source: trunk/data/plugin_configfile.xml @ 2975

Last change on this file since 2975 was 2975, checked in by Nicklas Nordborg, 15 years ago

Updated configuration files with correct column mappings.

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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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