source: trunk/src/plugins/core/core-plugins.xml @ 5614

Last change on this file since 5614 was 5612, checked in by Nicklas Nordborg, 11 years ago

References #1592: Unified installation procedure for plug-ins, extensions and more...

Moved remaining core plug-in definitions to the xml file. Removed the getAbout() method from all plugins.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 23.3 KB
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1<?xml version="1.0" encoding="UTF-8" ?>
2<!--
3  $Id: core-plugins.xml 5612 2011-04-18 11:23:57Z nicklas $
4
5  Copyright (C) Nicklas Nordborg
6
7  This file is part of BASE - BioArray Software Environment.
8  Available at http://base.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 BASE. If not, see <http://www.gnu.org/licenses/>.
22-->
23<extensions
24  xmlns="http://base.thep.lu.se/extensions.xsd"
25  id-base="net.sf.basedb.plugins."
26  >
27  <about>
28    <version>3.0</version>
29    <name>Core plug-in definitions</name>
30    <description>
31      This file contains information about all plug-ins
32      that are shipped as part of the BASE core.
33    </description>
34    <copyright>BASE development team</copyright>
35    <email>basedb-users@lists.sourceforge.net</email>
36    <url>http://base.thep.lu.se/</url>
37  </about>
38 
39  <plugin-definition id="Base1PluginExecuter">
40    <about>
41      <name>BASE 1 plug-in executor</name>
42      <description>
43        This plug-in simulates the plug-in runner from Base 1.2
44        to enable old plug-ins to be executed.
45      </description>
46    </about>
47    <plugin-class>net.sf.basedb.plugins.Base1PluginExecuter</plugin-class>
48    <settings>
49      <property name="everyone-use">1</property>
50    </settings>
51  </plugin-definition>
52
53  <plugin-definition id="BaseFileExporter">
54    <about>
55      <name>BASEfile exporter</name>
56      <description>
57        Exports bioassay set data to serial or matrix BASEfile format.
58      </description>
59    </about>
60    <plugin-class>net.sf.basedb.plugins.BaseFileExporterPlugin</plugin-class>
61    <settings>
62      <property name="everyone-use">1</property>
63      <property name="immediate-execution">1</property>
64    </settings>
65  </plugin-definition>
66
67  <plugin-definition id="BfsExporter">
68    <about>
69      <name>BFS exporter</name>
70      <description>
71        Exports bioassay set data to BFS format.
72      </description>
73    </about>
74    <plugin-class>net.sf.basedb.plugins.BfsExporterPlugin</plugin-class>
75    <settings>
76      <property name="everyone-use">1</property>
77      <property name="immediate-execution">1</property>
78    </settings>
79  </plugin-definition>
80
81  <plugin-definition id="FormulaFilter">
82    <about>
83      <name>Formula filter</name>
84      <description>
85        This plugin is used to filter a bioassay set, creating a new bioassay set with fewer spots in it.
86        The filter is based on expressions entered by the user, which are parsed with the JEP package.
87        Thus, the functionality of this plugin is very flexible.
88      </description>
89    </about>
90    <plugin-class>net.sf.basedb.plugins.FormulaFilter</plugin-class>
91    <settings>
92      <property name="everyone-use">1</property>
93    </settings>
94  </plugin-definition>
95
96  <plugin-definition id="HelpExporter">
97    <about>
98      <name>Help texts exporter</name>
99      <description>
100        This plugin is used to export a client applications help texts to a XML-file. The help
101        texts can later be imported by the corresponding import plugin.
102      </description>
103    </about>
104    <plugin-class>net.sf.basedb.plugins.HelpExporter</plugin-class>
105    <settings>
106      <property name="immediate-execution">1</property>
107    </settings>
108  </plugin-definition>
109
110  <plugin-definition id="HelpImporter">
111    <about>
112      <name>Help texts importer</name>
113      <description>
114        This plugin is used to import help texts from a XML-file to BASE.
115      </description>
116    </about>
117    <plugin-class>net.sf.basedb.plugins.HelpImporter</plugin-class>
118  </plugin-definition>
119 
120  <plugin-definition id="IntensityCalculator">
121    <about>
122      <name>Formula intensity calculator</name>
123      <description>
124        This plugin is used to calculate intensities from raw data creating an initial root bioassay set.
125        The intensities are calculated using Formula objects registered for the experiment's raw data type.
126        Thus, the functionality of this plugin can be extended by adding more formula objects to the database.
127      </description>
128    </about>
129    <plugin-class>net.sf.basedb.plugins.IntensityCalculatorPlugin</plugin-class>
130    <settings>
131      <property name="everyone-use">1</property>
132    </settings>
133  </plugin-definition>
134 
135  <plugin-definition id="JepExtraValueCalculator">
136    <about>
137      <name>Formula extra value calculator</name>
138      <description>
139        This plugin is used to calculate extra values for a bioassay set using
140        formulas entered by the user.
141      </description>
142    </about>
143    <plugin-class>net.sf.basedb.plugins.JepExtraValueCalculator</plugin-class>
144    <settings>
145      <property name="everyone-use">1</property>
146    </settings>
147  </plugin-definition>
148 
149  <plugin-definition id="JepIntensityTransformer">
150    <about>
151      <name>Formula intensity transformer</name>
152      <description>
153        This plugin is used to transform the intensities of a bioassayset using
154        formulas entered by the user.
155      </description>
156    </about>
157    <plugin-class>net.sf.basedb.plugins.JepIntensityTransformer</plugin-class>
158    <settings>
159      <property name="everyone-use">1</property>
160    </settings>
161  </plugin-definition>
162 
163  <plugin-definition id="LowessNormalization">
164    <about>
165      <name>Normalization: Lowess</name>
166      <description>
167        This is an efficient java implementation by Johan Enell
168        of the LOWESS algorithm. It provides intensity-based normalization.
169        The window size is the only smoothness parameter available
170        in this implementation. The higher it is, the smoother the
171        function will be. Tweaking the other two parameters allows
172        you to gain performance at the price of a small precision loss.
173        The default values are usually good.
174       
175        This plug-in supports the use of reporter lists for exclusion of
176        reporters in the LOWESS calculation. The option to select reporter
177        lists is visible for users with access to defined reporter lists.
178
179        For more info on LOWESS:
180        Cleveland WS, Devlin SJ: Locally weighted regression: an
181        approach to regression analysis by local fitting. J Am Stat
182        Assoc 1988, 83:596-610.
183        Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP:
184        Normalization for cDNA microarray data: a robust composite
185        method addressing single and multiple slide systematic
186        variation. Nucleic Acids Res 2002, 30:e15.
187      </description>
188    </about>
189    <plugin-class>net.sf.basedb.plugins.LowessNormalization</plugin-class>
190    <settings>
191      <property name="everyone-use">1</property>
192    </settings>
193  </plugin-definition>
194 
195  <plugin-definition id="MedianRatioNormalization">
196    <about>
197      <name>Normalization: Median ratio</name>
198      <description>
199        This normalizer behaves differently depending on the array type.
200
201        1-channel arrays: Intensities are changed in two different ways
202        depending on user selection.
203        a) For absolute intensity data the intensities should be scaled
204        with the median intensity, Inew=Iold/Imedian, such that resulting
205        median is 1.
206        b) For log intensity data the intensities should be subtracted with
207        the median intensity, log(Inew)=log(Iold)-log(Imedian), such that
208        resulting median is 0.
209
210        2-channel arrays: Intensities are scaled such that their geometric
211        mean (sqrt(i1 * i2)) is kept constant but the median of their ratios
212        (i1/i2) is shifted to 1.
213
214        All array types: The user can optionally exclude spots; all spots
215        with at least one intensity below a user selectable threshold are
216        removed. User selectable (low/high intensity) fractions of the
217        remaining spots are ignored in median calculation.
218      </description>
219    </about>
220    <plugin-class>net.sf.basedb.plugins.MedianRatioNormalization</plugin-class>
221    <settings>
222      <property name="everyone-use">1</property>
223    </settings>
224  </plugin-definition>
225
226  <plugin-definition id="PlateFlatFileImporter">
227    <about>
228      <name>Plate importer</name>
229      <description>
230        This plugin is used to import plates from a simple flat file.
231      </description>
232    </about>
233    <plugin-class>net.sf.basedb.plugins.PlateFlatFileImporter</plugin-class>
234  </plugin-definition>
235
236  <plugin-definition id="PlateMappingExporter">
237    <about>
238      <name>Plate mapping exporter</name>
239      <description>
240        This plugin is used to export plate mappings, which maps the
241        coordinates of one or more source plates to coordinates on
242        one or more destination plates. Use the "Plate mapping importer"
243        to import the files produced by this plugin.
244      </description>
245    </about>
246    <plugin-class>net.sf.basedb.plugins.PlateMappingExporter</plugin-class>
247    <settings>
248      <property name="immediate-execution">1</property>
249    </settings>
250  </plugin-definition>
251
252  <plugin-definition id="PlateMappingImporter">
253    <about>
254      <name>Plate mapping importer</name>
255      <description>
256        This plugin is used to import plate mapping files created
257        by the "Plate mapping exporter". The file maps the
258        coordinates of one or more source plates to coordinates
259        on one or more destination plates.
260      </description>
261    </about>
262    <plugin-class>net.sf.basedb.plugins.PlateMappingImporter</plugin-class>
263  </plugin-definition>
264
265  <plugin-definition id="RawDataFlatFileImporter">
266    <about>
267      <name>Raw data importer</name>
268      <description>
269        This plugin is used to import raw data from a simple text file.
270      </description>
271    </about>
272    <plugin-class>net.sf.basedb.plugins.RawDataFlatFileImporter</plugin-class>
273    <settings>
274      <property name="everyone-use">1</property>
275    </settings>
276  </plugin-definition>
277
278  <plugin-definition id="ReporterFlatFileImporter">
279    <about>
280      <name>Reporter importer</name>
281      <description>
282        This plugin is used to import reporters from a simple flat file.
283      </description>
284    </about>
285    <plugin-class>net.sf.basedb.plugins.ReporterFlatFileImporter</plugin-class>
286    <settings>
287      <property name="everyone-use">1</property>
288    </settings>
289  </plugin-definition>
290
291  <plugin-definition id="ReporterMapFlatFileImporter">
292    <about>
293      <name>Reporter map importer</name>
294      <description>
295        This plugin is used to import features to an ArrayDesign from a simple flat file.
296      </description>
297    </about>
298    <plugin-class>net.sf.basedb.plugins.ReporterMapFlatFileImporter</plugin-class>
299  </plugin-definition>
300
301  <plugin-definition id="SpotImageCreator">
302    <about>
303      <name>Spot images creator</name>
304      <description>
305        Converts a full-size scanned image into smaller preview jpg images for each individual spot.
306      </description>
307    </about>
308    <plugin-class>net.sf.basedb.plugins.SpotImageCreator</plugin-class>
309    <settings>
310      <property name="everyone-use">1</property>
311    </settings>
312  </plugin-definition>
313
314  <plugin-definition id="ZipFileUnpacker">
315    <about>
316      <name>ZIP file unpacker</name>
317      <description>
318        This plugin unpacks a zip file on the BASE file system.
319        It supports zip and jar files.
320      </description>
321    </about>
322    <plugin-class>net.sf.basedb.plugins.ZipFileUnpacker</plugin-class>
323    <settings>
324      <property name="everyone-use">1</property>
325      <property name="immediate-execution">1</property>
326    </settings>
327  </plugin-definition>
328
329  <plugin-definition id="TarFileUnpacker">
330    <about>
331      <name>TAR file unpacker</name>
332      <description>
333        This plugin unpacks a tar file on the BASE file system.
334        It also supports TAR files compressed with the GZIP and
335        BZIP algorithms.
336      </description>
337    </about>
338    <plugin-class>net.sf.basedb.plugins.TarFileUnpacker</plugin-class>
339    <settings>
340      <property name="everyone-use">1</property>
341      <property name="immediate-execution">1</property>
342    </settings>
343  </plugin-definition>
344
345  <plugin-definition id="PluginConfigurationExporter">
346    <about>
347      <name>Plugin configuration exporter</name>
348      <description>
349        This plugin is used to export selected plugin configurations
350        to an XML-file. The plugin configurations can later be imported
351        by the "Plugin configuration importer".
352      </description>
353    </about>
354    <plugin-class>net.sf.basedb.plugins.PluginConfigurationExporter</plugin-class>
355    <settings>
356      <property name="everyone-use">1</property>
357      <property name="immediate-execution">1</property>
358    </settings>
359  </plugin-definition>
360
361  <plugin-definition id="PluginConfigurationImporter">
362    <about>
363      <name>Plugin configuration importer</name>
364      <description>
365        This plugin is used to import configuration for a BASE plugin from
366        an XML-file created by the "Plugin configuration exporter".
367      </description>
368    </about>
369    <plugin-class>net.sf.basedb.plugins.PluginConfigurationImporter</plugin-class>
370  </plugin-definition>
371
372  <plugin-definition id="CdfFileReporterImporter">
373    <about>
374      <name>Affymetrix CDF probeset importer</name>
375      <description>
376        This plug-in is used to import probesets from an Affymetrix
377        CDF file as reporters. It can be used in import mode from the
378        reporter list view and from the array design view and in
379        verification mode from the array design view. The plug-in can
380        only set the name and ID of the reporters, since the CDF file
381        doesn't contains any annotation information. Probesets already
382        in BASE will not be affected by the import.
383      </description>
384    </about>
385    <plugin-class>net.sf.basedb.plugins.CdfFileReporterImporter</plugin-class>
386  </plugin-definition>
387
388  <plugin-definition id="PackedFileExporter">
389    <about>
390      <name>Packed file exporter</name>
391      <description>
392        This plugin is used to pack one or more files/directories
393        into a single file. Items should be selected before starting
394        the plug-in and they must all be located in the same parent
395        directory. The compressed file can be downloaded immediately
396        or stored in the BASE file system. The user can choose to have
397        the selected files and directories removed after they've been
398        packed.
399      </description>
400    </about>
401    <plugin-class>net.sf.basedb.plugins.PackedFileExporter</plugin-class>
402    <settings>
403      <property name="everyone-use">1</property>
404      <property name="immediate-execution">1</property>
405    </settings>
406  </plugin-definition>
407
408  <plugin-definition id="AnnotationFlatFileImporter">
409    <about>
410      <name>Annotation importer</name>
411      <description>
412        This plugin is used to import annotations to any annotatable items.
413      </description>
414    </about>
415    <plugin-class>net.sf.basedb.plugins.AnnotationFlatFileImporter</plugin-class>
416    <settings>
417      <property name="everyone-use">1</property>
418    </settings>
419  </plugin-definition>
420
421  <plugin-definition id="IlluminaRawDataImporter">
422    <about>
423      <name>Illumina raw data importer</name>
424      <description>
425        This plugin is used to import raw data from Illumina data files.
426        The plug-in can be executed from the list of raw bioassays and
427        will then only create new raw bioassays, or from within an experiment,
428        in which case the imported data will also be associated with
429        the experiment.
430      </description>
431    </about>
432    <plugin-class>net.sf.basedb.plugins.IlluminaRawDataImporter</plugin-class>
433    <settings>
434      <property name="everyone-use">1</property>
435    </settings>
436  </plugin-definition>
437
438  <plugin-definition id="GalExporter">
439    <about>
440      <name>GAL exporter</name>
441      <description>
442        This plugin exports the features of an array design to a
443        GAL file. The plugin only works for array designs that
444        has features in the database and is disabled for other
445        array designs.
446      </description>
447    </about>
448    <plugin-class>net.sf.basedb.plugins.GalExporter</plugin-class>
449    <settings>
450      <property name="everyone-use">1</property>
451      <property name="immediate-execution">1</property>
452    </settings>
453  </plugin-definition>
454
455  <plugin-definition id="ManualTransformCreator">
456    <about>
457      <name>Manual transform</name>
458      <description>
459        This plug-in allows a user to manually register an external
460        analysis procedure that has happened outside of BASE and to
461        register the parameters used and the output files that was
462        generated. Before this plug-in can be used a configuration
463        that represents the external tool must be created. The
464        configuration will be used to register possible parameters
465        and output files.
466      </description>
467    </about>
468    <plugin-class>net.sf.basedb.plugins.ManualTransformCreator</plugin-class>
469    <settings>
470      <property name="everyone-use">1</property>
471      <property name="immediate-execution">1</property>
472    </settings>
473  </plugin-definition>
474
475  <plugin-definition id="BioSourceImporter">
476    <about>
477      <name>Biosource importer</name>
478      <description>
479        Imports and updates biosources in a batch.
480      </description>
481    </about>
482    <plugin-class>net.sf.basedb.plugins.batchimport.BioSourceImporter</plugin-class>
483    <settings>
484      <property name="everyone-use">1</property>
485    </settings>
486  </plugin-definition>
487 
488  <plugin-definition id="BioPlateImporter">
489    <about>
490      <name>Bioplate importer</name>
491      <description>
492        Imports and updates bioplates in a batch.
493      </description>
494    </about>
495    <plugin-class>net.sf.basedb.plugins.batchimport.BioPlateImporter</plugin-class>
496    <settings>
497      <property name="everyone-use">1</property>
498    </settings>
499  </plugin-definition>
500
501  <plugin-definition id="SampleImporter">
502    <about>
503      <name>Sample importer</name>
504      <description>
505        Imports and updates samples in a batch.
506      </description>
507    </about>
508    <plugin-class>net.sf.basedb.plugins.batchimport.SampleImporter</plugin-class>
509    <settings>
510      <property name="everyone-use">1</property>
511    </settings>
512  </plugin-definition>
513
514  <plugin-definition id="ExtractImporter">
515    <about>
516      <name>Extract importer</name>
517      <description>
518        Imports and updates extracts in a batch.
519      </description>
520    </about>
521    <plugin-class>net.sf.basedb.plugins.batchimport.ExtractImporter</plugin-class>
522    <settings>
523      <property name="everyone-use">1</property>
524    </settings>
525  </plugin-definition>
526
527  <plugin-definition id="LabeledExtractImporter">
528    <about>
529      <name>Labeled extract importer</name>
530      <description>
531        Imports and updates labeled extracts in a batch.
532      </description>
533    </about>
534    <plugin-class>net.sf.basedb.plugins.batchimport.LabeledExtractImporter</plugin-class>
535    <settings>
536      <property name="everyone-use">1</property>
537    </settings>
538  </plugin-definition>
539
540  <plugin-definition id="HybridizationImporter">
541    <about>
542      <name>Hybridization importer</name>
543      <description>
544        Imports and updates hybridizations in a batch.
545      </description>
546    </about>
547    <plugin-class>net.sf.basedb.plugins.batchimport.HybridizationImporter</plugin-class>
548    <settings>
549      <property name="everyone-use">1</property>
550    </settings>
551  </plugin-definition>
552
553  <plugin-definition id="ScanImporter">
554    <about>
555      <name>Scan importer</name>
556      <description>
557        Imports and updates scans in a batch.
558      </description>
559    </about>
560    <plugin-class>net.sf.basedb.plugins.batchimport.ScanImporter</plugin-class>
561    <settings>
562      <property name="everyone-use">1</property>
563    </settings>
564  </plugin-definition>
565
566  <plugin-definition id="RawBioAssayImporter">
567    <about>
568      <name>Raw bioassay importer</name>
569      <description>
570        Imports and updates raw bioassays in a batch.
571      </description>
572    </about>
573    <plugin-class>net.sf.basedb.plugins.batchimport.RawBioAssayImporter</plugin-class>
574    <settings>
575      <property name="everyone-use">1</property>
576    </settings>
577  </plugin-definition>
578
579  <plugin-definition id="ArrayDesignImporter">
580    <about>
581      <name>Array design importer</name>
582      <description>
583        Imports and updates array designs in a batch.
584      </description>
585    </about>
586    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayDesignImporter</plugin-class>
587  </plugin-definition>
588
589  <plugin-definition id="ArrayBatchImporter">
590    <about>
591      <name>Array batch importer</name>
592      <description>
593        Imports and updates array batches in a batch.
594      </description>
595    </about>
596    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayBatchImporter</plugin-class>
597  </plugin-definition>
598
599  <plugin-definition id="ArraySlideImporter">
600    <about>
601      <name>Array slide importer</name>
602      <description>
603        Imports and updates array slides in a batch.
604      </description>
605    </about>
606    <plugin-class>net.sf.basedb.plugins.batchimport.ArraySlideImporter</plugin-class>
607  </plugin-definition>
608
609  <plugin-definition id="ExternalProgramExecutor">
610    <about>
611      <name>External program executor</name>
612      <description>
613        This plug-in is used to export data from BASE to an external
614        program, run the program, and import the result back into BASE.
615        The export and import format is set by the user but must be a
616        format supported by the external program. The export also handles
617        the parameters needed to run the external program.
618      </description>
619    </about>
620    <plugin-class>net.sf.basedb.plugins.executor.ExternalProgramExecutor</plugin-class>
621    <settings>
622      <property name="everyone-use">1</property>
623    </settings>
624  </plugin-definition>
625
626  <plugin-definition id="BfsExporterSupport">
627    <about>
628      <name>BFS exporter for the ExternalProgramExecutor</name>
629      <description>
630        Support plug-in for the external program executor that
631        exports data to the external program in BFS format. This
632        plug-in can't be used as a standalone plug-in.
633      </description>
634    </about>
635    <plugin-class>net.sf.basedb.plugins.executor.BfsExporterSupport</plugin-class>
636    <settings>
637      <property name="everyone-use">1</property>
638    </settings>
639  </plugin-definition>
640
641  <plugin-definition id="BfsImporterSupport">
642    <about>
643      <name>BFS importer for the ExternalProgramExecutor</name>
644      <description>
645        Support plug-in for the external program executor that
646        imports BFS formatted data from the external program to
647        BASE. This plug-in can't be used as a standalone plug-in.
648      </description>
649    </about>
650    <plugin-class>net.sf.basedb.plugins.executor.BfsImporterSupport</plugin-class>
651    <settings>
652      <property name="everyone-use">1</property>
653    </settings>
654  </plugin-definition>
655
656  <plugin-definition id="BaseFileExporterSupport">
657    <about>
658      <name>BASEFile exporter for the ExternalProgramExecutor</name>
659      <description>
660        Support plug-in for the external program executor that
661        exports data to the external program in BASEFile format.
662        This plug-in can't be used as a standalone plug-in.
663      </description>
664    </about>
665    <plugin-class>net.sf.basedb.plugins.executor.BaseFileExporterSupport</plugin-class>
666    <settings>
667      <property name="everyone-use">1</property>
668    </settings>
669  </plugin-definition>
670
671  <plugin-definition id="BaseFileImporterSupport">
672    <about>
673      <name>BASEfile importer for the ExternalProgramExecutor</name>
674      <description>
675        Support plug-in for the external program executor that
676        imports BASEfile formatted data from the external program
677        to BASE. This plug-in can't be used as a standalone plug-in.
678      </description>
679    </about>
680    <plugin-class>net.sf.basedb.plugins.executor.BaseFileImporterSupport</plugin-class>
681    <settings>
682      <property name="everyone-use">1</property>
683    </settings>
684  </plugin-definition>
685
686  <plugin-definition id="FileOnlyImporterSupport">
687    <about>
688      <name>File-only importer for the ExternalProgramExecutor</name>
689      <description>
690        Support plug-in for the external program executor that
691        uploads all created files to BASE and attaches them to
692        a child bioassay set. This plug-in can't be used as a
693        standalone plug-in.
694      </description>
695    </about>
696    <plugin-class>net.sf.basedb.plugins.executor.FileOnlyImporterSupport</plugin-class>
697    <settings>
698      <property name="everyone-use">1</property>
699    </settings>
700  </plugin-definition>
701
702  <!--
703  <plugin-definition id="">
704    <about>
705      <name></name>
706      <description>
707      </description>
708    </about>
709    <plugin-class>net.sf.basedb.plugins.</plugin-class>
710    <settings>
711      <property name="everyone-use">1</property>
712      <property name="immediate-execution">1</property>
713    </settings>
714  </plugin-definition>
715  -->
716
717
718</extensions>
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