Ticket #441: agilent.import.xml

File agilent.import.xml, 20.2 KB (added by Nicklas Nordborg, 18 years ago)

Test of import configurations for Agilent raw data and reporters

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.RawDataFlatFileImporter">
4 <configname>Agilent raw data</configname>
5 <description />
6 <parameter>
7 <name>propertyMapping.rPValFeatEqBG</name>
8 <label>R p-value</label>
9 <class />
10 <value />
11 </parameter>
12 <parameter>
13 <name>propertyMapping.rSpatialDetrendIsInFilteredSet</name>
14 <label>R spatial trend</label>
15 <class />
16 <value />
17 </parameter>
18 <parameter>
19 <name>propertyMapping.gBGSubSignal</name>
20 <label>G net signal</label>
21 <class />
22 <value />
23 </parameter>
24 <parameter>
25 <name>propertyMapping.BGPixCorrelation</name>
26 <label>BG pix correlation</label>
27 <class />
28 <value />
29 </parameter>
30 <parameter>
31 <name>propertyMapping.rMedianSignal</name>
32 <label>R median signal</label>
33 <class>java.lang.String</class>
34 <value>\rMedianSignal\</value>
35 </parameter>
36 <parameter>
37 <name>propertyMapping.gIsPosAndSignif</name>
38 <label>G &gt; 0 and significant</label>
39 <class />
40 <value />
41 </parameter>
42 <parameter>
43 <name>propertyMapping.IsManualFlag</name>
44 <label>Manual flag</label>
45 <class />
46 <value />
47 </parameter>
48 <parameter>
49 <name>propertyMapping.gNumPixOLHi</name>
50 <label>G high outlier pixels</label>
51 <class>java.lang.String</class>
52 <value>\gNumPixOLHi\</value>
53 </parameter>
54 <parameter>
55 <name>propertyMapping.rIsPosAndSignif</name>
56 <label>R &gt; 0 and significant</label>
57 <class />
58 <value />
59 </parameter>
60 <parameter>
61 <name>propertyMapping.IsNormalization</name>
62 <label>Normalization</label>
63 <class />
64 <value />
65 </parameter>
66 <parameter>
67 <name>propertyMapping.ErrorModel</name>
68 <label>Error model</label>
69 <class />
70 <value />
71 </parameter>
72 <parameter>
73 <name>propertyMapping.gIsSaturated</name>
74 <label>G is saturated</label>
75 <class />
76 <value />
77 </parameter>
78 <parameter>
79 <name>propertyMapping.gPValFeatEqBG</name>
80 <label>G p-value</label>
81 <class />
82 <value />
83 </parameter>
84 <parameter>
85 <name>propertyMapping.rNumSatPix</name>
86 <label>R saturated pixels</label>
87 <class />
88 <value />
89 </parameter>
90 <parameter>
91 <name>propertyMapping.rIsSaturated</name>
92 <label>R is saturated</label>
93 <class />
94 <value />
95 </parameter>
96 <parameter>
97 <name>propertyMapping.gNumPixOLLo</name>
98 <label>G low outlier pixels</label>
99 <class>java.lang.String</class>
100 <value>\gNumPixOLLo\</value>
101 </parameter>
102 <parameter>
103 <name>propertyMapping.DyeNormCorrelation</name>
104 <label>Normalized correlation</label>
105 <class />
106 <value />
107 </parameter>
108 <parameter>
109 <name>reporterIdColumnMapping</name>
110 <label>Reporter ID</label>
111 <class>java.lang.String</class>
112 <value>\ProbeUID\</value>
113 </parameter>
114 <parameter>
115 <name>propertyMapping.gIsBGNonUnifOL</name>
116 <label>G bg non-uniform outlier</label>
117 <class />
118 <value />
119 </parameter>
120 <parameter>
121 <name>propertyMapping.gIsFeatNonUnifOL</name>
122 <label>G non-uniform outlier</label>
123 <class />
124 <value />
125 </parameter>
126 <parameter>
127 <name>rowColumnMapping</name>
128 <label>Row</label>
129 <class>java.lang.String</class>
130 <value>\Row\</value>
131 </parameter>
132 <parameter>
133 <name>propertyMapping.rNumPixOLLo</name>
134 <label>R low outlier pixels</label>
135 <class>java.lang.String</class>
136 <value>\rNumPixOLLo\</value>
137 </parameter>
138 <parameter>
139 <name>propertyMapping.gSurrogateUsed</name>
140 <label>G surrogate used</label>
141 <class>java.lang.String</class>
142 <value>\gSurrogateUsed\</value>
143 </parameter>
144 <parameter>
145 <name>dataHeaderRegexp</name>
146 <label>Data header</label>
147 <class>java.lang.String</class>
148 <value>\QFEATURES FeatureNum Row Col accessions ProbeUID ControlType ProbeName GeneName SystematicName Description PositionX PositionY LogRatio LogRatioError PValueLogRatio gSurrogateUsed rSurrogateUsed gIsFound rIsFound gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gNumPixOLHi rNumPixOLHi gNumPixOLLo rNumPixOLLo gNumPix rNumPix gMeanSignal rMeanSignal gMedianSignal rMedianSignal gPixSDev rPixSDev gBGNumPix rBGNumPix gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gNumSatPix rNumSatPix gIsSaturated rIsSaturated PixCorrelation BGPixCorrelation gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gBGSubSigError rBGSubSigError BGSubSigCorrelation gIsPosAndSignif rIsPosAndSignif gPValFeatEqBG rPValFeatEqBG gNumBGUsed rNumBGUsed gIsWellAboveBG rIsWellAboveBG gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel xDev gSpatialDetrendIsInFilteredSet rSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue rSpatialDetrendSurfaceValue\E</value>
149 </parameter>
150 <parameter>
151 <name>propertyMapping.rBGNumPix</name>
152 <label>R background pixels</label>
153 <class />
154 <value />
155 </parameter>
156 <parameter>
157 <name>propertyMapping.rSurrogateUsed</name>
158 <label>R surrogate used</label>
159 <class>java.lang.String</class>
160 <value>\rSurrogateUsed\</value>
161 </parameter>
162 <parameter>
163 <name>columnColumnMapping</name>
164 <label>Column</label>
165 <class>java.lang.String</class>
166 <value>\Col\</value>
167 </parameter>
168 <parameter>
169 <name>propertyMapping.gIsFound</name>
170 <label>G is found</label>
171 <class>java.lang.String</class>
172 <value>\gIsFound\</value>
173 </parameter>
174 <parameter>
175 <name>metaGridXColumnMapping</name>
176 <label>MetaGridX</label>
177 <class />
178 <value />
179 </parameter>
180 <parameter>
181 <name>propertyMapping.gNumPix</name>
182 <label>G pixels</label>
183 <class>java.lang.String</class>
184 <value>\gNumPix\</value>
185 </parameter>
186 <parameter>
187 <name>propertyMapping.gIsWellAboveBG</name>
188 <label>G well above bg</label>
189 <class />
190 <value />
191 </parameter>
192 <parameter>
193 <name>propertyMapping.gSpatialDetrendSurfaceValue</name>
194 <label>G surface value</label>
195 <class />
196 <value />
197 </parameter>
198 <parameter>
199 <name>metaGridYColumnMapping</name>
200 <label>MetaGridY</label>
201 <class />
202 <value />
203 </parameter>
204 <parameter>
205 <name>propertyMapping.gBGMedianSignal</name>
206 <label>G median background</label>
207 <class />
208 <value />
209 </parameter>
210 <parameter>
211 <name>propertyMapping.rIsBGPopnOL</name>
212 <label>R bg population outlier</label>
213 <class />
214 <value />
215 </parameter>
216 <parameter>
217 <name>rawDataType</name>
218 <label>Raw data type</label>
219 <class>java.lang.String</class>
220 <value>agilent</value>
221 </parameter>
222 <parameter>
223 <name>dataFooterRegexp</name>
224 <label>Data footer</label>
225 <class />
226 <value />
227 </parameter>
228 <parameter>
229 <name>propertyMapping.rNumPix</name>
230 <label>R pixels</label>
231 <class>java.lang.String</class>
232 <value>\rNumPix\</value>
233 </parameter>
234 <parameter>
235 <name>propertyMapping.gBGMeanSignal</name>
236 <label>G mean background</label>
237 <class />
238 <value />
239 </parameter>
240 <parameter>
241 <name>propertyMapping.gMedianSignal</name>
242 <label>G median signal</label>
243 <class>java.lang.String</class>
244 <value>\gMedianSignal\</value>
245 </parameter>
246 <parameter>
247 <name>blockColumnMapping</name>
248 <label>Block</label>
249 <class>java.lang.String</class>
250 <value>\FeatureNum\</value>
251 </parameter>
252 <parameter>
253 <name>propertyMapping.rBGMeanSignal</name>
254 <label>R mean background</label>
255 <class />
256 <value />
257 </parameter>
258 <parameter>
259 <name>yColumnMapping</name>
260 <label>Y</label>
261 <class>java.lang.String</class>
262 <value>\PositionY\</value>
263 </parameter>
264 <parameter>
265 <name>propertyMapping.LogRatio</name>
266 <label>Log ratio</label>
267 <class>java.lang.String</class>
268 <value>\LogRatio\</value>
269 </parameter>
270 <parameter>
271 <name>propertyMapping.rIsFeatPopnOL</name>
272 <label>R population outlier</label>
273 <class />
274 <value />
275 </parameter>
276 <parameter>
277 <name>maxDataColumns</name>
278 <label>Max data columns</label>
279 <class />
280 <value />
281 </parameter>
282 <parameter>
283 <name>propertyMapping.gNumBGUsed</name>
284 <label>G background pixels</label>
285 <class />
286 <value />
287 </parameter>
288 <parameter>
289 <name>propertyMapping.gMeanSignal</name>
290 <label>G mean signal</label>
291 <class>java.lang.String</class>
292 <value>\gMeanSignal\</value>
293 </parameter>
294 <parameter>
295 <name>trimQuotes</name>
296 <label>Remove quotes</label>
297 <class>java.lang.Boolean</class>
298 <value>true</value>
299 </parameter>
300 <parameter>
301 <name>propertyMapping.PValueLogRatio</name>
302 <label>P value log ratio</label>
303 <class>java.lang.String</class>
304 <value>\PValueLogRatio\</value>
305 </parameter>
306 <parameter>
307 <name>propertyMapping.rIsFeatNonUnifOL</name>
308 <label>R non-uniform outlier</label>
309 <class />
310 <value />
311 </parameter>
312 <parameter>
313 <name>propertyMapping.rNumPixOLHi</name>
314 <label>R high outlier pixels</label>
315 <class>java.lang.String</class>
316 <value>\rNumPixOLHi\</value>
317 </parameter>
318 <parameter>
319 <name>propertyMapping.gBGUsed</name>
320 <label>G bg used</label>
321 <class />
322 <value />
323 </parameter>
324 <parameter>
325 <name>propertyMapping.gNumSatPix</name>
326 <label>G saturated pixels</label>
327 <class />
328 <value />
329 </parameter>
330 <parameter>
331 <name>propertyMapping.rIsWellAboveBG</name>
332 <label>R well above bg</label>
333 <class />
334 <value />
335 </parameter>
336 <parameter>
337 <name>propertyMapping.rProcessedSignal</name>
338 <label>R processed signal</label>
339 <class>java.lang.String</class>
340 <value>\rProcessedSignal\</value>
341 </parameter>
342 <parameter>
343 <name>propertyMapping.gBGNumPix</name>
344 <label>G background pixels</label>
345 <class />
346 <value />
347 </parameter>
348 <parameter>
349 <name>headerRegexp</name>
350 <label>Header</label>
351 <class />
352 <value />
353 </parameter>
354 <parameter>
355 <name>propertyMapping.gIsFeatPopnOL</name>
356 <label>G population outlier</label>
357 <class />
358 <value />
359 </parameter>
360 <parameter>
361 <name>propertyMapping.BGSubSigCorrelation</name>
362 <label>BG correlation</label>
363 <class />
364 <value />
365 </parameter>
366 <parameter>
367 <name>propertyMapping.gProcessedSignal</name>
368 <label>G processed signal</label>
369 <class>java.lang.String</class>
370 <value>\gProcessedSignal\</value>
371 </parameter>
372 <parameter>
373 <name>propertyMapping.gDyeNormSignal</name>
374 <label>G normalized signal</label>
375 <class />
376 <value />
377 </parameter>
378 <parameter>
379 <name>propertyMapping.rBGUsed</name>
380 <label>R bg used</label>
381 <class />
382 <value />
383 </parameter>
384 <parameter>
385 <name>propertyMapping.gIsBGPopnOL</name>
386 <label>G bg population outlier</label>
387 <class />
388 <value />
389 </parameter>
390 <parameter>
391 <name>dataSplitterRegexp</name>
392 <label>Data splitter</label>
393 <class>java.lang.String</class>
394 <value>\t</value>
395 </parameter>
396 <parameter>
397 <name>propertyMapping.rBGSubSignal</name>
398 <label>R net signal</label>
399 <class />
400 <value />
401 </parameter>
402 <parameter>
403 <name>propertyMapping.PixCorrelation</name>
404 <label>Pix correlation</label>
405 <class />
406 <value />
407 </parameter>
408 <parameter>
409 <name>propertyMapping.rIsFound</name>
410 <label>R is found</label>
411 <class>java.lang.String</class>
412 <value>\rIsFound\</value>
413 </parameter>
414 <parameter>
415 <name>propertyMapping.rBGMedianSignal</name>
416 <label>R median background</label>
417 <class />
418 <value />
419 </parameter>
420 <parameter>
421 <name>propertyMapping.rNumBGUsed</name>
422 <label>R background pixels</label>
423 <class />
424 <value />
425 </parameter>
426 <parameter>
427 <name>xColumnMapping</name>
428 <label>X</label>
429 <class>java.lang.String</class>
430 <value>\PositionX\</value>
431 </parameter>
432 <parameter>
433 <name>minDataColumns</name>
434 <label>Min data columns</label>
435 <class />
436 <value />
437 </parameter>
438 <parameter>
439 <name>ignoreRegexp</name>
440 <label>Ignore</label>
441 <class />
442 <value />
443 </parameter>
444 <parameter>
445 <name>propertyMapping.rIsBGNonUnifOL</name>
446 <label>R bg non-uniform outlier</label>
447 <class />
448 <value />
449 </parameter>
450 <parameter>
451 <name>propertyMapping.rMeanSignal</name>
452 <label>R mean signal</label>
453 <class>java.lang.String</class>
454 <value>\rMeanSignal\</value>
455 </parameter>
456 <parameter>
457 <name>propertyMapping.rSpatialDetrendSurfaceValue</name>
458 <label>R surface value</label>
459 <class />
460 <value />
461 </parameter>
462 <parameter>
463 <name>propertyMapping.rDyeNormSignal</name>
464 <label>R normalized signal</label>
465 <class />
466 <value />
467 </parameter>
468 <parameter>
469 <name>propertyMapping.xDev</name>
470 <label>X dev</label>
471 <class />
472 <value />
473 </parameter>
474 <parameter>
475 <name>propertyMapping.gSpatialDetrendIsInFilteredSet</name>
476 <label>G spatial trend</label>
477 <class />
478 <value />
479 </parameter>
480 </configuration>
481 <configuration pluginClassName="net.sf.basedb.plugins.ReporterFlatFileImporter">
482 <configname>Reporters from Agilent raw data</configname>
483 <description />
484 <parameter>
485 <name>maxDataColumns</name>
486 <label>Max data columns</label>
487 <class />
488 <value />
489 </parameter>
490 <parameter>
491 <name>extendedColumnMapping.locusLink</name>
492 <label>LocusLink</label>
493 <class />
494 <value />
495 </parameter>
496 <parameter>
497 <name>trimQuotes</name>
498 <label>Remove quotes</label>
499 <class>java.lang.Boolean</class>
500 <value>true</value>
501 </parameter>
502 <parameter>
503 <name>scoreColumnMapping</name>
504 <label>Score</label>
505 <class />
506 <value />
507 </parameter>
508 <parameter>
509 <name>nameColumnMapping</name>
510 <label>Name</label>
511 <class>java.lang.String</class>
512 <value>\ProbeName\</value>
513 </parameter>
514 <parameter>
515 <name>extendedColumnMapping.markers</name>
516 <label>Markers</label>
517 <class />
518 <value />
519 </parameter>
520 <parameter>
521 <name>extendedColumnMapping.vector</name>
522 <label>Vector</label>
523 <class />
524 <value />
525 </parameter>
526 <parameter>
527 <name>extendedColumnMapping.nid</name>
528 <label>NID</label>
529 <class />
530 <value />
531 </parameter>
532 <parameter>
533 <name>descriptionColumnMapping</name>
534 <label>Description</label>
535 <class>java.lang.String</class>
536 <value>\Description\</value>
537 </parameter>
538 <parameter>
539 <name>symbolColumnMapping</name>
540 <label>Gene symbol</label>
541 <class />
542 <value />
543 </parameter>
544 <parameter>
545 <name>reporterIdColumnMapping</name>
546 <label>Reporter ID</label>
547 <class>java.lang.String</class>
548 <value>\ProbeUID\</value>
549 </parameter>
550 <parameter>
551 <name>headerRegexp</name>
552 <label>Header</label>
553 <class />
554 <value />
555 </parameter>
556 <parameter>
557 <name>extendedColumnMapping.antibiotics</name>
558 <label>Antibiotics</label>
559 <class />
560 <value />
561 </parameter>
562 <parameter>
563 <name>extendedColumnMapping.omim</name>
564 <label>OMIM</label>
565 <class />
566 <value />
567 </parameter>
568 <parameter>
569 <name>extendedColumnMapping.chromosome</name>
570 <label>Chromosome</label>
571 <class />
572 <value />
573 </parameter>
574 <parameter>
575 <name>reporterType</name>
576 <label>Reporter type</label>
577 <class />
578 <value />
579 </parameter>
580 <parameter>
581 <name>dataHeaderRegexp</name>
582 <label>Data header</label>
583 <class>java.lang.String</class>
584 <value>\QFEATURES FeatureNum Row Col accessions ProbeUID ControlType ProbeName GeneName SystematicName Description PositionX PositionY LogRatio LogRatioError PValueLogRatio gSurrogateUsed rSurrogateUsed gIsFound rIsFound gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gNumPixOLHi rNumPixOLHi gNumPixOLLo rNumPixOLLo gNumPix rNumPix gMeanSignal rMeanSignal gMedianSignal rMedianSignal gPixSDev rPixSDev gBGNumPix rBGNumPix gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gNumSatPix rNumSatPix gIsSaturated rIsSaturated PixCorrelation BGPixCorrelation gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gBGSubSigError rBGSubSigError BGSubSigCorrelation gIsPosAndSignif rIsPosAndSignif gPValFeatEqBG rPValFeatEqBG gNumBGUsed rNumBGUsed gIsWellAboveBG rIsWellAboveBG gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel xDev gSpatialDetrendIsInFilteredSet rSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue rSpatialDetrendSurfaceValue\E</value>
585 </parameter>
586 <parameter>
587 <name>dataSplitterRegexp</name>
588 <label>Data splitter</label>
589 <class>java.lang.String</class>
590 <value>\t</value>
591 </parameter>
592 <parameter>
593 <name>extendedColumnMapping.length</name>
594 <label>Length</label>
595 <class />
596 <value />
597 </parameter>
598 <parameter>
599 <name>extendedColumnMapping.tissue</name>
600 <label>Tissue</label>
601 <class />
602 <value />
603 </parameter>
604 <parameter>
605 <name>extendedColumnMapping.accession</name>
606 <label>Accession</label>
607 <class />
608 <value />
609 </parameter>
610 <parameter>
611 <name>minDataColumns</name>
612 <label>Min data columns</label>
613 <class />
614 <value />
615 </parameter>
616 <parameter>
617 <name>ignoreRegexp</name>
618 <label>Ignore</label>
619 <class />
620 <value />
621 </parameter>
622 <parameter>
623 <name>extendedColumnMapping.library</name>
624 <label>Library</label>
625 <class />
626 <value />
627 </parameter>
628 <parameter>
629 <name>reporterTypeColumnMapping</name>
630 <label>Reporter type</label>
631 <class />
632 <value />
633 </parameter>
634 <parameter>
635 <name>extendedColumnMapping.clusterId</name>
636 <label>Cluster ID</label>
637 <class />
638 <value />
639 </parameter>
640 <parameter>
641 <name>dataFooterRegexp</name>
642 <label>Data footer</label>
643 <class />
644 <value />
645 </parameter>
646 <parameter>
647 <name>extendedColumnMapping.species</name>
648 <label>Species</label>
649 <class />
650 <value />
651 </parameter>
652 <parameter>
653 <name>extendedColumnMapping.sequence</name>
654 <label>Sequence</label>
655 <class />
656 <value />
657 </parameter>
658 <parameter>
659 <name>extendedColumnMapping.cytoband</name>
660 <label>Cytoband</label>
661 <class />
662 <value />
663 </parameter>
664 </configuration>
665</configfile>