apr 11 |
nicklas |
422 |
or stored in the BASE file system. The user can choose to have |
| 5612 |
18 Apr 11 |
nicklas |
423 |
the selected files and directories removed after they've been |
| 5612 |
18 Apr 11 |
nicklas |
424 |
packed. |
| 5612 |
18 Apr 11 |
nicklas |
425 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
426 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
427 |
<plugin-class>net.sf.basedb.plugins.PackedFileExporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
428 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
429 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
430 |
<property name="immediate-execution">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
431 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
432 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
433 |
|
| 5612 |
18 Apr 11 |
nicklas |
434 |
<plugin-definition id="AnnotationFlatFileImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
435 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
436 |
<name>Annotation importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
437 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
438 |
This plugin is used to import annotations to any annotatable items. |
| 5612 |
18 Apr 11 |
nicklas |
439 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
440 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
441 |
<plugin-class>net.sf.basedb.plugins.AnnotationFlatFileImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
442 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
443 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
444 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
445 |
</plugin-definition> |
| 7849 |
13 Oct 20 |
nicklas |
446 |
|
| 7849 |
13 Oct 20 |
nicklas |
447 |
<plugin-definition id="AnyToAnyImporter"> |
| 7849 |
13 Oct 20 |
nicklas |
448 |
<about> |
| 7849 |
13 Oct 20 |
nicklas |
449 |
<name>Any-to-any importer</name> |
| 7849 |
13 Oct 20 |
nicklas |
450 |
<description> |
| 7849 |
13 Oct 20 |
nicklas |
451 |
This plugin is used to batch manage any-to-any links between items. |
| 7849 |
13 Oct 20 |
nicklas |
452 |
</description> |
| 7849 |
13 Oct 20 |
nicklas |
453 |
</about> |
| 7849 |
13 Oct 20 |
nicklas |
454 |
<plugin-class>net.sf.basedb.plugins.batchimport.AnyToAnyImporter</plugin-class> |
| 7849 |
13 Oct 20 |
nicklas |
455 |
<settings> |
| 7849 |
13 Oct 20 |
nicklas |
456 |
<property name="everyone-use">1</property> |
| 7849 |
13 Oct 20 |
nicklas |
457 |
</settings> |
| 7849 |
13 Oct 20 |
nicklas |
458 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
459 |
|
| 5612 |
18 Apr 11 |
nicklas |
460 |
<plugin-definition id="IlluminaRawDataImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
461 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
462 |
<name>Illumina raw data importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
463 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
464 |
This plugin is used to import raw data from Illumina data files. |
| 5612 |
18 Apr 11 |
nicklas |
465 |
The plug-in can be executed from the list of raw bioassays and |
| 5612 |
18 Apr 11 |
nicklas |
466 |
will then only create new raw bioassays, or from within an experiment, |
| 5612 |
18 Apr 11 |
nicklas |
467 |
in which case the imported data will also be associated with |
| 5612 |
18 Apr 11 |
nicklas |
468 |
the experiment. |
| 5612 |
18 Apr 11 |
nicklas |
469 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
470 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
471 |
<plugin-class>net.sf.basedb.plugins.IlluminaRawDataImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
472 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
473 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
474 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
475 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
476 |
|
| 5612 |
18 Apr 11 |
nicklas |
477 |
<plugin-definition id="GalExporter"> |
| 5612 |
18 Apr 11 |
nicklas |
478 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
479 |
<name>GAL exporter</name> |
| 5612 |
18 Apr 11 |
nicklas |
480 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
481 |
This plugin exports the features of an array design to a |
| 5612 |
18 Apr 11 |
nicklas |
482 |
GAL file. The plugin only works for array designs that |
| 5612 |
18 Apr 11 |
nicklas |
483 |
has features in the database and is disabled for other |
| 5612 |
18 Apr 11 |
nicklas |
484 |
array designs. |
| 5612 |
18 Apr 11 |
nicklas |
485 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
486 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
487 |
<plugin-class>net.sf.basedb.plugins.GalExporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
488 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
489 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
490 |
<property name="immediate-execution">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
491 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
492 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
493 |
|
| 5612 |
18 Apr 11 |
nicklas |
494 |
<plugin-definition id="ManualTransformCreator"> |
| 5612 |
18 Apr 11 |
nicklas |
495 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
496 |
<name>Manual transform</name> |
| 5612 |
18 Apr 11 |
nicklas |
497 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
498 |
This plug-in allows a user to manually register an external |
| 5612 |
18 Apr 11 |
nicklas |
499 |
analysis procedure that has happened outside of BASE and to |
| 5612 |
18 Apr 11 |
nicklas |
500 |
register the parameters used and the output files that was |
| 5612 |
18 Apr 11 |
nicklas |
501 |
generated. Before this plug-in can be used a configuration |
| 5612 |
18 Apr 11 |
nicklas |
502 |
that represents the external tool must be created. The |
| 5612 |
18 Apr 11 |
nicklas |
503 |
configuration will be used to register possible parameters |
| 5612 |
18 Apr 11 |
nicklas |
504 |
and output files. |
| 5612 |
18 Apr 11 |
nicklas |
505 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
506 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
507 |
<plugin-class>net.sf.basedb.plugins.ManualTransformCreator</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
508 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
509 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
510 |
<property name="immediate-execution">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
511 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
512 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
513 |
|
| 5729 |
08 Sep 11 |
nicklas |
514 |
<plugin-definition id="ManualDerivedBioAssayCreator"> |
| 5729 |
08 Sep 11 |
nicklas |
515 |
<about> |
| 5729 |
08 Sep 11 |
nicklas |
516 |
<name>Manual derived bioassay creator</name> |
| 5729 |
08 Sep 11 |
nicklas |
517 |
<description> |
| 5729 |
08 Sep 11 |
nicklas |
518 |
This plug-in allows a user to manually register an external |
| 5729 |
08 Sep 11 |
nicklas |
519 |
analysis procedure that has happened outside of BASE and to |
| 5729 |
08 Sep 11 |
nicklas |
520 |
register the parameters used and the output files that was |
| 5729 |
08 Sep 11 |
nicklas |
521 |
generated. Before this plug-in can be used a configuration |
| 5729 |
08 Sep 11 |
nicklas |
522 |
that represents the external tool must be created. The |
| 5729 |
08 Sep 11 |
nicklas |
523 |
configuration will be used to register possible parameters |
| 5729 |
08 Sep 11 |
nicklas |
524 |
and output files. |
| 5729 |
08 Sep 11 |
nicklas |
525 |
</description> |
| 5729 |
08 Sep 11 |
nicklas |
526 |
</about> |
| 5729 |
08 Sep 11 |
nicklas |
527 |
<plugin-class>net.sf.basedb.plugins.ManualDerivedBioAssayCreator</plugin-class> |
| 5729 |
08 Sep 11 |
nicklas |
528 |
<settings> |
| 5729 |
08 Sep 11 |
nicklas |
529 |
<property name="everyone-use">1</property> |
| 5729 |
08 Sep 11 |
nicklas |
530 |
<property name="immediate-execution">1</property> |
| 5729 |
08 Sep 11 |
nicklas |
531 |
</settings> |
| 5729 |
08 Sep 11 |
nicklas |
532 |
</plugin-definition> |
| 5729 |
08 Sep 11 |
nicklas |
533 |
|
| 6520 |
18 Aug 14 |
nicklas |
534 |
<plugin-definition id="FileImporter"> |
| 6520 |
18 Aug 14 |
nicklas |
535 |
<about> |
| 6520 |
18 Aug 14 |
nicklas |
536 |
<name>File importer</name> |
| 6520 |
18 Aug 14 |
nicklas |
537 |
<description> |
| 6520 |
18 Aug 14 |
nicklas |
538 |
Imports and updates files in a batch. The importer |
| 6520 |
18 Aug 14 |
nicklas |
539 |
can create new OFFLINE or EXTERNAL files, and update |
| 6520 |
18 Aug 14 |
nicklas |
540 |
all types of files. |
| 6520 |
18 Aug 14 |
nicklas |
541 |
</description> |
| 6520 |
18 Aug 14 |
nicklas |
542 |
</about> |
| 6520 |
18 Aug 14 |
nicklas |
543 |
<plugin-class>net.sf.basedb.plugins.batchimport.FileImporter</plugin-class> |
| 6520 |
18 Aug 14 |
nicklas |
544 |
<settings> |
| 6520 |
18 Aug 14 |
nicklas |
545 |
<property name="everyone-use">1</property> |
| 6520 |
18 Aug 14 |
nicklas |
546 |
</settings> |
| 6520 |
18 Aug 14 |
nicklas |
547 |
</plugin-definition> |
| 6520 |
18 Aug 14 |
nicklas |
548 |
|
| 6998 |
04 Nov 15 |
nicklas |
549 |
<plugin-definition id="KitImporter"> |
| 6998 |
04 Nov 15 |
nicklas |
550 |
<about> |
| 6998 |
04 Nov 15 |
nicklas |
551 |
<name>Kit importer</name> |
| 6998 |
04 Nov 15 |
nicklas |
552 |
<description> |
| 6998 |
04 Nov 15 |
nicklas |
553 |
Imports and updates kit items in a batch. |
| 6998 |
04 Nov 15 |
nicklas |
554 |
</description> |
| 6998 |
04 Nov 15 |
nicklas |
555 |
</about> |
| 6998 |
04 Nov 15 |
nicklas |
556 |
<plugin-class>net.sf.basedb.plugins.batchimport.KitImporter</plugin-class> |
| 6998 |
04 Nov 15 |
nicklas |
557 |
<settings> |
| 6998 |
04 Nov 15 |
nicklas |
558 |
<property name="everyone-use">1</property> |
| 6998 |
04 Nov 15 |
nicklas |
559 |
</settings> |
| 6998 |
04 Nov 15 |
nicklas |
560 |
</plugin-definition> |
| 7747 |
16 Sep 19 |
nicklas |
561 |
|
| 7747 |
16 Sep 19 |
nicklas |
562 |
<plugin-definition id="TagImporter"> |
| 7747 |
16 Sep 19 |
nicklas |
563 |
<about> |
| 7747 |
16 Sep 19 |
nicklas |
564 |
<name>Tag importer</name> |
| 7747 |
16 Sep 19 |
nicklas |
565 |
<description> |
| 7747 |
16 Sep 19 |
nicklas |
566 |
Imports and updates tag items in a batch. |
| 7747 |
16 Sep 19 |
nicklas |
567 |
</description> |
| 7747 |
16 Sep 19 |
nicklas |
568 |
</about> |
| 7747 |
16 Sep 19 |
nicklas |
569 |
<plugin-class>net.sf.basedb.plugins.batchimport.TagImporter</plugin-class> |
| 7747 |
16 Sep 19 |
nicklas |
570 |
</plugin-definition> |
| 6998 |
04 Nov 15 |
nicklas |
571 |
|
| 5612 |
18 Apr 11 |
nicklas |
572 |
<plugin-definition id="BioSourceImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
573 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
574 |
<name>Biosource importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
575 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
576 |
Imports and updates biosources in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
577 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
578 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
579 |
<plugin-class>net.sf.basedb.plugins.batchimport.BioSourceImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
580 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
581 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
582 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
583 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
584 |
|
| 5612 |
18 Apr 11 |
nicklas |
585 |
<plugin-definition id="BioPlateImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
586 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
587 |
<name>Bioplate importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
588 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
589 |
Imports and updates bioplates in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
590 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
591 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
592 |
<plugin-class>net.sf.basedb.plugins.batchimport.BioPlateImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
593 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
594 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
595 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
596 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
597 |
|
| 5612 |
18 Apr 11 |
nicklas |
598 |
<plugin-definition id="SampleImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
599 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
600 |
<name>Sample importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
601 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
602 |
Imports and updates samples in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
603 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
604 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
605 |
<plugin-class>net.sf.basedb.plugins.batchimport.SampleImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
606 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
607 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
608 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
609 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
610 |
|
| 5612 |
18 Apr 11 |
nicklas |
611 |
<plugin-definition id="ExtractImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
612 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
613 |
<name>Extract importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
614 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
615 |
Imports and updates extracts in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
616 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
617 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
618 |
<plugin-class>net.sf.basedb.plugins.batchimport.ExtractImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
619 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
620 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
621 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
622 |
</plugin-definition> |
| 7098 |
07 Mar 16 |
nicklas |
623 |
|
| 7098 |
07 Mar 16 |
nicklas |
624 |
<plugin-definition id="AnnotationTypeImporter"> |
| 7098 |
07 Mar 16 |
nicklas |
625 |
<about> |
| 7098 |
07 Mar 16 |
nicklas |
626 |
<name>Annotation type importer</name> |
| 7098 |
07 Mar 16 |
nicklas |
627 |
<description> |
| 7098 |
07 Mar 16 |
nicklas |
628 |
Imports and updates annotation types in a batch. |
| 7098 |
07 Mar 16 |
nicklas |
629 |
</description> |
| 7098 |
07 Mar 16 |
nicklas |
630 |
</about> |
| 7098 |
07 Mar 16 |
nicklas |
631 |
<plugin-class>net.sf.basedb.plugins.batchimport.AnnotationTypeImporter</plugin-class> |
| 7098 |
07 Mar 16 |
nicklas |
632 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
633 |
|
| 5649 |
30 May 11 |
nicklas |
634 |
<plugin-definition id="PhysicalBioAssayImporter"> |
| 5649 |
30 May 11 |
nicklas |
635 |
<about> |
| 5649 |
30 May 11 |
nicklas |
636 |
<name>Physical bioassay importer</name> |
| 5649 |
30 May 11 |
nicklas |
637 |
<description> |
| 5649 |
30 May 11 |
nicklas |
638 |
Imports and updates physical bioassays in a batch. |
| 5649 |
30 May 11 |
nicklas |
639 |
</description> |
| 5649 |
30 May 11 |
nicklas |
640 |
</about> |
| 5649 |
30 May 11 |
nicklas |
641 |
<plugin-class>net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter</plugin-class> |
| 5649 |
30 May 11 |
nicklas |
642 |
<settings> |
| 5649 |
30 May 11 |
nicklas |
643 |
<property name="everyone-use">1</property> |
| 5649 |
30 May 11 |
nicklas |
644 |
</settings> |
| 5649 |
30 May 11 |
nicklas |
645 |
</plugin-definition> |
| 5649 |
30 May 11 |
nicklas |
646 |
|
| 5696 |
12 Aug 11 |
nicklas |
647 |
<plugin-definition id="DerivedBioAssayImporter"> |
| 5696 |
12 Aug 11 |
nicklas |
648 |
<about> |
| 5696 |
12 Aug 11 |
nicklas |
649 |
<name>Derived bioassay importer</name> |
| 5696 |
12 Aug 11 |
nicklas |
650 |
<description> |
| 5696 |
12 Aug 11 |
nicklas |
651 |
Imports and updates derived bioassays in a batch. |
| 5696 |
12 Aug 11 |
nicklas |
652 |
</description> |
| 5696 |
12 Aug 11 |
nicklas |
653 |
</about> |
| 5696 |
12 Aug 11 |
nicklas |
654 |
<plugin-class>net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter</plugin-class> |
| 5696 |
12 Aug 11 |
nicklas |
655 |
<settings> |
| 5696 |
12 Aug 11 |
nicklas |
656 |
<property name="everyone-use">1</property> |
| 5696 |
12 Aug 11 |
nicklas |
657 |
</settings> |
| 5696 |
12 Aug 11 |
nicklas |
658 |
</plugin-definition> |
| 5696 |
12 Aug 11 |
nicklas |
659 |
|
| 5612 |
18 Apr 11 |
nicklas |
660 |
<plugin-definition id="RawBioAssayImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
661 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
662 |
<name>Raw bioassay importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
663 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
664 |
Imports and updates raw bioassays in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
665 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
666 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
667 |
<plugin-class>net.sf.basedb.plugins.batchimport.RawBioAssayImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
668 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
669 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
670 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
671 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
672 |
|
| 5612 |
18 Apr 11 |
nicklas |
673 |
<plugin-definition id="ArrayDesignImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
674 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
675 |
<name>Array design importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
676 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
677 |
Imports and updates array designs in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
678 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
679 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
680 |
<plugin-class>net.sf.basedb.plugins.batchimport.ArrayDesignImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
681 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
682 |
|
| 5612 |
18 Apr 11 |
nicklas |
683 |
<plugin-definition id="ArrayBatchImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
684 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
685 |
<name>Array batch importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
686 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
687 |
Imports and updates array batches in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
688 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
689 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
690 |
<plugin-class>net.sf.basedb.plugins.batchimport.ArrayBatchImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
691 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
692 |
|
| 5612 |
18 Apr 11 |
nicklas |
693 |
<plugin-definition id="ArraySlideImporter"> |
| 5612 |
18 Apr 11 |
nicklas |
694 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
695 |
<name>Array slide importer</name> |
| 5612 |
18 Apr 11 |
nicklas |
696 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
697 |
Imports and updates array slides in a batch. |
| 5612 |
18 Apr 11 |
nicklas |
698 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
699 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
700 |
<plugin-class>net.sf.basedb.plugins.batchimport.ArraySlideImporter</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
701 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
702 |
|
| 5612 |
18 Apr 11 |
nicklas |
703 |
<plugin-definition id="ExternalProgramExecutor"> |
| 5612 |
18 Apr 11 |
nicklas |
704 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
705 |
<name>External program executor</name> |
| 5612 |
18 Apr 11 |
nicklas |
706 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
707 |
This plug-in is used to export data from BASE to an external |
| 5612 |
18 Apr 11 |
nicklas |
708 |
program, run the program, and import the result back into BASE. |
| 5612 |
18 Apr 11 |
nicklas |
709 |
The export and import format is set by the user but must be a |
| 5612 |
18 Apr 11 |
nicklas |
710 |
format supported by the external program. The export also handles |
| 5612 |
18 Apr 11 |
nicklas |
711 |
the parameters needed to run the external program. |
| 5612 |
18 Apr 11 |
nicklas |
712 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
713 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
714 |
<plugin-class>net.sf.basedb.plugins.executor.ExternalProgramExecutor</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
715 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
716 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
717 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
718 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
719 |
|
| 5612 |
18 Apr 11 |
nicklas |
720 |
<plugin-definition id="BfsExporterSupport"> |
| 5612 |
18 Apr 11 |
nicklas |
721 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
722 |
<name>BFS exporter for the ExternalProgramExecutor</name> |
| 5612 |
18 Apr 11 |
nicklas |
723 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
724 |
Support plug-in for the external program executor that |
| 5612 |
18 Apr 11 |
nicklas |
725 |
exports data to the external program in BFS format. This |
| 5612 |
18 Apr 11 |
nicklas |
726 |
plug-in can't be used as a standalone plug-in. |
| 5612 |
18 Apr 11 |
nicklas |
727 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
728 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
729 |
<plugin-class>net.sf.basedb.plugins.executor.BfsExporterSupport</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
730 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
731 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
732 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
733 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
734 |
|
| 5612 |
18 Apr 11 |
nicklas |
735 |
<plugin-definition id="BfsImporterSupport"> |
| 5612 |
18 Apr 11 |
nicklas |
736 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
737 |
<name>BFS importer for the ExternalProgramExecutor</name> |
| 5612 |
18 Apr 11 |
nicklas |
738 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
739 |
Support plug-in for the external program executor that |
| 5612 |
18 Apr 11 |
nicklas |
740 |
imports BFS formatted data from the external program to |
| 5612 |
18 Apr 11 |
nicklas |
741 |
BASE. This plug-in can't be used as a standalone plug-in. |
| 5612 |
18 Apr 11 |
nicklas |
742 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
743 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
744 |
<plugin-class>net.sf.basedb.plugins.executor.BfsImporterSupport</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
745 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
746 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
747 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
748 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
749 |
|
| 5612 |
18 Apr 11 |
nicklas |
750 |
<plugin-definition id="BaseFileExporterSupport"> |
| 5612 |
18 Apr 11 |
nicklas |
751 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
752 |
<name>BASEFile exporter for the ExternalProgramExecutor</name> |
| 5612 |
18 Apr 11 |
nicklas |
753 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
754 |
Support plug-in for the external program executor that |
| 5612 |
18 Apr 11 |
nicklas |
755 |
exports data to the external program in BASEFile format. |
| 5612 |
18 Apr 11 |
nicklas |
756 |
This plug-in can't be used as a standalone plug-in. |
| 5612 |
18 Apr 11 |
nicklas |
757 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
758 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
759 |
<plugin-class>net.sf.basedb.plugins.executor.BaseFileExporterSupport</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
760 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
761 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
762 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
763 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
764 |
|
| 5612 |
18 Apr 11 |
nicklas |
765 |
<plugin-definition id="BaseFileImporterSupport"> |
| 5612 |
18 Apr 11 |
nicklas |
766 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
767 |
<name>BASEfile importer for the ExternalProgramExecutor</name> |
| 5612 |
18 Apr 11 |
nicklas |
768 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
769 |
Support plug-in for the external program executor that |
| 5612 |
18 Apr 11 |
nicklas |
770 |
imports BASEfile formatted data from the external program |
| 5612 |
18 Apr 11 |
nicklas |
771 |
to BASE. This plug-in can't be used as a standalone plug-in. |
| 5612 |
18 Apr 11 |
nicklas |
772 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
773 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
774 |
<plugin-class>net.sf.basedb.plugins.executor.BaseFileImporterSupport</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
775 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
776 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
777 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
778 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
779 |
|
| 5612 |
18 Apr 11 |
nicklas |
780 |
<plugin-definition id="FileOnlyImporterSupport"> |
| 5612 |
18 Apr 11 |
nicklas |
781 |
<about> |
| 5612 |
18 Apr 11 |
nicklas |
782 |
<name>File-only importer for the ExternalProgramExecutor</name> |
| 5612 |
18 Apr 11 |
nicklas |
783 |
<description> |
| 5612 |
18 Apr 11 |
nicklas |
784 |
Support plug-in for the external program executor that |
| 5612 |
18 Apr 11 |
nicklas |
785 |
uploads all created files to BASE and attaches them to |
| 5612 |
18 Apr 11 |
nicklas |
786 |
a child bioassay set. This plug-in can't be used as a |
| 5612 |
18 Apr 11 |
nicklas |
787 |
standalone plug-in. |
| 5612 |
18 Apr 11 |
nicklas |
788 |
</description> |
| 5612 |
18 Apr 11 |
nicklas |
789 |
</about> |
| 5612 |
18 Apr 11 |
nicklas |
790 |
<plugin-class>net.sf.basedb.plugins.executor.FileOnlyImporterSupport</plugin-class> |
| 5612 |
18 Apr 11 |
nicklas |
791 |
<settings> |
| 5612 |
18 Apr 11 |
nicklas |
792 |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
793 |
</settings> |
| 5612 |
18 Apr 11 |
nicklas |
794 |
</plugin-definition> |
| 5612 |
18 Apr 11 |
nicklas |
795 |
|
| 5759 |
26 Sep 11 |
nicklas |
796 |
<plugin-definition id="GtfReporterImporter"> |
| 5759 |
26 Sep 11 |
nicklas |
797 |
<about> |
| 5759 |
26 Sep 11 |
nicklas |
798 |
<name>GTF reporter importer</name> |
| 5759 |
26 Sep 11 |
nicklas |
799 |
<description> |
| 5764 |
27 Sep 11 |
nicklas |
800 |
Creates reporters and reporter lists from GTF (Gene transfer format) |
| 5770 |
29 Sep 11 |
nicklas |
801 |
files. The default configuration uses the transcript_id+seqname value |
| 5770 |
29 Sep 11 |
nicklas |
802 |
as the reporter id and name, and gene_id as "symbol". This can |
| 5759 |
26 Sep 11 |
nicklas |
803 |
be changed by user configurations. For example, to use the gene_id |
| 5759 |
26 Sep 11 |
nicklas |
804 |
instead or to add prefixes to the id values. The importer |
| 5759 |
26 Sep 11 |
nicklas |
805 |
builds on the regular reporter importer and performs on-the-fly |
| 5759 |
26 Sep 11 |
nicklas |
806 |
transformation of GTF attributes to a completely column-based format. |
| 5759 |
26 Sep 11 |
nicklas |
807 |
</description> |
| 5759 |
26 Sep 11 |
nicklas |
808 |
</about> |
| 5759 |
26 Sep 11 |
nicklas |
809 |
<plugin-class>net.sf.basedb.plugins.gtf.GtfReporterImporter</plugin-class> |
| 5759 |
26 Sep 11 |
nicklas |
810 |
<settings> |
| 5759 |
26 Sep 11 |
nicklas |
811 |
<property name="everyone-use">1</property> |
| 5759 |
26 Sep 11 |
nicklas |
812 |
</settings> |
| 5759 |
26 Sep 11 |
nicklas |
813 |
</plugin-definition> |
| 5759 |
26 Sep 11 |
nicklas |
814 |
|
| 5764 |
27 Sep 11 |
nicklas |
815 |
<plugin-definition id="GtfReporterMapImporter"> |
| 5764 |
27 Sep 11 |
nicklas |
816 |
<about> |
| 5764 |
27 Sep 11 |
nicklas |
817 |
<name>GTF reporter map importer</name> |
| 5764 |
27 Sep 11 |
nicklas |
818 |
<description> |
| 5764 |
27 Sep 11 |
nicklas |
819 |
Maps reporters to array design features from GTF files. The default |
| 5764 |
27 Sep 11 |
nicklas |
820 |
implementation use the transcript_id as both the feature id and |
| 5764 |
27 Sep 11 |
nicklas |
821 |
reporter id, but this can be changed by user configuration. For |
| 5764 |
27 Sep 11 |
nicklas |
822 |
example, to use the gene_id instead or to add prefixes to the id |
| 5764 |
27 Sep 11 |
nicklas |
823 |
values. The importer build on the regular reporter map importer |
| 5764 |
27 Sep 11 |
nicklas |
824 |
and perform on-the-fly transformation of GTF attributes to a |
| 5764 |
27 Sep 11 |
nicklas |
825 |
completely column-based format. |
| 5764 |
27 Sep 11 |
nicklas |
826 |
</description> |
| 5764 |
27 Sep 11 |
nicklas |
827 |
</about> |
| 5764 |
27 Sep 11 |
nicklas |
828 |
<plugin-class>net.sf.basedb.plugins.gtf.GtfReporterMapImporter</plugin-class> |
| 5764 |
27 Sep 11 |
nicklas |
829 |
</plugin-definition> |
| 5764 |
27 Sep 11 |
nicklas |
830 |
|
| 5878 |
17 Nov 11 |
nicklas |
831 |
<plugin-definition id="CloneReportersPlugin"> |
| 5878 |
17 Nov 11 |
nicklas |
832 |
<about> |
| 5878 |
17 Nov 11 |
nicklas |
833 |
<name>Clone reporters</name> |
| 5878 |
17 Nov 11 |
nicklas |
834 |
<description> |
| 5878 |
17 Nov 11 |
nicklas |
835 |
Clone reporter annotations to a per-experiment storage in the |
| 5878 |
17 Nov 11 |
nicklas |
836 |
dynamic database. The cloned table contains only those reporters that |
| 5878 |
17 Nov 11 |
nicklas |
837 |
have been used in the experiment and it is also possible to select |
| 5878 |
17 Nov 11 |
nicklas |
838 |
a subset of all available reporter annotations (eg. by a template). |
| 5878 |
17 Nov 11 |
nicklas |
839 |
After the cloning operation all tools/plug-ins working on the experiment |
| 5878 |
17 Nov 11 |
nicklas |
840 |
will use the cloned annotations which protects the analysis from accidental |
| 5878 |
17 Nov 11 |
nicklas |
841 |
updates to the main reporter annotations. The cloned reporter annotations |
| 5878 |
17 Nov 11 |
nicklas |
842 |
can be removed and/or updated at any time. |
| 5878 |
17 Nov 11 |
nicklas |
843 |
</description> |
| 5878 |
17 Nov 11 |
nicklas |
844 |
</about> |
| 5878 |
17 Nov 11 |
nicklas |
845 |
<plugin-class>net.sf.basedb.plugins.CloneReportersPlugin</plugin-class> |
| 5878 |
17 Nov 11 |
nicklas |
846 |
<settings> |
| 5878 |
17 Nov 11 |
nicklas |
847 |
<property name="everyone-use">1</property> |
| 5878 |
17 Nov 11 |
nicklas |
848 |
</settings> |
| 5878 |
17 Nov 11 |
nicklas |
849 |
</plugin-definition> |
| 5878 |
17 Nov 11 |
nicklas |
850 |
|
| 5610 |
15 Apr 11 |
nicklas |
851 |
<!-- |
| 5610 |
15 Apr 11 |
nicklas |
<plugin-definition id=""> |
| 5610 |
15 Apr 11 |
nicklas |
<about> |
| 5610 |
15 Apr 11 |
nicklas |
<name></name> |
| 5610 |
15 Apr 11 |
nicklas |
<description> |
| 5610 |
15 Apr 11 |
nicklas |
</description> |
| 5610 |
15 Apr 11 |
nicklas |
</about> |
| 5610 |
15 Apr 11 |
nicklas |
<plugin-class>net.sf.basedb.plugins.</plugin-class> |
| 5610 |
15 Apr 11 |
nicklas |
<settings> |
| 5610 |
15 Apr 11 |
nicklas |
<property name="everyone-use">1</property> |
| 5612 |
18 Apr 11 |
nicklas |
<property name="immediate-execution">1</property> |
| 5610 |
15 Apr 11 |
nicklas |
</settings> |
| 5610 |
15 Apr 11 |
nicklas |
</plugin-definition> |
| 5610 |
15 Apr 11 |
nicklas |
864 |
--> |
| 5610 |
15 Apr 11 |
nicklas |
865 |
|
| 5610 |
15 Apr 11 |
nicklas |
866 |
|
| 5610 |
15 Apr 11 |
nicklas |
867 |
</extensions> |