source: trunk/src/plugins/core/core-plugins.xml @ 7098

Last change on this file since 7098 was 7098, checked in by Nicklas Nordborg, 6 years ago

References #1987: Batch importer for annotation types

First version of the annotation type importer. So far it can only create new annotation types and set the name and description.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 29.7 KB
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1<?xml version="1.0" encoding="UTF-8" ?>
2<!--
3  $Id: core-plugins.xml 7098 2016-03-07 10:49:45Z 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 source data.
203        a) For absolute intensity data the intensities are scaled
204        with the median intensity, Inew=Iold/Imedian, such that resulting
205        median is 1.
206        b) For log intensity data the intensities are 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="GzipFileUnpacker">
346    <about>
347      <name>GZip file unpacker</name>
348      <description>
349        This plugin unpacks gzip compressed files to the BASE file system.
350      </description>
351    </about>
352    <plugin-class>net.sf.basedb.plugins.GzipFileUnpacker</plugin-class>
353    <settings>
354      <property name="everyone-use">1</property>
355      <property name="immediate-execution">1</property>
356    </settings>
357  </plugin-definition>
358
359  <plugin-definition id="Bzip2FileUnpacker">
360    <about>
361      <name>BZip2 file unpacker</name>
362      <description>
363        This plugin unpacks BZip2 compressed files to the BASE file system.
364      </description>
365    </about>
366    <plugin-class>net.sf.basedb.plugins.Bzip2FileUnpacker</plugin-class>
367    <settings>
368      <property name="everyone-use">1</property>
369      <property name="immediate-execution">1</property>
370    </settings>
371  </plugin-definition>
372
373
374  <plugin-definition id="PluginConfigurationExporter">
375    <about>
376      <name>Plugin configuration exporter</name>
377      <description>
378        This plugin is used to export selected plugin configurations
379        to an XML-file. The plugin configurations can later be imported
380        by the "Plugin configuration importer".
381      </description>
382    </about>
383    <plugin-class>net.sf.basedb.plugins.PluginConfigurationExporter</plugin-class>
384    <settings>
385      <property name="everyone-use">1</property>
386      <property name="immediate-execution">1</property>
387    </settings>
388  </plugin-definition>
389
390  <plugin-definition id="PluginConfigurationImporter">
391    <about>
392      <name>Plugin configuration importer</name>
393      <description>
394        This plugin is used to import configuration for a BASE plugin from
395        an XML-file created by the "Plugin configuration exporter".
396      </description>
397    </about>
398    <plugin-class>net.sf.basedb.plugins.PluginConfigurationImporter</plugin-class>
399  </plugin-definition>
400
401  <plugin-definition id="PrintMapFlatFileImporter">
402    <about>
403      <name>Print map importer</name>
404      <description>
405        This plugin is used to import arraydesign from a print map.
406      </description>
407    </about>
408    <plugin-class>net.sf.basedb.plugins.PrintMapFlatFileImporter</plugin-class>
409  </plugin-definition>
410
411  <plugin-definition id="CdfFileReporterImporter">
412    <about>
413      <name>Affymetrix CDF probeset importer</name>
414      <description>
415        This plug-in is used to import probesets from an Affymetrix
416        CDF file as reporters. It can be used in import mode from the
417        reporter list view and from the array design view and in
418        verification mode from the array design view. The plug-in can
419        only set the name and ID of the reporters, since the CDF file
420        doesn't contains any annotation information. Probesets already
421        in BASE will not be affected by the import.
422      </description>
423    </about>
424    <plugin-class>net.sf.basedb.plugins.CdfFileReporterImporter</plugin-class>
425  </plugin-definition>
426
427  <plugin-definition id="PackedFileExporter">
428    <about>
429      <name>Packed file exporter</name>
430      <description>
431        This plugin is used to pack one or more files/directories
432        into a single file. Items should be selected before starting
433        the plug-in and they must all be located in the same parent
434        directory. The compressed file can be downloaded immediately
435        or stored in the BASE file system. The user can choose to have
436        the selected files and directories removed after they've been
437        packed.
438      </description>
439    </about>
440    <plugin-class>net.sf.basedb.plugins.PackedFileExporter</plugin-class>
441    <settings>
442      <property name="everyone-use">1</property>
443      <property name="immediate-execution">1</property>
444    </settings>
445  </plugin-definition>
446
447  <plugin-definition id="AnnotationFlatFileImporter">
448    <about>
449      <name>Annotation importer</name>
450      <description>
451        This plugin is used to import annotations to any annotatable items.
452      </description>
453    </about>
454    <plugin-class>net.sf.basedb.plugins.AnnotationFlatFileImporter</plugin-class>
455    <settings>
456      <property name="everyone-use">1</property>
457    </settings>
458  </plugin-definition>
459
460  <plugin-definition id="IlluminaRawDataImporter">
461    <about>
462      <name>Illumina raw data importer</name>
463      <description>
464        This plugin is used to import raw data from Illumina data files.
465        The plug-in can be executed from the list of raw bioassays and
466        will then only create new raw bioassays, or from within an experiment,
467        in which case the imported data will also be associated with
468        the experiment.
469      </description>
470    </about>
471    <plugin-class>net.sf.basedb.plugins.IlluminaRawDataImporter</plugin-class>
472    <settings>
473      <property name="everyone-use">1</property>
474    </settings>
475  </plugin-definition>
476
477  <plugin-definition id="GalExporter">
478    <about>
479      <name>GAL exporter</name>
480      <description>
481        This plugin exports the features of an array design to a
482        GAL file. The plugin only works for array designs that
483        has features in the database and is disabled for other
484        array designs.
485      </description>
486    </about>
487    <plugin-class>net.sf.basedb.plugins.GalExporter</plugin-class>
488    <settings>
489      <property name="everyone-use">1</property>
490      <property name="immediate-execution">1</property>
491    </settings>
492  </plugin-definition>
493
494  <plugin-definition id="ManualTransformCreator">
495    <about>
496      <name>Manual transform</name>
497      <description>
498        This plug-in allows a user to manually register an external
499        analysis procedure that has happened outside of BASE and to
500        register the parameters used and the output files that was
501        generated. Before this plug-in can be used a configuration
502        that represents the external tool must be created. The
503        configuration will be used to register possible parameters
504        and output files.
505      </description>
506    </about>
507    <plugin-class>net.sf.basedb.plugins.ManualTransformCreator</plugin-class>
508    <settings>
509      <property name="everyone-use">1</property>
510      <property name="immediate-execution">1</property>
511    </settings>
512  </plugin-definition>
513
514  <plugin-definition id="ManualDerivedBioAssayCreator">
515    <about>
516      <name>Manual derived bioassay creator</name>
517      <description>
518        This plug-in allows a user to manually register an external
519        analysis procedure that has happened outside of BASE and to
520        register the parameters used and the output files that was
521        generated. Before this plug-in can be used a configuration
522        that represents the external tool must be created. The
523        configuration will be used to register possible parameters
524        and output files.
525      </description>
526    </about>
527    <plugin-class>net.sf.basedb.plugins.ManualDerivedBioAssayCreator</plugin-class>
528    <settings>
529      <property name="everyone-use">1</property>
530      <property name="immediate-execution">1</property>
531    </settings>
532  </plugin-definition>
533
534  <plugin-definition id="FileImporter">
535    <about>
536      <name>File importer</name>
537      <description>
538        Imports and updates files in a batch. The importer
539        can create new OFFLINE or EXTERNAL files, and update
540        all types of files.
541      </description>
542    </about>
543    <plugin-class>net.sf.basedb.plugins.batchimport.FileImporter</plugin-class>
544    <settings>
545      <property name="everyone-use">1</property>
546    </settings>
547  </plugin-definition>
548
549  <plugin-definition id="KitImporter">
550    <about>
551      <name>Kit importer</name>
552      <description>
553        Imports and updates kit items in a batch.
554      </description>
555    </about>
556    <plugin-class>net.sf.basedb.plugins.batchimport.KitImporter</plugin-class>
557    <settings>
558      <property name="everyone-use">1</property>
559    </settings>
560  </plugin-definition>
561
562  <plugin-definition id="BioSourceImporter">
563    <about>
564      <name>Biosource importer</name>
565      <description>
566        Imports and updates biosources in a batch.
567      </description>
568    </about>
569    <plugin-class>net.sf.basedb.plugins.batchimport.BioSourceImporter</plugin-class>
570    <settings>
571      <property name="everyone-use">1</property>
572    </settings>
573  </plugin-definition>
574 
575  <plugin-definition id="BioPlateImporter">
576    <about>
577      <name>Bioplate importer</name>
578      <description>
579        Imports and updates bioplates in a batch.
580      </description>
581    </about>
582    <plugin-class>net.sf.basedb.plugins.batchimport.BioPlateImporter</plugin-class>
583    <settings>
584      <property name="everyone-use">1</property>
585    </settings>
586  </plugin-definition>
587
588  <plugin-definition id="SampleImporter">
589    <about>
590      <name>Sample importer</name>
591      <description>
592        Imports and updates samples in a batch.
593      </description>
594    </about>
595    <plugin-class>net.sf.basedb.plugins.batchimport.SampleImporter</plugin-class>
596    <settings>
597      <property name="everyone-use">1</property>
598    </settings>
599  </plugin-definition>
600
601  <plugin-definition id="ExtractImporter">
602    <about>
603      <name>Extract importer</name>
604      <description>
605        Imports and updates extracts in a batch.
606      </description>
607    </about>
608    <plugin-class>net.sf.basedb.plugins.batchimport.ExtractImporter</plugin-class>
609    <settings>
610      <property name="everyone-use">1</property>
611    </settings>
612  </plugin-definition>
613 
614  <plugin-definition id="AnnotationTypeImporter">
615    <about>
616      <name>Annotation type importer</name>
617      <description>
618        Imports and updates annotation types in a batch.
619      </description>
620    </about>
621    <plugin-class>net.sf.basedb.plugins.batchimport.AnnotationTypeImporter</plugin-class>
622  </plugin-definition>
623
624  <!-- Used for backwards compatibility with older server installations -->
625  <plugin-definition id="LabeledExtractImporter">
626    <about>
627      <name>Labeled extract importer (deprecated)</name>
628      <description>
629        Imports and updates labeled extracts in a batch.
630      </description>
631    </about>
632    <plugin-class>net.sf.basedb.plugins.batchimport.LabeledExtractImporter</plugin-class>
633    <settings>
634      <property name="everyone-use">1</property>
635      <property name="deprecated">1</property>
636    </settings>
637  </plugin-definition>
638
639  <!-- Used for backwards compatibility with older server installations -->
640  <plugin-definition id="HybridizationImporter">
641    <about>
642      <name>Hybridization importer (deprecated)</name>
643      <description>
644        Imports and updates hybridizations in a batch.
645      </description>
646    </about>
647    <plugin-class>net.sf.basedb.plugins.batchimport.HybridizationImporter</plugin-class>
648    <settings>
649      <property name="everyone-use">1</property>
650      <property name="deprecated">1</property>
651    </settings>
652  </plugin-definition>
653
654  <plugin-definition id="PhysicalBioAssayImporter">
655    <about>
656      <name>Physical bioassay importer</name>
657      <description>
658        Imports and updates physical bioassays in a batch.
659      </description>
660    </about>
661    <plugin-class>net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter</plugin-class>
662    <settings>
663      <property name="everyone-use">1</property>
664    </settings>
665  </plugin-definition>
666 
667  <!-- Used for backwards compatibility with older server installations -->
668  <plugin-definition id="ScanImporter">
669    <about>
670      <name>Scan importer (deprecated)</name>
671      <description>
672        Imports and updates scans in a batch.
673      </description>
674    </about>
675    <plugin-class>net.sf.basedb.plugins.batchimport.ScanImporter</plugin-class>
676    <settings>
677      <property name="everyone-use">1</property>
678      <property name="deprecated">1</property>
679    </settings>
680  </plugin-definition>
681 
682  <plugin-definition id="DerivedBioAssayImporter">
683    <about>
684      <name>Derived bioassay importer</name>
685      <description>
686        Imports and updates derived bioassays in a batch.
687      </description>
688    </about>
689    <plugin-class>net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter</plugin-class>
690    <settings>
691      <property name="everyone-use">1</property>
692    </settings>
693  </plugin-definition>
694 
695  <plugin-definition id="RawBioAssayImporter">
696    <about>
697      <name>Raw bioassay importer</name>
698      <description>
699        Imports and updates raw bioassays in a batch.
700      </description>
701    </about>
702    <plugin-class>net.sf.basedb.plugins.batchimport.RawBioAssayImporter</plugin-class>
703    <settings>
704      <property name="everyone-use">1</property>
705    </settings>
706  </plugin-definition>
707
708  <plugin-definition id="ArrayDesignImporter">
709    <about>
710      <name>Array design importer</name>
711      <description>
712        Imports and updates array designs in a batch.
713      </description>
714    </about>
715    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayDesignImporter</plugin-class>
716  </plugin-definition>
717
718  <plugin-definition id="ArrayBatchImporter">
719    <about>
720      <name>Array batch importer</name>
721      <description>
722        Imports and updates array batches in a batch.
723      </description>
724    </about>
725    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayBatchImporter</plugin-class>
726  </plugin-definition>
727
728  <plugin-definition id="ArraySlideImporter">
729    <about>
730      <name>Array slide importer</name>
731      <description>
732        Imports and updates array slides in a batch.
733      </description>
734    </about>
735    <plugin-class>net.sf.basedb.plugins.batchimport.ArraySlideImporter</plugin-class>
736  </plugin-definition>
737
738  <plugin-definition id="ExternalProgramExecutor">
739    <about>
740      <name>External program executor</name>
741      <description>
742        This plug-in is used to export data from BASE to an external
743        program, run the program, and import the result back into BASE.
744        The export and import format is set by the user but must be a
745        format supported by the external program. The export also handles
746        the parameters needed to run the external program.
747      </description>
748    </about>
749    <plugin-class>net.sf.basedb.plugins.executor.ExternalProgramExecutor</plugin-class>
750    <settings>
751      <property name="everyone-use">1</property>
752    </settings>
753  </plugin-definition>
754
755  <plugin-definition id="BfsExporterSupport">
756    <about>
757      <name>BFS exporter for the ExternalProgramExecutor</name>
758      <description>
759        Support plug-in for the external program executor that
760        exports data to the external program in BFS format. This
761        plug-in can't be used as a standalone plug-in.
762      </description>
763    </about>
764    <plugin-class>net.sf.basedb.plugins.executor.BfsExporterSupport</plugin-class>
765    <settings>
766      <property name="everyone-use">1</property>
767    </settings>
768  </plugin-definition>
769
770  <plugin-definition id="BfsImporterSupport">
771    <about>
772      <name>BFS importer for the ExternalProgramExecutor</name>
773      <description>
774        Support plug-in for the external program executor that
775        imports BFS formatted data from the external program to
776        BASE. This plug-in can't be used as a standalone plug-in.
777      </description>
778    </about>
779    <plugin-class>net.sf.basedb.plugins.executor.BfsImporterSupport</plugin-class>
780    <settings>
781      <property name="everyone-use">1</property>
782    </settings>
783  </plugin-definition>
784
785  <plugin-definition id="BaseFileExporterSupport">
786    <about>
787      <name>BASEFile exporter for the ExternalProgramExecutor</name>
788      <description>
789        Support plug-in for the external program executor that
790        exports data to the external program in BASEFile format.
791        This plug-in can't be used as a standalone plug-in.
792      </description>
793    </about>
794    <plugin-class>net.sf.basedb.plugins.executor.BaseFileExporterSupport</plugin-class>
795    <settings>
796      <property name="everyone-use">1</property>
797    </settings>
798  </plugin-definition>
799
800  <plugin-definition id="BaseFileImporterSupport">
801    <about>
802      <name>BASEfile importer for the ExternalProgramExecutor</name>
803      <description>
804        Support plug-in for the external program executor that
805        imports BASEfile formatted data from the external program
806        to BASE. This plug-in can't be used as a standalone plug-in.
807      </description>
808    </about>
809    <plugin-class>net.sf.basedb.plugins.executor.BaseFileImporterSupport</plugin-class>
810    <settings>
811      <property name="everyone-use">1</property>
812    </settings>
813  </plugin-definition>
814
815  <plugin-definition id="FileOnlyImporterSupport">
816    <about>
817      <name>File-only importer for the ExternalProgramExecutor</name>
818      <description>
819        Support plug-in for the external program executor that
820        uploads all created files to BASE and attaches them to
821        a child bioassay set. This plug-in can't be used as a
822        standalone plug-in.
823      </description>
824    </about>
825    <plugin-class>net.sf.basedb.plugins.executor.FileOnlyImporterSupport</plugin-class>
826    <settings>
827      <property name="everyone-use">1</property>
828    </settings>
829  </plugin-definition>
830
831  <plugin-definition id="GtfReporterImporter">
832    <about>
833      <name>GTF reporter importer</name>
834      <description>
835        Creates reporters and reporter lists from GTF (Gene transfer format)
836        files. The default configuration uses the transcript_id+seqname value
837        as the reporter id and name, and gene_id as "symbol". This can
838        be changed by user configurations. For example, to use the gene_id
839        instead or to add prefixes to the id values. The importer
840        builds on the regular reporter importer and performs on-the-fly
841        transformation of GTF attributes to a completely column-based format.
842      </description>
843    </about>
844    <plugin-class>net.sf.basedb.plugins.gtf.GtfReporterImporter</plugin-class>
845    <settings>
846      <property name="everyone-use">1</property>
847    </settings>
848  </plugin-definition>
849
850  <plugin-definition id="GtfReporterMapImporter">
851    <about>
852      <name>GTF reporter map importer</name>
853      <description>
854        Maps reporters to array design features from GTF files. The default
855        implementation use the transcript_id as both the feature id and
856        reporter id, but this can be changed by user configuration. For
857        example, to use the gene_id instead or to add prefixes to the id
858        values. The importer build on the regular reporter map importer
859        and perform on-the-fly transformation of GTF attributes to a
860        completely column-based format.
861      </description>
862    </about>
863    <plugin-class>net.sf.basedb.plugins.gtf.GtfReporterMapImporter</plugin-class>
864  </plugin-definition>
865
866  <plugin-definition id="CloneReportersPlugin">
867    <about>
868      <name>Clone reporters</name>
869      <description>
870        Clone reporter annotations to a per-experiment storage in the
871        dynamic database. The cloned table contains only those reporters that
872        have been used in the experiment and it is also possible to select
873        a subset of all available reporter annotations (eg. by a template).
874        After the cloning operation all tools/plug-ins working on the experiment
875        will use the cloned annotations which protects the analysis from accidental
876        updates to the main reporter annotations. The cloned reporter annotations
877        can be removed and/or updated at any time.
878      </description>
879    </about>
880    <plugin-class>net.sf.basedb.plugins.CloneReportersPlugin</plugin-class>
881    <settings>
882      <property name="everyone-use">1</property>
883    </settings>
884  </plugin-definition>
885
886  <!--
887  <plugin-definition id="">
888    <about>
889      <name></name>
890      <description>
891      </description>
892    </about>
893    <plugin-class>net.sf.basedb.plugins.</plugin-class>
894    <settings>
895      <property name="everyone-use">1</property>
896      <property name="immediate-execution">1</property>
897    </settings>
898  </plugin-definition>
899  -->
900
901
902</extensions>
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