source: trunk/doc/src/docbook/appendix/coreplugins.xml

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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE appendix PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: coreplugins.xml 7982 2021-06-14 08:01:21Z nicklas $
7 
8  Copyright (C) 2007 Jari Häkkinen, Nicklas Nordborg
9  Copyright (C) 2008 Jari Häkkinen
10 
11  This file is part of BASE - BioArray Software Environment.
12  Available at http://base.thep.lu.se/
13 
14  BASE is free software; you can redistribute it and/or
15  modify it under the terms of the GNU General Public License
16  as published by the Free Software Foundation; either version 3
17  of the License, or (at your option) any later version.
18 
19  BASE is distributed in the hope that it will be useful,
20  but WITHOUT ANY WARRANTY; without even the implied warranty of
21  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
22  GNU General Public License for more details.
23 
24  You should have received a copy of the GNU General Public License
25  along with BASE. If not, see <http://www.gnu.org/licenses/>.
26-->
27
28<appendix id="appendix.coreplugins">
29  <?dbhtml filename="coreplugins.html" ?>
30  <title>Core plug-ins shipped with BASE</title>
31
32  <para>
33    Here is a categorized list of all plug-ins installed with a pristine BASE
34    installation. Some plug-ins must be configured before use. The
35    requirements are listed below and configuration samples are given
36    for for plug-ins that supports/requires configurations. Use the
37    right-click menu of the mouse to download these XML files for
38    further import into BASE (see <xref
39    linkend="plugins.configuration.importexport" />).
40  </para>
41
42  <para>
43    Contributed plug-ins are available at <ulink
44    url="https://baseplugins.thep.lu.se" >https://baseplugins.thep.lu.se
45    </ulink>. These plug-ins are either developed outside the core team
46    or require external non-Java compilers and tools. These packages
47    are excluded from the BASE package to make the installation
48    process somewhat simpler.
49  </para>
50     
51  <sect1 id="coreplugins.analyze">
52    <title>Core analysis plug-ins</title>
53
54    <variablelist>
55      <varlistentry>
56        <term>BASE 1 plug-in executor</term>
57        <listitem>
58          <para>
59            Simulates the plug-in runner from Base 1.2. Must be configured
60            before use. The recommended approach is to use the plug-in configuration
61            file from the BASE 1.2 installation. See <xref linkend="plugins.installation.base1"
62            /> for more information.
63          </para>
64        </listitem>
65      </varlistentry>
66
67      <varlistentry>
68        <term>External program executor</term>
69        <listitem>
70          <para>
71            Export data from BASE and execute an external program for analysis.
72            Afterwards, data can be imported back to BASE. A configuration is needed
73            to run this plug-in. The plug-in is very flexible and can handle several
74            export/import data formats (which can be extended by
75            adding special export/import plug-ins). Here is a list of the built-in
76            exporter/importer implementations.
77          </para>
78         
79          <itemizedlist>
80            <listitem>
81              <para>
82              <emphasis>BASEFile exporter for the ExternalProgramExecutor</emphasis>: Exporter implementation
83              that export data in BASE file format.
84              </para>
85            </listitem>
86            <listitem>
87              <para>
88              <emphasis>BASEfile importer for the ExternalProgramExecutor</emphasis>: Importer implementation
89              that can import data in BASEfile format.
90              </para>
91            </listitem>
92            <listitem>
93              <para>
94              <emphasis>BFS exporter for the ExternalProgramExecutor</emphasis>: Exporter implementation
95              that export data in BFS file format.
96              </para>
97            </listitem>
98            <listitem>
99              <para>
100              <emphasis>BFS importer for the ExternalProgramExecutor</emphasis>: Importer implementation
101              that can import data in BFS file format.
102              </para>
103            </listitem>
104            <listitem>
105              <para>
106              <emphasis>File-only importer for the ExternalProgramExecutor</emphasis>: Importer implementation
107              that simply upload all created files to BASE.
108              </para>
109            </listitem>
110          </itemizedlist>
111         
112          <note>
113            <para>
114            This plug-in can in theory handle everything (and more) that the
115            <emphasis>BASE 1 plug-in executor</emphasis> can, except that it doesn't do
116            any translation of field names used in BASE 1.
117            </para> 
118          </note>
119         
120        </listitem>
121      </varlistentry>
122
123      <varlistentry>
124        <term>Formula extra value calculator</term>
125        <listitem>
126          <para>
127            Calculates extra values for a bioassay set using a user-defined
128            formula. No configuration is needed.
129          </para>
130        </listitem>
131      </varlistentry>
132
133      <varlistentry>
134        <term>Formula filter</term>
135        <listitem>
136          <para>
137            Filters a bioassay set using a user-defined formula.
138            No configuration is needed.
139          </para>
140        </listitem>
141      </varlistentry>
142
143      <varlistentry>
144        <term>Formula intensity transformer</term>
145        <listitem>
146          <para>
147            Creates a new bioassay set with transformed intensity values using a
148            user-defined formula. No configuration is needed.
149          </para>
150        </listitem>
151      </varlistentry>
152
153      <varlistentry>
154        <term>Manual derived bioassay creator</term>
155        <term>Manual transformation</term>
156        <listitem>
157          <para>
158            Allows a user to manually register an external analysis procedure that has
159            happened outside of BASE and to register the parameters used and the generated
160            output files. On plug-in create a derived bioassay set and the other
161            a transformation/bioassay set. Both plug-ins need a configuration to
162            register possible parameters and output files.
163          </para>
164        </listitem>
165      </varlistentry>
166
167      <varlistentry>
168        <term>Normalisation: Lowess</term>
169        <listitem>
170          <para>
171            Normalisation using LOWESS algorithm. No configuration is
172            needed.
173          </para>
174        </listitem>
175      </varlistentry>
176
177      <varlistentry>
178        <term>Normalisation: Median ratio</term>
179        <listitem>
180          <para>
181            Normalisation based on median ratio. No configuration is needed.
182          </para>
183        </listitem>
184      </varlistentry>
185    </variablelist>
186
187  </sect1>
188
189  <sect1 id="coreplugins.export">
190    <title>Core export plug-ins</title>
191
192    <para>
193      Unless otherwise noted, none of the export plug-ins
194      need a configuration.
195    </para>
196
197    <variablelist>
198      <varlistentry>
199        <term>BASEfile exporter</term>
200        <listitem>
201          <para>
202            Exports bioassay set data to serial or matrix BASEfile format.
203          </para>
204        </listitem>
205      </varlistentry>
206     
207      <varlistentry>
208        <term>BFS exporter</term>
209        <listitem>
210          <para>
211            Exports bioassay set data to BFS format.
212          </para>
213        </listitem>
214      </varlistentry>
215     
216      <varlistentry>
217        <term>GAL exporter</term>
218        <listitem>
219          <para>
220            Exports the features of an array design to a GAL file.
221          </para>
222        </listitem>
223      </varlistentry>
224
225      <varlistentry>
226        <term>Help texts exporter</term>
227        <listitem>
228          <para>
229            Exports help texts to an XML file.
230          </para>
231        </listitem>
232      </varlistentry>
233
234      <varlistentry>
235        <term>Packed file exporter</term>
236        <listitem>
237          <para>
238            Exports files and directories as an archive-file. A configuration
239            is needed to specify compression format. Support for the following
240            formats are included in BASE:
241          </para>
242         
243          <itemizedlist>
244            <listitem>
245              <para>
246              <emphasis>BZipped TAR archive</emphasis>: Collects the selected files/directories
247              into a TAR file and compress it with BZIP2.
248              </para>
249            </listitem>
250            <listitem>
251              <para>
252              <emphasis>GZipped TAR archive</emphasis>: Collects the selected files/directories
253              into a TAR file and compress it with GZIP.
254              </para>
255            </listitem>
256            <listitem>
257              <para>
258              <emphasis>TAR archive</emphasis>: Collects the selected files/directories
259              into an uncompressed TAR file.
260              </para>
261            </listitem>
262            <listitem>
263              <para>
264              <emphasis>ZIP archive</emphasis>: Collects the selected files/directories
265              into a ZIP file.
266              </para>
267            </listitem>
268          </itemizedlist>
269         
270          <para>
271            See <xref linkend="plugin_developer.other.packer"/> for information
272            about implementing support for other file formats. 
273          </para>
274         
275        </listitem>
276      </varlistentry>
277
278      <varlistentry>
279        <term>Plate mapping exporter</term>
280        <listitem>
281          <para>
282            Exports plate mappings.
283          </para>
284        </listitem>
285      </varlistentry>
286
287      <varlistentry>
288        <term>Plugin configuration exporter</term>
289        <listitem>
290          <para>
291            Exports plug-in configurations to an XML file.
292          </para>
293        </listitem>
294      </varlistentry>
295
296      <varlistentry>
297        <term>Table exporter</term>
298        <listitem>
299          <para>
300            Exports data from table listings in the web-interface to
301            a TAB-separated text file or XML file.
302          </para>
303        </listitem>
304      </varlistentry>
305
306    </variablelist>
307
308  </sect1>
309
310  <sect1 id="coreplugins.import">
311    <title>Core import plug-ins</title>
312
313    <para>
314      There are many import plug-ins in BASE. Their use are in most
315      cases seamless and the user does not need to be aware of
316      detailed plug-in usage. However, there is a set of batch import
317      plug-ins that are targeted for importing multiple items into
318      BASE. These batch importers require some user knowledge for
319      proper and efficient use of them. The batch plug-ins are listed
320      in the <xref linkend="coreplugins.import.batch" /> sub-section
321      below together with pointers to further reading on how to use
322      the plug-ins.
323    </para>
324
325    <variablelist>
326
327      <varlistentry>
328        <term>Affymetrix CDF probeset importer</term>
329        <listitem>
330          <para>
331            This plug-in is used to import probesets (reporters in
332            BASE language) from an Affymetrix CDF file. It can be used
333            in import mode from the reporter list view and from the
334            array design view and in verification mode from the array
335            design view. The plug-in can only set the name and ID of
336            the reporters, since the CDF file doesn't contains any
337            annotation information. Probesets already in BASE will not
338            be affected by the import. No configuration is needed.
339          </para>
340        </listitem>
341      </varlistentry>
342
343      <varlistentry>
344        <term>Annotation importer</term>
345        <listitem>
346          <para>
347            Imports annotation to any annotatable item in BASE.
348            Configurations are supported but not required.
349          </para>
350        </listitem>
351      </varlistentry>
352
353      <varlistentry>
354        <term>GTF reporter importer</term>
355        <listitem>
356          <para>
357            Imports reporter information from GTF (Gene transfer format)
358            files. Configurations are supported but not required. BASE
359            has pre-installed configurations that uses the gene_id or transcript_id
360            as reporter id.
361          </para>
362        </listitem>
363      </varlistentry>
364
365      <varlistentry>
366        <term>GTF reporter map importer</term>
367        <listitem>
368          <para>
369            Imports array design features from GTF (Gene transfer format)
370            files. A configuration is needed. BASE has pre-installed
371            configurations that uses the gene_id or transcript_id
372            as reporter id.
373          </para>
374        </listitem>
375      </varlistentry>
376
377      <varlistentry>
378        <term>Help texts importer</term>
379        <listitem>
380          <para>
381            Imports help texts from an XML file into BASE.
382            No configuration is needed.
383          </para>
384        </listitem>
385      </varlistentry>
386
387      <varlistentry>
388        <term>Illumina raw data importer</term>
389        <listitem>
390          <para>
391            This plug-in is used to import raw data from Illumina BeadStudion
392            data files. No configuration is needed.
393          </para>
394        </listitem>
395      </varlistentry>
396
397      <varlistentry>
398        <term>Plate importer</term>
399        <listitem>
400          <para>
401            Imports plates from a simple flat file. A configuration is needed.
402            BASE has pre-installed configurations for 96- and 384-well plates.
403          </para>
404        </listitem>
405      </varlistentry>
406
407      <varlistentry>
408        <term>Plate mapping importer</term>
409        <listitem>
410          <para>
411            Imports plate mappings exported by the <emphasis>Plate mapping exporter</emphasis>.
412            No configuration is needed.
413          </para>
414        </listitem>
415      </varlistentry>
416
417             
418      <varlistentry>
419        <term>Plugin configuration importer</term>
420        <listitem>
421          <para>
422            Imports plug-in configurations from an XML file. No configuration
423            is needed.
424          </para>
425        </listitem>
426      </varlistentry>
427
428      <varlistentry>
429        <term>Print map importer</term>
430        <listitem>
431          <para>
432            Imports array design features from TAM or MwBR files. This plug-in
433            require that the array design is connected with plates. No
434            configuration is needed.
435          </para>
436        </listitem>
437      </varlistentry>
438
439      <varlistentry>
440        <term>Raw data importer</term>
441        <listitem>
442          <para>
443            Imports raw data from a text file. A configuration is needed.
444            BASE has pre-installed configurations for GenePix and Cufflinks
445            data files.
446          </para>
447        </listitem>
448      </varlistentry>
449
450      <varlistentry>
451        <term>Reporter importer</term>
452        <listitem>
453          <para>
454            Import reporter (probeset) information from a file. A configuration
455            is not needed, but is recommended. BASE has pre-installed configurations
456            for several different file types.
457          </para>
458          <para>
459            <emphasis>Since BASE 2.0, available
460            configurations:</emphasis>
461          </para>
462        </listitem>
463      </varlistentry>
464
465      <varlistentry>
466        <term>Reporter map importer</term>
467        <listitem>
468          <para>
469            Imports array design features from text files. This plug-in can
470            be used without connection to plates. A configuration is needed.
471            BASE has pre-installed configurations for some file formats.
472          </para>
473        </listitem>
474      </varlistentry>
475
476    </variablelist>
477
478    <sect2 id="coreplugins.import.batch">
479      <title>Core batch import plug-ins</title>
480
481      <para>
482        The batch import plug-ins all work similarly and their usage
483        is described in <xref linkend="import_data.batch" />. All
484        batch importers have support for configurations but can also
485        be used without.
486      </para>
487
488      <variablelist>
489        <varlistentry>
490          <term>Array batch importer</term>
491          <listitem>
492            <para>
493              Imports and updates array batches in a batch.
494            </para>
495          </listitem>
496        </varlistentry>
497 
498        <varlistentry>
499          <term>Array design importer</term>
500          <listitem>
501            <para>
502              Imports and updates array designs in a batch.
503            </para>
504          </listitem>
505        </varlistentry>
506       
507        <varlistentry>
508          <term>Array slide importer</term>
509          <listitem>
510            <para>
511              Imports and updates array slides in a batch.
512            </para>
513          </listitem>
514        </varlistentry>
515
516        <varlistentry>
517          <term>Bioplate importer</term>
518          <listitem>
519            <para>
520              Imports and updates bioplates in a batch. Note that this
521              import can't be used to put biomaterial on the bioplates.
522            </para>
523          </listitem>
524        </varlistentry>
525
526        <varlistentry>
527          <term>Biosource importer</term>
528          <listitem>
529            <para>
530              Imports and updates biosources in a batch.
531            </para>
532          </listitem>
533        </varlistentry>
534
535        <varlistentry>
536          <term>Derived bioassay importer</term>
537          <listitem>
538            <para>
539              Imports and updates derived bioassays in a batch.
540            </para>
541          </listitem>
542        </varlistentry>
543
544        <varlistentry>
545          <term>Extract importer</term>
546          <listitem>
547            <para>
548              Imports and updates extracts in a batch.
549            </para>
550          </listitem>
551        </varlistentry>
552
553        <varlistentry>
554          <term>Physical bioassay importer</term>
555          <listitem>
556            <para>
557              Imports and updates physical bioassays in a batch.
558            </para>
559          </listitem>
560        </varlistentry>
561
562        <varlistentry>
563          <term>Raw bioassay importer</term>
564          <listitem>
565            <para>
566              Imports and updates raw bioassays in a batch.
567            </para>
568          </listitem>
569        </varlistentry>
570
571        <varlistentry>
572          <term>Sample importer</term>
573          <listitem>
574            <para>
575              Imports and updates samples in a batch.
576            </para>
577          </listitem>
578        </varlistentry>
579
580      </variablelist>
581
582    </sect2>
583
584  </sect1>
585
586  <sect1 id="coreplugins.intensity">
587    <title>Core intensity plug-ins</title>
588
589    <variablelist>
590      <varlistentry>
591        <term>Formula intensity calculator</term>
592        <listitem>
593          <para>
594            Calculate intensities from raw data using a user-defined formula.
595            No configuration is needed, but formulas must be defined using
596            <menuchoice>
597              <guimenu>View</guimenu>
598              <guimenuitem>Formulas</guimenuitem>
599            </menuchoice>.
600          </para>
601        </listitem>
602      </varlistentry>
603
604    </variablelist>
605
606  </sect1>
607
608  <sect1 id="coreplugins.other">
609    <title>Uncategorized core plug-ins</title>
610
611    <variablelist>
612
613      <varlistentry>
614        <term>TAR file unpacker</term>
615        <listitem>
616          <para>
617            Unpacks a tar file on the BASE file system. It also
618            supports TAR files compressed with GZIP or BZIP
619            algorithms. This plug-in can be used to automatically
620            unpack files during upload. No configuration is needed.
621          </para>
622        </listitem>
623      </varlistentry>
624
625      <varlistentry>
626        <term>ZIP file unpacker</term>
627        <listitem>
628          <para>
629            Unpacks ZIP and JAR files on the BASE's file system.
630            This plug-in can be used to automatically unpack files
631            during upload. No configuration is needed.
632          </para>
633        </listitem>
634      </varlistentry>
635
636      <varlistentry>
637        <term>BZip2 file unpacker</term>
638        <listitem>
639          <para>
640            Unpacks BZip2 compressed files to the BASE file
641            system. This plug-in can be used to automatically unpack files
642            during upload. No configuration is needed.
643          </para>
644        </listitem>
645      </varlistentry>
646     
647      <varlistentry>
648        <term>GZip file unpacker</term>
649        <listitem>
650          <para>
651            Unpacks GZip compressed files to the BASE file
652            system. This plug-in can be used to automatically unpack files
653            during upload. No configuration is needed.
654          </para>
655        </listitem>
656      </varlistentry>
657
658    </variablelist>
659
660  </sect1>
661
662</appendix>
663
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