source: branches/2.1/src/core/plugin_configfile.xml @ 2974

Last change on this file since 2974 was 2974, checked in by Nicklas Nordborg, 17 years ago

Fixed issues with incorrect column mappings and swithced channels in default configuration files.
  • Property svn:keywords set to Id
File size: 62.8 KB
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
3  <configuration pluginClassName="net.sf.basedb.plugins.PlateFlatFileImporter">
4    <configname>384_wells plate import</configname>
5    <description>This configuration is for the Plate importer plugin when to import 384-well plates.</description>
6    <parameter>
7      <name>maxDataColumns</name>
8      <label>Max data columns</label>
9      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
10      <class />
11      <value />
12    </parameter>
13    <parameter>
14      <name>reporterColumnMapping</name>
15      <label>Reporter ID</label>
16      <description>Mapping that picks the well's reporter id from the data columns. For example: \ID\</description>
17      <class>java.lang.String</class>
18      <value>\oligo_id\</value>
19    </parameter>
20    <parameter>
21      <name>dataHeaderRegexp</name>
22      <label>Data header</label>
23      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
24      <class>java.lang.String</class>
25      <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
26    </parameter>
27    <parameter>
28      <name>barcodeColumnMapping</name>
29      <label>Plate barcode</label>
30      <description>Mapping that picks the plate barcode from the data columns. For example: \Barcode\</description>
31      <class />
32      <value />
33    </parameter>
34    <parameter>
35      <name>trimQuotes</name>
36      <label>Remove quotes</label>
37      <description>If true quotes (" or ') around data value will be removed.</description>
38      <class>java.lang.Boolean</class>
39      <value>true</value>
40    </parameter>
41    <parameter>
42      <name>dataSplitterRegexp</name>
43      <label>Data splitter</label>
44      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
45      <class>java.lang.String</class>
46      <value>\t</value>
47    </parameter>
48    <parameter>
49      <name>charset</name>
50      <label>Character set</label>
51      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
52      <class>java.lang.String</class>
53      <value>ISO-8859-1</value>
54    </parameter>
55    <parameter>
56      <name>columnColumnMapping</name>
57      <label>Column</label>
58      <description>Mapping that picks the well's column in the plate from the data columns. For example: \Column\</description>
59      <class>java.lang.String</class>
60      <value>\384_column\</value>
61    </parameter>
62    <parameter>
63      <name>nameColumnMapping</name>
64      <label>Plate number/name</label>
65      <description>Mapping that picks the plate name from the data columns. For example: \Plate\</description>
66      <class>java.lang.String</class>
67      <value>\384_number\</value>
68    </parameter>
69    <parameter>
70      <name>minDataColumns</name>
71      <label>Min data columns</label>
72      <description>The minimum number of columns for a line to be counted as a data line.</description>
73      <class />
74      <value />
75    </parameter>
76    <parameter>
77      <name>ignoreRegexp</name>
78      <label>Ignore</label>
79      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
80      <class />
81      <value />
82    </parameter>
83    <parameter>
84      <name>dataFooterRegexp</name>
85      <label>Data footer</label>
86      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
87      <class />
88      <value />
89    </parameter>
90    <parameter>
91      <name>headerRegexp</name>
92      <label>Header</label>
93      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
94      <class />
95      <value />
96    </parameter>
97    <parameter>
98      <name>rowColumnMapping</name>
99      <label>Row</label>
100      <description>Mapping that picks the well's row in the plate from the data columns. For example: \Row\</description>
101      <class>java.lang.String</class>
102      <value>\384_row\</value>
103    </parameter>
104  </configuration>
105  <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
106    <configname>Reporters from 384well plates file</configname>
107    <description>This configuration is for importing reporters from the same text file as 384well plates are imported from.</description>
108    <parameter>
109      <name>maxDataColumns</name>
110      <label>Max data columns</label>
111      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
112      <class />
113      <value />
114    </parameter>
115    <parameter>
116      <name>extendedColumnMapping.locusLink</name>
117      <label>LocusLink</label>
118      <description />
119      <class />
120      <value />
121    </parameter>
122    <parameter>
123      <name>trimQuotes</name>
124      <label>Remove quotes</label>
125      <description>If true quotes (" or ') around data value will be removed.</description>
126      <class>java.lang.Boolean</class>
127      <value>true</value>
128    </parameter>
129    <parameter>
130      <name>charset</name>
131      <label>Character set</label>
132      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
133      <class>java.lang.String</class>
134      <value>ISO-8859-1</value>
135    </parameter>
136    <parameter>
137      <name>scoreColumnMapping</name>
138      <label>Score</label>
139      <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
140      <class />
141      <value />
142    </parameter>
143    <parameter>
144      <name>nameColumnMapping</name>
145      <label>Name</label>
146      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
147      <class>java.lang.String</class>
148      <value>\oligo_id\</value>
149    </parameter>
150    <parameter>
151      <name>extendedColumnMapping.markers</name>
152      <label>Markers</label>
153      <description />
154      <class />
155      <value />
156    </parameter>
157    <parameter>
158      <name>extendedColumnMapping.vector</name>
159      <label>Vector</label>
160      <description>The vector from which the reporter is derived</description>
161      <class />
162      <value />
163    </parameter>
164    <parameter>
165      <name>extendedColumnMapping.nid</name>
166      <label>NID</label>
167      <description />
168      <class />
169      <value />
170    </parameter>
171    <parameter>
172      <name>descriptionColumnMapping</name>
173      <label>Description</label>
174      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
175      <class>java.lang.String</class>
176      <value>\description_Ensembl*\</value>
177    </parameter>
178    <parameter>
179      <name>headerRegexp</name>
180      <label>Header</label>
181      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
182      <class />
183      <value />
184    </parameter>
185    <parameter>
186      <name>reporterIdColumnMapping</name>
187      <label>Reporter ID</label>
188      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
189      <class>java.lang.String</class>
190      <value>\oligo_id\</value>
191    </parameter>
192    <parameter>
193      <name>symbolColumnMapping</name>
194      <label>Gene symbol</label>
195      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
196      <class>java.lang.String</class>
197      <value>\gene_symbol_Ensembl*\</value>
198    </parameter>
199    <parameter>
200      <name>extendedColumnMapping.antibiotics</name>
201      <label>Antibiotics</label>
202      <description />
203      <class />
204      <value />
205    </parameter>
206    <parameter>
207      <name>extendedColumnMapping.omim</name>
208      <label>OMIM</label>
209      <description />
210      <class />
211      <value />
212    </parameter>
213    <parameter>
214      <name>extendedColumnMapping.chromosome</name>
215      <label>Chromosome</label>
216      <description>The chromosome from which the reporter is derived</description>
217      <class />
218      <value />
219    </parameter>
220    <parameter>
221      <name>reporterType</name>
222      <label>Reporter type</label>
223      <description>The reporter type assigned to the imported reporters</description>
224      <class />
225      <value />
226    </parameter>
227    <parameter>
228      <name>dataHeaderRegexp</name>
229      <label>Data header</label>
230      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
231      <class>java.lang.String</class>
232      <value>384_number\t384_column\t384_row\t384_position\toligo_id.*</value>
233    </parameter>
234    <parameter>
235      <name>dataSplitterRegexp</name>
236      <label>Data splitter</label>
237      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
238      <class>java.lang.String</class>
239      <value>\t</value>
240    </parameter>
241    <parameter>
242      <name>extendedColumnMapping.length</name>
243      <label>Length</label>
244      <description>The length of the sequence</description>
245      <class />
246      <value />
247    </parameter>
248    <parameter>
249      <name>extendedColumnMapping.tissue</name>
250      <label>Tissue</label>
251      <description>The tissue from which the reporter is derived</description>
252      <class />
253      <value />
254    </parameter>
255    <parameter>
256      <name>extendedColumnMapping.accession</name>
257      <label>Accession</label>
258      <description />
259      <class />
260      <value />
261    </parameter>
262    <parameter>
263      <name>minDataColumns</name>
264      <label>Min data columns</label>
265      <description>The minimum number of columns for a line to be counted as a data line.</description>
266      <class />
267      <value />
268    </parameter>
269    <parameter>
270      <name>ignoreRegexp</name>
271      <label>Ignore</label>
272      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
273      <class />
274      <value />
275    </parameter>
276    <parameter>
277      <name>reporterTypeColumnMapping</name>
278      <label>Reporter type</label>
279      <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
280      <class />
281      <value />
282    </parameter>
283    <parameter>
284      <name>extendedColumnMapping.library</name>
285      <label>Library</label>
286      <description>The library from which the reporter is derived</description>
287      <class />
288      <value />
289    </parameter>
290    <parameter>
291      <name>extendedColumnMapping.clusterId</name>
292      <label>Cluster ID</label>
293      <description>A unique identifier for a Unigene entry</description>
294      <class />
295      <value />
296    </parameter>
297    <parameter>
298      <name>dataFooterRegexp</name>
299      <label>Data footer</label>
300      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
301      <class />
302      <value />
303    </parameter>
304    <parameter>
305      <name>extendedColumnMapping.cytoband</name>
306      <label>Cytoband</label>
307      <description>The cytoband from which the reporter is derived</description>
308      <class />
309      <value />
310    </parameter>
311    <parameter>
312      <name>extendedColumnMapping.sequence</name>
313      <label>Sequence</label>
314      <description>The nucleotide sequence of the reporter</description>
315      <class>java.lang.String</class>
316      <value>\oligo_sequence\</value>
317    </parameter>
318    <parameter>
319      <name>extendedColumnMapping.species</name>
320      <label>Species</label>
321      <description>The organism from which the reporter is derived</description>
322      <class />
323      <value />
324    </parameter>
325  </configuration>
326  <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
327    <configname>Reporters from GenePix file</configname>
328    <description>This  configuration is for importing reporters from a GenePix file (*.gpr)</description>
329    <parameter>
330      <name>maxDataColumns</name>
331      <label>Max data columns</label>
332      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
333      <class />
334      <value />
335    </parameter>
336    <parameter>
337      <name>extendedColumnMapping.locusLink</name>
338      <label>LocusLink</label>
339      <description />
340      <class />
341      <value />
342    </parameter>
343    <parameter>
344      <name>trimQuotes</name>
345      <label>Remove quotes</label>
346      <description>If true quotes (" or ') around data value will be removed.</description>
347      <class>java.lang.Boolean</class>
348      <value>true</value>
349    </parameter>
350    <parameter>
351      <name>charset</name>
352      <label>Character set</label>
353      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
354      <class>java.lang.String</class>
355      <value>ISO-8859-1</value>
356    </parameter>
357    <parameter>
358      <name>scoreColumnMapping</name>
359      <label>Score</label>
360      <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
361      <class />
362      <value />
363    </parameter>
364    <parameter>
365      <name>nameColumnMapping</name>
366      <label>Name</label>
367      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
368      <class>java.lang.String</class>
369      <value>\Name\</value>
370    </parameter>
371    <parameter>
372      <name>extendedColumnMapping.markers</name>
373      <label>Markers</label>
374      <description />
375      <class />
376      <value />
377    </parameter>
378    <parameter>
379      <name>extendedColumnMapping.vector</name>
380      <label>Vector</label>
381      <description>The vector from which the reporter is derived</description>
382      <class />
383      <value />
384    </parameter>
385    <parameter>
386      <name>extendedColumnMapping.nid</name>
387      <label>NID</label>
388      <description />
389      <class />
390      <value />
391    </parameter>
392    <parameter>
393      <name>descriptionColumnMapping</name>
394      <label>Description</label>
395      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
396      <class />
397      <value />
398    </parameter>
399    <parameter>
400      <name>headerRegexp</name>
401      <label>Header</label>
402      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
403      <class />
404      <value />
405    </parameter>
406    <parameter>
407      <name>reporterIdColumnMapping</name>
408      <label>Reporter ID</label>
409      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
410      <class>java.lang.String</class>
411      <value>\ID\</value>
412    </parameter>
413    <parameter>
414      <name>symbolColumnMapping</name>
415      <label>Gene symbol</label>
416      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
417      <class />
418      <value />
419    </parameter>
420    <parameter>
421      <name>extendedColumnMapping.antibiotics</name>
422      <label>Antibiotics</label>
423      <description />
424      <class />
425      <value />
426    </parameter>
427    <parameter>
428      <name>extendedColumnMapping.omim</name>
429      <label>OMIM</label>
430      <description />
431      <class />
432      <value />
433    </parameter>
434    <parameter>
435      <name>extendedColumnMapping.chromosome</name>
436      <label>Chromosome</label>
437      <description>The chromosome from which the reporter is derived</description>
438      <class />
439      <value />
440    </parameter>
441    <parameter>
442      <name>reporterType</name>
443      <label>Reporter type</label>
444      <description>The reporter type assigned to the imported reporters</description>
445      <class />
446      <value />
447    </parameter>
448    <parameter>
449      <name>dataHeaderRegexp</name>
450      <label>Data header</label>
451      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
452      <class>java.lang.String</class>
453      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</value>
454    </parameter>
455    <parameter>
456      <name>dataSplitterRegexp</name>
457      <label>Data splitter</label>
458      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
459      <class>java.lang.String</class>
460      <value>\t</value>
461    </parameter>
462    <parameter>
463      <name>extendedColumnMapping.length</name>
464      <label>Length</label>
465      <description>The length of the sequence</description>
466      <class />
467      <value />
468    </parameter>
469    <parameter>
470      <name>extendedColumnMapping.tissue</name>
471      <label>Tissue</label>
472      <description>The tissue from which the reporter is derived</description>
473      <class />
474      <value />
475    </parameter>
476    <parameter>
477      <name>extendedColumnMapping.accession</name>
478      <label>Accession</label>
479      <description />
480      <class />
481      <value />
482    </parameter>
483    <parameter>
484      <name>minDataColumns</name>
485      <label>Min data columns</label>
486      <description>The minimum number of columns for a line to be counted as a data line.</description>
487      <class />
488      <value />
489    </parameter>
490    <parameter>
491      <name>ignoreRegexp</name>
492      <label>Ignore</label>
493      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
494      <class />
495      <value />
496    </parameter>
497    <parameter>
498      <name>reporterTypeColumnMapping</name>
499      <label>Reporter type</label>
500      <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
501      <class />
502      <value />
503    </parameter>
504    <parameter>
505      <name>extendedColumnMapping.library</name>
506      <label>Library</label>
507      <description>The library from which the reporter is derived</description>
508      <class />
509      <value />
510    </parameter>
511    <parameter>
512      <name>extendedColumnMapping.clusterId</name>
513      <label>Cluster ID</label>
514      <description>A unique identifier for a Unigene entry</description>
515      <class />
516      <value />
517    </parameter>
518    <parameter>
519      <name>dataFooterRegexp</name>
520      <label>Data footer</label>
521      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
522      <class />
523      <value />
524    </parameter>
525    <parameter>
526      <name>extendedColumnMapping.cytoband</name>
527      <label>Cytoband</label>
528      <description>The cytoband from which the reporter is derived</description>
529      <class />
530      <value />
531    </parameter>
532    <parameter>
533      <name>extendedColumnMapping.sequence</name>
534      <label>Sequence</label>
535      <description>The nucleotide sequence of the reporter</description>
536      <class />
537      <value />
538    </parameter>
539    <parameter>
540      <name>extendedColumnMapping.species</name>
541      <label>Species</label>
542      <description>The organism from which the reporter is derived</description>
543      <class />
544      <value />
545    </parameter>
546  </configuration>
547  <configuration pluginClassName="net.sf.basedb.plugins.ReporterMapFlatFileImporter">
548    <configname>Features from Genepix file</configname>
549    <description>This configuration is for import features from a GenePix file.&#xD;
550Block mapping is used in this configuration.</description>
551    <parameter>
552      <name>maxDataColumns</name>
553      <label>Max data columns</label>
554      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
555      <class />
556      <value />
557    </parameter>
558    <parameter>
559      <name>dataHeaderRegexp</name>
560      <label>Data header</label>
561      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
562      <class>java.lang.String</class>
563      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</value>
564    </parameter>
565    <parameter>
566      <name>trimQuotes</name>
567      <label>Remove quotes</label>
568      <description>If true quotes (" or ') around data value will be removed.</description>
569      <class>java.lang.Boolean</class>
570      <value>true</value>
571    </parameter>
572    <parameter>
573      <name>dataSplitterRegexp</name>
574      <label>Data splitter</label>
575      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
576      <class>java.lang.String</class>
577      <value>\t</value>
578    </parameter>
579    <parameter>
580      <name>charset</name>
581      <label>Character set</label>
582      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
583      <class>java.lang.String</class>
584      <value>ISO-8859-1</value>
585    </parameter>
586    <parameter>
587      <name>columnColumnMapping</name>
588      <label>Column</label>
589      <description>Mapping that picks the feature's column position in a block from the data columns. For example: \Column\</description>
590      <class>java.lang.String</class>
591      <value>\Column\</value>
592    </parameter>
593    <parameter>
594      <name>metaGridXColumnMapping</name>
595      <label>Meta grid X</label>
596      <description>Mapping that picks the feature's meta grid X coordinate from the data columns. Required if you don't specify a block mapping. Example: \Meta grid X\</description>
597      <class />
598      <value />
599    </parameter>
600    <parameter>
601      <name>metaGridYColumnMapping</name>
602      <label>Meta grid Y</label>
603      <description>Mapping that picks the feature's meta grid Y coordinate from the data columns. Required if you don't specify a block mapping. Example: \Meta grid Y\</description>
604      <class />
605      <value />
606    </parameter>
607    <parameter>
608      <name>minDataColumns</name>
609      <label>Min data columns</label>
610      <description>The minimum number of columns for a line to be counted as a data line.</description>
611      <class />
612      <value />
613    </parameter>
614    <parameter>
615      <name>ignoreRegexp</name>
616      <label>Ignore</label>
617      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
618      <class />
619      <value />
620    </parameter>
621    <parameter>
622      <name>dataFooterRegexp</name>
623      <label>Data footer</label>
624      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
625      <class />
626      <value />
627    </parameter>
628    <parameter>
629      <name>reporterIdColumnMapping</name>
630      <label>Reporter ID</label>
631      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
632      <class>java.lang.String</class>
633      <value>\ID\</value>
634    </parameter>
635    <parameter>
636      <name>headerRegexp</name>
637      <label>Header</label>
638      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
639      <class />
640      <value />
641    </parameter>
642    <parameter>
643      <name>blockColumnMapping</name>
644      <label>Block</label>
645      <description>Mapping that picks the feature's block number from the data columns. You must specify either this mapping or mappings for the meta coordinates. Example: \Block\</description>
646      <class>java.lang.String</class>
647      <value>\Block\</value>
648    </parameter>
649    <parameter>
650      <name>rowColumnMapping</name>
651      <label>Row</label>
652      <description>Mapping that picks the feature's row position in a block from the data columns. For example: \Row\</description>
653      <class>java.lang.String</class>
654      <value>\Row\</value>
655    </parameter>
656  </configuration>
657  <configuration pluginClassName="net.sf.basedb.plugins.RawDataFlatFileImporter">
658    <configname>GenePix raw data import (cy5/cy3)</configname>
659    <description>Configuration to import raw data from a genepix file(*.gpr).&#xD;
660The wavelengths should be 635nm for channel_1 and 532nm for channel_2.</description>
661    <parameter>
662      <name>yColumnMapping</name>
663      <label>Y</label>
664      <description>Mapping that picks the spot's physical Y coordinate from the data columns. For example: \Y\</description>
665      <class>java.lang.String</class>
666      <value>\Y\</value>
667    </parameter>
668    <parameter>
669      <name>maxDataColumns</name>
670      <label>Max data columns</label>
671      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
672      <class />
673      <value />
674    </parameter>
675    <parameter>
676      <name>propertyMapping.flags</name>
677      <label>Flags</label>
678      <description>Flags</description>
679      <class>java.lang.String</class>
680      <value>\Flags\</value>
681    </parameter>
682    <parameter>
683      <name>propertyMapping.ch2BgMean</name>
684      <label>Channel 2 background mean</label>
685      <description>The mean of the background intensity in channel 2</description>
686      <class>java.lang.String</class>
687      <value>\B532 Mean\</value>
688    </parameter>
689    <parameter>
690      <name>propertyMapping.mValue</name>
691      <label>M value</label>
692      <description>M value</description>
693      <class>java.lang.String</class>
694      <value>\Log Ratio (635/532)\</value>
695    </parameter>
696    <parameter>
697      <name>trimQuotes</name>
698      <label>Remove quotes</label>
699      <description>If true quotes (" or ') around data value will be removed.</description>
700      <class>java.lang.Boolean</class>
701      <value>true</value>
702    </parameter>
703    <parameter>
704      <name>charset</name>
705      <label>Character set</label>
706      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
707      <class>java.lang.String</class>
708      <value>ISO-8859-1</value>
709    </parameter>
710    <parameter>
711      <name>propertyMapping.diameter</name>
712      <label>Spot diameter</label>
713      <description>The diameter of the spot in pixels</description>
714      <class>java.lang.String</class>
715      <value>\Dia.\</value>
716    </parameter>
717    <parameter>
718      <name>propertyMapping.ch2PercSat</name>
719      <label>Percent saturated pixels</label>
720      <description>Percentage of saturated pixels in channel 2</description>
721      <class>java.lang.String</class>
722      <value>\F532 % Sat.\</value>
723    </parameter>
724    <parameter>
725      <name>propertyMapping.ch1FgSd</name>
726      <label>Channel 1 foreground standard deviation</label>
727      <description>The standard deviation of the foreground intensity in channel 1</description>
728      <class>java.lang.String</class>
729      <value>\F635 SD\</value>
730    </parameter>
731    <parameter>
732      <name>propertyMapping.ch2PercSd1</name>
733      <label>Percent pixels within 1 standard deviation</label>
734      <description>Percentage of pixels within 1 standard deviation in channel 2</description>
735      <class>java.lang.String</class>
736      <value>\% &gt; B532+1SD\</value>
737    </parameter>
738    <parameter>
739      <name>propertyMapping.fgPixels</name>
740      <label>Foreground pixels</label>
741      <description>Number of foreground pixels</description>
742      <class>java.lang.String</class>
743      <value>\F Pixels\</value>
744    </parameter>
745    <parameter>
746      <name>propertyMapping.ch2FgSd</name>
747      <label>Channel 2 foreground standard deviation</label>
748      <description>The standard deviation of the foreground intensity in channel 2</description>
749      <class>java.lang.String</class>
750      <value>\F532 SD\</value>
751    </parameter>
752    <parameter>
753      <name>propertyMapping.ch2BgSd</name>
754      <label>Channel 2 background standard deviation</label>
755      <description>The standard deviation of the background intensity in channel 2</description>
756      <class>java.lang.String</class>
757      <value>\B532 SD\</value>
758    </parameter>
759    <parameter>
760      <name>reporterIdColumnMapping</name>
761      <label>Reporter ID</label>
762      <description>Mapping that picks the spot's reporter from the data columns. For example: \ID\</description>
763      <class>java.lang.String</class>
764      <value>\ID\</value>
765    </parameter>
766    <parameter>
767      <name>headerRegexp</name>
768      <label>Header</label>
769      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
770      <class>java.lang.String</class>
771      <value>"(.+)=(.*)"</value>
772    </parameter>
773    <parameter>
774      <name>propertyMapping.ch1FgMedian</name>
775      <label>Channel 1 foreground median</label>
776      <description>The median of the foreground intensity in channel 1</description>
777      <class>java.lang.String</class>
778      <value>\F635 Median\</value>
779    </parameter>
780    <parameter>
781      <name>propertyMapping.ch1BgMean</name>
782      <label>Channel 1 background mean</label>
783      <description>The mean of the background intensity in channel 1</description>
784      <class>java.lang.String</class>
785      <value>\B635 Mean\</value>
786    </parameter>
787    <parameter>
788      <name>rowColumnMapping</name>
789      <label>Row</label>
790      <description>Mapping that picks the spot's row in the block from the data columns. For example: \Row\</description>
791      <class>java.lang.String</class>
792      <value>\Row\</value>
793    </parameter>
794    <parameter>
795      <name>propertyMapping.ch2BgMedian</name>
796      <label>Channel 2 background median</label>
797      <description>The median of the background intensity in channel 2</description>
798      <class>java.lang.String</class>
799      <value>\B532 Median\</value>
800    </parameter>
801    <parameter>
802      <name>propertyMapping.ch1BgMedian</name>
803      <label>Channel 1 background median</label>
804      <description>The median of the background intensity in channel 1</description>
805      <class>java.lang.String</class>
806      <value>\B635 Median\</value>
807    </parameter>
808    <parameter>
809      <name>propertyMapping.ch2FgMean</name>
810      <label>Channel 2 foreground mean</label>
811      <description>The mean of the foreground intensity in channel 2</description>
812      <class>java.lang.String</class>
813      <value>\F532 Mean\</value>
814    </parameter>
815    <parameter>
816      <name>propertyMapping.rgnR2</name>
817      <label>Rgn R2</label>
818      <description>Rgn R2</description>
819      <class>java.lang.String</class>
820      <value>\Rgn R² (635/532)\</value>
821    </parameter>
822    <parameter>
823      <name>dataHeaderRegexp</name>
824      <label>Data header</label>
825      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
826      <class>java.lang.String</class>
827      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(635\/532\)".*</value>
828    </parameter>
829    <parameter>
830      <name>propertyMapping.ch2FgMedian</name>
831      <label>Channel 2 foreground median</label>
832      <description>The median of the foreground intensity in channel 2</description>
833      <class>java.lang.String</class>
834      <value>\F532 Median\</value>
835    </parameter>
836    <parameter>
837      <name>propertyMapping.ratiosSd</name>
838      <label>Standard deviation of ratios</label>
839      <description>Standard deviation of the intensity ratios for all pixels</description>
840      <class>java.lang.String</class>
841      <value>\Ratios SD (635/532)\</value>
842    </parameter>
843    <parameter>
844      <name>propertyMapping.ch1PercSat</name>
845      <label>Percent saturated pixels</label>
846      <description>Percentage of saturated pixels in channel 1</description>
847      <class>java.lang.String</class>
848      <value>\F635 % Sat.\</value>
849    </parameter>
850    <parameter>
851      <name>dataSplitterRegexp</name>
852      <label>Data splitter</label>
853      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
854      <class>java.lang.String</class>
855      <value>\t</value>
856    </parameter>
857    <parameter>
858      <name>columnColumnMapping</name>
859      <label>Column</label>
860      <description>Mapping that picks the spot's column in the block from the data columns. For example: \Column\</description>
861      <class>java.lang.String</class>
862      <value>\Column\</value>
863    </parameter>
864    <parameter>
865      <name>propertyMapping.bgPixels</name>
866      <label>Background pixels</label>
867      <description>Number of background pixels</description>
868      <class>java.lang.String</class>
869      <value>\B Pixels\</value>
870    </parameter>
871    <parameter>
872      <name>propertyMapping.ch1PercSd2</name>
873      <label>Percent pixels within 2 standard deviations</label>
874      <description>Percentage of pixels within 2 standard deviations in channel 1</description>
875      <class>java.lang.String</class>
876      <value>\% &gt; B635+2SD\</value>
877    </parameter>
878    <parameter>
879      <name>metaGridXColumnMapping</name>
880      <label>MetaGridX</label>
881      <description>Mapping that picks the spot's meta-Grid X-axis from the data columns. For example: \Meta grid X\</description>
882      <class />
883      <value />
884    </parameter>
885    <parameter>
886      <name>propertyMapping.ch1FgMean</name>
887      <label>Channel 1 foreground mean</label>
888      <description>The mean of the foreground intensity in channel 1</description>
889      <class>java.lang.String</class>
890      <value>\F635 Mean\</value>
891    </parameter>
892    <parameter>
893      <name>xColumnMapping</name>
894      <label>X</label>
895      <description>Mapping that picks the spot's physical X coordinate from the data columns. For example: \X\</description>
896      <class>java.lang.String</class>
897      <value>\X\</value>
898    </parameter>
899    <parameter>
900      <name>metaGridYColumnMapping</name>
901      <label>MetaGridY</label>
902      <description>Mapping that picks the spot's meta-Grid Y-axis from the data columns. For example: \Meta grid Y\</description>
903      <class />
904      <value />
905    </parameter>
906    <parameter>
907      <name>propertyMapping.ch1BgSd</name>
908      <label>Channel 1 background standard deviation</label>
909      <description>The standard deviation of the background intensity in channel 1</description>
910      <class>java.lang.String</class>
911      <value>\B635 SD\</value>
912    </parameter>
913    <parameter>
914      <name>minDataColumns</name>
915      <label>Min data columns</label>
916      <description>The minimum number of columns for a line to be counted as a data line.</description>
917      <class />
918      <value />
919    </parameter>
920    <parameter>
921      <name>propertyMapping.rgnRatio</name>
922      <label>Rgn ratio</label>
923      <description>Rgn ratio</description>
924      <class>java.lang.String</class>
925      <value>\Rgn Ratio (635/532)\</value>
926    </parameter>
927    <parameter>
928      <name>ignoreRegexp</name>
929      <label>Ignore</label>
930      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
931      <class />
932      <value />
933    </parameter>
934    <parameter>
935      <name>propertyMapping.CV</name>
936      <label>CV</label>
937      <description>CV</description>
938      <class />
939      <value />
940    </parameter>
941    <parameter>
942      <name>propertyMapping.ch1PercSd1</name>
943      <label>Percent pixels within 1 standard deviation</label>
944      <description>Percentage of pixels within 1 standard deviation in channel 1</description>
945      <class>java.lang.String</class>
946      <value>\% &gt; B635+1SD\</value>
947    </parameter>
948    <parameter>
949      <name>rawDataType</name>
950      <label>Raw data type</label>
951      <description>The type of raw data that this importer will import.</description>
952      <class>java.lang.String</class>
953      <value>genepix</value>
954    </parameter>
955    <parameter>
956      <name>dataFooterRegexp</name>
957      <label>Data footer</label>
958      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
959      <class />
960      <value />
961    </parameter>
962    <parameter>
963      <name>propertyMapping.ch2PercSd2</name>
964      <label>Percent pixels within 2 standard deviations</label>
965      <description>Percentage of pixels within 2 standard deviations in channel 2</description>
966      <class>java.lang.String</class>
967      <value>\% &gt; B532+2SD\</value>
968    </parameter>
969    <parameter>
970      <name>blockColumnMapping</name>
971      <label>Block</label>
972      <description>Mapping that picks the spot's block from the data columns. For example: \Block\</description>
973      <class>java.lang.String</class>
974      <value>\Block\</value>
975    </parameter>
976  </configuration>
977  <configuration pluginClassName="net.sf.basedb.plugins.RawDataFlatFileImporter">
978    <configname>GenePix raw data import (cy3/cy5)</configname>
979    <description>Configuration to import raw data from a genepix file(*.gpr).&#xD;
980The wavelengths should be 532nm for channel_1 and 635nm for channel_2.</description>
981    <parameter>
982      <name>yColumnMapping</name>
983      <label>Y</label>
984      <description>Mapping that picks the spot's physical Y coordinate from the data columns. For example: \Y\</description>
985      <class>java.lang.String</class>
986      <value>\Y\</value>
987    </parameter>
988    <parameter>
989      <name>maxDataColumns</name>
990      <label>Max data columns</label>
991      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
992      <class />
993      <value />
994    </parameter>
995    <parameter>
996      <name>propertyMapping.ch2BgMean</name>
997      <label>Channel 2 background mean</label>
998      <description>The mean of the background intensity in channel 2</description>
999      <class>java.lang.String</class>
1000      <value>\B635 Mean\</value>
1001    </parameter>
1002    <parameter>
1003      <name>propertyMapping.flags</name>
1004      <label>Flags</label>
1005      <description>Flags</description>
1006      <class>java.lang.String</class>
1007      <value>\Flags\</value>
1008    </parameter>
1009    <parameter>
1010      <name>propertyMapping.mValue</name>
1011      <label>M value</label>
1012      <description>M value</description>
1013      <class>java.lang.String</class>
1014      <value>\Log Ratio (532/635)\</value>
1015    </parameter>
1016    <parameter>
1017      <name>trimQuotes</name>
1018      <label>Remove quotes</label>
1019      <description>If true quotes (" or ') around data value will be removed.</description>
1020      <class>java.lang.Boolean</class>
1021      <value>true</value>
1022    </parameter>
1023    <parameter>
1024      <name>charset</name>
1025      <label>Character set</label>
1026      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
1027      <class>java.lang.String</class>
1028      <value>ISO-8859-1</value>
1029    </parameter>
1030    <parameter>
1031      <name>propertyMapping.diameter</name>
1032      <label>Spot diameter</label>
1033      <description>The diameter of the spot in pixels</description>
1034      <class>java.lang.String</class>
1035      <value>\Dia.\</value>
1036    </parameter>
1037    <parameter>
1038      <name>propertyMapping.ch2PercSat</name>
1039      <label>Percent saturated pixels</label>
1040      <description>Percentage of saturated pixels in channel 2</description>
1041      <class>java.lang.String</class>
1042      <value>\F635 % Sat.\</value>
1043    </parameter>
1044    <parameter>
1045      <name>propertyMapping.ch1FgSd</name>
1046      <label>Channel 1 foreground standard deviation</label>
1047      <description>The standard deviation of the foreground intensity in channel 1</description>
1048      <class>java.lang.String</class>
1049      <value>\F532 SD\</value>
1050    </parameter>
1051    <parameter>
1052      <name>propertyMapping.ch2PercSd1</name>
1053      <label>Percent pixels within 1 standard deviation</label>
1054      <description>Percentage of pixels within 1 standard deviation in channel 2</description>
1055      <class>java.lang.String</class>
1056      <value>\% &gt; B635+1SD\</value>
1057    </parameter>
1058    <parameter>
1059      <name>propertyMapping.fgPixels</name>
1060      <label>Foreground pixels</label>
1061      <description>Number of foreground pixels</description>
1062      <class>java.lang.String</class>
1063      <value>\F Pixels\</value>
1064    </parameter>
1065    <parameter>
1066      <name>propertyMapping.ch2FgSd</name>
1067      <label>Channel 2 foreground standard deviation</label>
1068      <description>The standard deviation of the foreground intensity in channel 2</description>
1069      <class>java.lang.String</class>
1070      <value>\F635 SD\</value>
1071    </parameter>
1072    <parameter>
1073      <name>propertyMapping.ch2BgSd</name>
1074      <label>Channel 2 background standard deviation</label>
1075      <description>The standard deviation of the background intensity in channel 2</description>
1076      <class>java.lang.String</class>
1077      <value>\B635 SD\</value>
1078    </parameter>
1079    <parameter>
1080      <name>reporterIdColumnMapping</name>
1081      <label>Reporter ID</label>
1082      <description>Mapping that picks the spot's reporter from the data columns. For example: \ID\</description>
1083      <class>java.lang.String</class>
1084      <value>\ID\</value>
1085    </parameter>
1086    <parameter>
1087      <name>headerRegexp</name>
1088      <label>Header</label>
1089      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
1090      <class>java.lang.String</class>
1091      <value>"(.+)=(.*)"</value>
1092    </parameter>
1093    <parameter>
1094      <name>propertyMapping.ch1FgMedian</name>
1095      <label>Channel 1 foreground median</label>
1096      <description>The median of the foreground intensity in channel 1</description>
1097      <class>java.lang.String</class>
1098      <value>\F532 Median\</value>
1099    </parameter>
1100    <parameter>
1101      <name>propertyMapping.ch1BgMean</name>
1102      <label>Channel 1 background mean</label>
1103      <description>The mean of the background intensity in channel 1</description>
1104      <class>java.lang.String</class>
1105      <value>\B532 Mean\</value>
1106    </parameter>
1107    <parameter>
1108      <name>propertyMapping.ch2BgMedian</name>
1109      <label>Channel 2 background median</label>
1110      <description>The median of the background intensity in channel 2</description>
1111      <class>java.lang.String</class>
1112      <value>\B635 Median\</value>
1113    </parameter>
1114    <parameter>
1115      <name>rowColumnMapping</name>
1116      <label>Row</label>
1117      <description>Mapping that picks the spot's row in the block from the data columns. For example: \Row\</description>
1118      <class>java.lang.String</class>
1119      <value>\Row\</value>
1120    </parameter>
1121    <parameter>
1122      <name>propertyMapping.ch1BgMedian</name>
1123      <label>Channel 1 background median</label>
1124      <description>The median of the background intensity in channel 1</description>
1125      <class>java.lang.String</class>
1126      <value>\B532 Median\</value>
1127    </parameter>
1128    <parameter>
1129      <name>propertyMapping.ch2FgMean</name>
1130      <label>Channel 2 foreground mean</label>
1131      <description>The mean of the foreground intensity in channel 2</description>
1132      <class>java.lang.String</class>
1133      <value>\F635 Mean\</value>
1134    </parameter>
1135    <parameter>
1136      <name>propertyMapping.rgnR2</name>
1137      <label>Rgn R2</label>
1138      <description>Rgn R2</description>
1139      <class>java.lang.String</class>
1140      <value>\Rgn R² (532/635)\</value>
1141    </parameter>
1142    <parameter>
1143      <name>propertyMapping.ch2FgMedian</name>
1144      <label>Channel 2 foreground median</label>
1145      <description>The median of the foreground intensity in channel 2</description>
1146      <class>java.lang.String</class>
1147      <value>\F635 Median\</value>
1148    </parameter>
1149    <parameter>
1150      <name>dataHeaderRegexp</name>
1151      <label>Data header</label>
1152      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
1153      <class>java.lang.String</class>
1154      <value>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(532\/635\)".*</value>
1155    </parameter>
1156    <parameter>
1157      <name>propertyMapping.ratiosSd</name>
1158      <label>Standard deviation of ratios</label>
1159      <description>Standard deviation of the intensity ratios for all pixels</description>
1160      <class>java.lang.String</class>
1161      <value>\Ratios SD (532/635)\</value>
1162    </parameter>
1163    <parameter>
1164      <name>propertyMapping.ch1PercSat</name>
1165      <label>Percent saturated pixels</label>
1166      <description>Percentage of saturated pixels in channel 1</description>
1167      <class>java.lang.String</class>
1168      <value>\F532 % Sat.\</value>
1169    </parameter>
1170    <parameter>
1171      <name>dataSplitterRegexp</name>
1172      <label>Data splitter</label>
1173      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
1174      <class>java.lang.String</class>
1175      <value>\t</value>
1176    </parameter>
1177    <parameter>
1178      <name>columnColumnMapping</name>
1179      <label>Column</label>
1180      <description>Mapping that picks the spot's column in the block from the data columns. For example: \Column\</description>
1181      <class>java.lang.String</class>
1182      <value>\Column\</value>
1183    </parameter>
1184    <parameter>
1185      <name>propertyMapping.bgPixels</name>
1186      <label>Background pixels</label>
1187      <description>Number of background pixels</description>
1188      <class>java.lang.String</class>
1189      <value>\B Pixels\</value>
1190    </parameter>
1191    <parameter>
1192      <name>propertyMapping.ch1PercSd2</name>
1193      <label>Percent pixels within 2 standard deviations</label>
1194      <description>Percentage of pixels within 2 standard deviations in channel 1</description>
1195      <class>java.lang.String</class>
1196      <value>\% &gt; B532+2SD\</value>
1197    </parameter>
1198    <parameter>
1199      <name>metaGridXColumnMapping</name>
1200      <label>MetaGridX</label>
1201      <description>Mapping that picks the spot's meta-Grid X-axis from the data columns. For example: \Meta grid X\</description>
1202      <class />
1203      <value />
1204    </parameter>
1205    <parameter>
1206      <name>propertyMapping.ch1FgMean</name>
1207      <label>Channel 1 foreground mean</label>
1208      <description>The mean of the foreground intensity in channel 1</description>
1209      <class>java.lang.String</class>
1210      <value>\F532 Mean\</value>
1211    </parameter>
1212    <parameter>
1213      <name>xColumnMapping</name>
1214      <label>X</label>
1215      <description>Mapping that picks the spot's physical X coordinate from the data columns. For example: \X\</description>
1216      <class>java.lang.String</class>
1217      <value>\X\</value>
1218    </parameter>
1219    <parameter>
1220      <name>metaGridYColumnMapping</name>
1221      <label>MetaGridY</label>
1222      <description>Mapping that picks the spot's meta-Grid Y-axis from the data columns. For example: \Meta grid Y\</description>
1223      <class />
1224      <value />
1225    </parameter>
1226    <parameter>
1227      <name>propertyMapping.ch1BgSd</name>
1228      <label>Channel 1 background standard deviation</label>
1229      <description>The standard deviation of the background intensity in channel 1</description>
1230      <class>java.lang.String</class>
1231      <value>\B532 SD\</value>
1232    </parameter>
1233    <parameter>
1234      <name>minDataColumns</name>
1235      <label>Min data columns</label>
1236      <description>The minimum number of columns for a line to be counted as a data line.</description>
1237      <class />
1238      <value />
1239    </parameter>
1240    <parameter>
1241      <name>propertyMapping.rgnRatio</name>
1242      <label>Rgn ratio</label>
1243      <description>Rgn ratio</description>
1244      <class>java.lang.String</class>
1245      <value>\Rgn Ratio (532/635)\</value>
1246    </parameter>
1247    <parameter>
1248      <name>ignoreRegexp</name>
1249      <label>Ignore</label>
1250      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
1251      <class />
1252      <value />
1253    </parameter>
1254    <parameter>
1255      <name>propertyMapping.ch1PercSd1</name>
1256      <label>Percent pixels within 1 standard deviation</label>
1257      <description>Percentage of pixels within 1 standard deviation in channel 1</description>
1258      <class>java.lang.String</class>
1259      <value>\% &gt; B532+1SD\</value>
1260    </parameter>
1261    <parameter>
1262      <name>propertyMapping.CV</name>
1263      <label>CV</label>
1264      <description>CV</description>
1265      <class />
1266      <value />
1267    </parameter>
1268    <parameter>
1269      <name>rawDataType</name>
1270      <label>Raw data type</label>
1271      <description>The type of raw data that this importer will import.</description>
1272      <class>java.lang.String</class>
1273      <value>genepix</value>
1274    </parameter>
1275    <parameter>
1276      <name>dataFooterRegexp</name>
1277      <label>Data footer</label>
1278      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
1279      <class />
1280      <value />
1281    </parameter>
1282    <parameter>
1283      <name>propertyMapping.ch2PercSd2</name>
1284      <label>Percent pixels within 2 standard deviations</label>
1285      <description>Percentage of pixels within 2 standard deviations in channel 2</description>
1286      <class>java.lang.String</class>
1287      <value>\% &gt; B635+2SD\</value>
1288    </parameter>
1289    <parameter>
1290      <name>blockColumnMapping</name>
1291      <label>Block</label>
1292      <description>Mapping that picks the spot's block from the data columns. For example: \Block\</description>
1293      <class>java.lang.String</class>
1294      <value>\Block\</value>
1295    </parameter>
1296  </configuration>
1297  <configuration pluginClassName="net.sf.basedb.plugins.PlateFlatFileImporter">
1298    <configname>96_well plate import</configname>
1299    <description>This configuration is for the Plate importer plugin when to import 96-well plates.</description>
1300    <parameter>
1301      <name>maxDataColumns</name>
1302      <label>Max data columns</label>
1303      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
1304      <class />
1305      <value />
1306    </parameter>
1307    <parameter>
1308      <name>reporterColumnMapping</name>
1309      <label>Reporter ID</label>
1310      <description>Mapping that picks the well's reporter id from the data columns. For example: \ID\</description>
1311      <class>java.lang.String</class>
1312      <value>\oligo_id\</value>
1313    </parameter>
1314    <parameter>
1315      <name>dataHeaderRegexp</name>
1316      <label>Data header</label>
1317      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
1318      <class>java.lang.String</class>
1319      <value>96_number\t96_column\t96_row\t96_position\toligo_id.*</value>
1320    </parameter>
1321    <parameter>
1322      <name>barcodeColumnMapping</name>
1323      <label>Plate barcode</label>
1324      <description>Mapping that picks the plate barcode from the data columns. For example: \Barcode\</description>
1325      <class />
1326      <value />
1327    </parameter>
1328    <parameter>
1329      <name>trimQuotes</name>
1330      <label>Remove quotes</label>
1331      <description>If true quotes (" or ') around data value will be removed.</description>
1332      <class>java.lang.Boolean</class>
1333      <value>true</value>
1334    </parameter>
1335    <parameter>
1336      <name>dataSplitterRegexp</name>
1337      <label>Data splitter</label>
1338      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
1339      <class>java.lang.String</class>
1340      <value>\t</value>
1341    </parameter>
1342    <parameter>
1343      <name>charset</name>
1344      <label>Character set</label>
1345      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
1346      <class>java.lang.String</class>
1347      <value>ISO-8859-1</value>
1348    </parameter>
1349    <parameter>
1350      <name>columnColumnMapping</name>
1351      <label>Column</label>
1352      <description>Mapping that picks the well's column in the plate from the data columns. For example: \Column\</description>
1353      <class>java.lang.String</class>
1354      <value>\96_column\</value>
1355    </parameter>
1356    <parameter>
1357      <name>nameColumnMapping</name>
1358      <label>Plate number/name</label>
1359      <description>Mapping that picks the plate name from the data columns. For example: \Plate\</description>
1360      <class>java.lang.String</class>
1361      <value>\96_number\</value>
1362    </parameter>
1363    <parameter>
1364      <name>minDataColumns</name>
1365      <label>Min data columns</label>
1366      <description>The minimum number of columns for a line to be counted as a data line.</description>
1367      <class />
1368      <value />
1369    </parameter>
1370    <parameter>
1371      <name>ignoreRegexp</name>
1372      <label>Ignore</label>
1373      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
1374      <class />
1375      <value />
1376    </parameter>
1377    <parameter>
1378      <name>dataFooterRegexp</name>
1379      <label>Data footer</label>
1380      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
1381      <class />
1382      <value />
1383    </parameter>
1384    <parameter>
1385      <name>headerRegexp</name>
1386      <label>Header</label>
1387      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
1388      <class />
1389      <value />
1390    </parameter>
1391    <parameter>
1392      <name>rowColumnMapping</name>
1393      <label>Row</label>
1394      <description>Mapping that picks the well's row in the plate from the data columns. For example: \Row\</description>
1395      <class>java.lang.String</class>
1396      <value>\96_row\</value>
1397    </parameter>
1398  </configuration>
1399  <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
1400    <configname>Reporters from 96well plates file</configname>
1401    <description>This configuration is for importing reporters from the same text file as 96well plates are imported from.</description>
1402    <parameter>
1403      <name>maxDataColumns</name>
1404      <label>Max data columns</label>
1405      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
1406      <class />
1407      <value />
1408    </parameter>
1409    <parameter>
1410      <name>extendedColumnMapping.locusLink</name>
1411      <label>LocusLink</label>
1412      <description />
1413      <class />
1414      <value />
1415    </parameter>
1416    <parameter>
1417      <name>trimQuotes</name>
1418      <label>Remove quotes</label>
1419      <description>If true quotes (" or ') around data value will be removed.</description>
1420      <class>java.lang.Boolean</class>
1421      <value>true</value>
1422    </parameter>
1423    <parameter>
1424      <name>charset</name>
1425      <label>Character set</label>
1426      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
1427      <class>java.lang.String</class>
1428      <value>ISO-8859-1</value>
1429    </parameter>
1430    <parameter>
1431      <name>scoreColumnMapping</name>
1432      <label>Score</label>
1433      <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
1434      <class />
1435      <value />
1436    </parameter>
1437    <parameter>
1438      <name>nameColumnMapping</name>
1439      <label>Name</label>
1440      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
1441      <class>java.lang.String</class>
1442      <value>\oligo_id\</value>
1443    </parameter>
1444    <parameter>
1445      <name>extendedColumnMapping.markers</name>
1446      <label>Markers</label>
1447      <description />
1448      <class />
1449      <value />
1450    </parameter>
1451    <parameter>
1452      <name>extendedColumnMapping.vector</name>
1453      <label>Vector</label>
1454      <description>The vector from which the reporter is derived</description>
1455      <class />
1456      <value />
1457    </parameter>
1458    <parameter>
1459      <name>extendedColumnMapping.nid</name>
1460      <label>NID</label>
1461      <description />
1462      <class />
1463      <value />
1464    </parameter>
1465    <parameter>
1466      <name>descriptionColumnMapping</name>
1467      <label>Description</label>
1468      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
1469      <class>java.lang.String</class>
1470      <value>\description_Ensembl*\</value>
1471    </parameter>
1472    <parameter>
1473      <name>headerRegexp</name>
1474      <label>Header</label>
1475      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
1476      <class />
1477      <value />
1478    </parameter>
1479    <parameter>
1480      <name>reporterIdColumnMapping</name>
1481      <label>Reporter ID</label>
1482      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
1483      <class>java.lang.String</class>
1484      <value>\oligo_id\</value>
1485    </parameter>
1486    <parameter>
1487      <name>symbolColumnMapping</name>
1488      <label>Gene symbol</label>
1489      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
1490      <class>java.lang.String</class>
1491      <value>\gene_symbol_Ensembl*\</value>
1492    </parameter>
1493    <parameter>
1494      <name>extendedColumnMapping.antibiotics</name>
1495      <label>Antibiotics</label>
1496      <description />
1497      <class />
1498      <value />
1499    </parameter>
1500    <parameter>
1501      <name>extendedColumnMapping.omim</name>
1502      <label>OMIM</label>
1503      <description />
1504      <class />
1505      <value />
1506    </parameter>
1507    <parameter>
1508      <name>extendedColumnMapping.chromosome</name>
1509      <label>Chromosome</label>
1510      <description>The chromosome from which the reporter is derived</description>
1511      <class />
1512      <value />
1513    </parameter>
1514    <parameter>
1515      <name>reporterType</name>
1516      <label>Reporter type</label>
1517      <description>The reporter type assigned to the imported reporters</description>
1518      <class />
1519      <value />
1520    </parameter>
1521    <parameter>
1522      <name>dataHeaderRegexp</name>
1523      <label>Data header</label>
1524      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
1525      <class>java.lang.String</class>
1526      <value>96_number\t96_column\t96_row\t96_position\toligo_id.*</value>
1527    </parameter>
1528    <parameter>
1529      <name>dataSplitterRegexp</name>
1530      <label>Data splitter</label>
1531      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
1532      <class>java.lang.String</class>
1533      <value>\t</value>
1534    </parameter>
1535    <parameter>
1536      <name>extendedColumnMapping.length</name>
1537      <label>Length</label>
1538      <description>The length of the sequence</description>
1539      <class />
1540      <value />
1541    </parameter>
1542    <parameter>
1543      <name>extendedColumnMapping.tissue</name>
1544      <label>Tissue</label>
1545      <description>The tissue from which the reporter is derived</description>
1546      <class />
1547      <value />
1548    </parameter>
1549    <parameter>
1550      <name>extendedColumnMapping.accession</name>
1551      <label>Accession</label>
1552      <description />
1553      <class />
1554      <value />
1555    </parameter>
1556    <parameter>
1557      <name>minDataColumns</name>
1558      <label>Min data columns</label>
1559      <description>The minimum number of columns for a line to be counted as a data line.</description>
1560      <class />
1561      <value />
1562    </parameter>
1563    <parameter>
1564      <name>ignoreRegexp</name>
1565      <label>Ignore</label>
1566      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
1567      <class />
1568      <value />
1569    </parameter>
1570    <parameter>
1571      <name>reporterTypeColumnMapping</name>
1572      <label>Reporter type</label>
1573      <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
1574      <class />
1575      <value />
1576    </parameter>
1577    <parameter>
1578      <name>extendedColumnMapping.library</name>
1579      <label>Library</label>
1580      <description>The library from which the reporter is derived</description>
1581      <class />
1582      <value />
1583    </parameter>
1584    <parameter>
1585      <name>extendedColumnMapping.clusterId</name>
1586      <label>Cluster ID</label>
1587      <description>A unique identifier for a Unigene entry</description>
1588      <class />
1589      <value />
1590    </parameter>
1591    <parameter>
1592      <name>dataFooterRegexp</name>
1593      <label>Data footer</label>
1594      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
1595      <class />
1596      <value />
1597    </parameter>
1598    <parameter>
1599      <name>extendedColumnMapping.cytoband</name>
1600      <label>Cytoband</label>
1601      <description>The cytoband from which the reporter is derived</description>
1602      <class />
1603      <value />
1604    </parameter>
1605    <parameter>
1606      <name>extendedColumnMapping.sequence</name>
1607      <label>Sequence</label>
1608      <description>The nucleotide sequence of the reporter</description>
1609      <class>java.lang.String</class>
1610      <value>\oligo_sequence\</value>
1611    </parameter>
1612    <parameter>
1613      <name>extendedColumnMapping.species</name>
1614      <label>Species</label>
1615      <description>The organism from which the reporter is derived</description>
1616      <class />
1617      <value />
1618    </parameter>
1619  </configuration>
1620</configfile>
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