Changeset 1148
- Timestamp:
- Jul 31, 2009, 3:27:20 PM (14 years ago)
- File:
-
- 1 edited
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- Added
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plugins/base2/net.sf.basedb.illumina/trunk/META-INF/base-configurations.xml
r624 r1148 291 291 <class>java.lang.String</class> 292 292 <value>\Probe_Sequence\</value> 293 </parameter> 294 <parameter> 295 <name>nameColumnMapping</name> 296 <label>Name</label> 297 <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description> 298 <class>java.lang.String</class> 299 <value>\Probe_Id\</value> 300 </parameter> 301 <parameter> 302 <name>extendedColumnMapping.vector</name> 303 <label>Vector</label> 304 <description>The vector from which the reporter is derived</description> 305 <class /> 306 <value /> 307 </parameter> 308 <parameter> 309 <name>extendedColumnMapping.nid</name> 310 <label>NID</label> 311 <description /> 312 <class /> 313 <value /> 314 </parameter> 315 </configuration> 316 <configuration pluginClassName="net.sf.basedb.illumina.plugins.BgxReporterImporter"> 317 <configname>Illumina MicroRNA BGX file</configname> 318 <description>A configuration for MicroRNA BGX files which contains a different set of reporter annotation columns than an ordinary BGX file.</description> 319 <parameter> 320 <name>extendedColumnMapping.accession</name> 321 <label>Accession</label> 322 <description /> 323 <class /> 324 <value /> 325 </parameter> 326 <parameter> 327 <name>minDataColumns</name> 328 <label>Min data columns</label> 329 <description>The minimum number of columns for a line to be counted as a data line.</description> 330 <class /> 331 <value /> 332 </parameter> 333 <parameter> 334 <name>extendedColumnMapping.cytoband</name> 335 <label>Cytoband</label> 336 <description>The cytoband from which the reporter is derived</description> 337 <class /> 338 <value /> 339 </parameter> 340 <parameter> 341 <name>dataFooterRegexp</name> 342 <label>Data footer</label> 343 <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description> 344 <class /> 345 <value /> 346 </parameter> 347 <parameter> 348 <name>extendedColumnMapping.source</name> 349 <label>Source</label> 350 <description /> 351 <class>java.lang.String</class> 352 <value>\Source\</value> 353 </parameter> 354 <parameter> 355 <name>extendedColumnMapping.markers</name> 356 <label>Markers</label> 357 <description /> 358 <class /> 359 <value /> 360 </parameter> 361 <parameter> 362 <name>extendedColumnMapping.omim</name> 363 <label>OMIM</label> 364 <description /> 365 <class /> 366 <value /> 367 </parameter> 368 <parameter> 369 <name>extendedColumnMapping.searchKey</name> 370 <label>Search key</label> 371 <description /> 372 <class>java.lang.String</class> 373 <value>\Search_Key\</value> 374 </parameter> 375 <parameter> 376 <name>extendedColumnMapping.tissue</name> 377 <label>Tissue</label> 378 <description>The tissue from which the reporter is derived</description> 379 <class /> 380 <value /> 381 </parameter> 382 <parameter> 383 <name>ignoreRegexp</name> 384 <label>Ignore</label> 385 <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description> 386 <class /> 387 <value /> 388 </parameter> 389 <parameter> 390 <name>descriptionColumnMapping</name> 391 <label>Description</label> 392 <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description> 393 <class /> 394 <value /> 395 </parameter> 396 <parameter> 397 <name>extendedColumnMapping.clusterId</name> 398 <label>Cluster ID</label> 399 <description>A unique identifier for a Unigene entry</description> 400 <class /> 401 <value /> 402 </parameter> 403 <parameter> 404 <name>decimalSeparator</name> 405 <label>Decimal separator</label> 406 <description>The decimal separator used in numeric values, if not specified dot is assumed.</description> 407 <class>java.lang.String</class> 408 <value>dot</value> 409 </parameter> 410 <parameter> 411 <name>extendedColumnMapping.ilmnStrand</name> 412 <label>Ilmn strand</label> 413 <description>Strand definition of the SNP</description> 414 <class /> 415 <value /> 416 </parameter> 417 <parameter> 418 <name>trimQuotes</name> 419 <label>Remove quotes</label> 420 <description>If true quotes (" or ') around data value will be removed.</description> 421 <class>java.lang.Boolean</class> 422 <value>true</value> 423 </parameter> 424 <parameter> 425 <name>extendedColumnMapping.snp</name> 426 <label>SNP</label> 427 <description>Type of SNP</description> 428 <class /> 429 <value /> 430 </parameter> 431 <parameter> 432 <name>extendedColumnMapping.locusLink</name> 433 <label>LocusLink</label> 434 <description /> 435 <class /> 436 <value /> 437 </parameter> 438 <parameter> 439 <name>extendedColumnMapping.synonyms</name> 440 <label>Synonyms</label> 441 <description /> 442 <class /> 443 <value /> 444 </parameter> 445 <parameter> 446 <name>extendedColumnMapping.isoformType</name> 447 <label>Isoform type</label> 448 <description /> 449 <class /> 450 <value /> 451 </parameter> 452 <parameter> 453 <name>extendedColumnMapping.sourceReferenceId</name> 454 <label>Source reference id</label> 455 <description /> 456 <class /> 457 <value /> 458 </parameter> 459 <parameter> 460 <name>extendedColumnMapping.ilmnGene</name> 461 <label>ILMN Gene</label> 462 <description /> 463 <class>java.lang.String</class> 464 <value>\ILMN_Gene\</value> 465 </parameter> 466 <parameter> 467 <name>extendedColumnMapping.library</name> 468 <label>Library</label> 469 <description>The library from which the reporter is derived</description> 470 <class /> 471 <value /> 472 </parameter> 473 <parameter> 474 <name>maxDataColumns</name> 475 <label>Max data columns</label> 476 <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> 477 <class /> 478 <value /> 479 </parameter> 480 <parameter> 481 <name>extendedColumnMapping.chromosome</name> 482 <label>Chromosome</label> 483 <description>The chromosome from which the reporter is derived</description> 484 <class>java.lang.String</class> 485 <value>\Chromosome\</value> 486 </parameter> 487 <parameter> 488 <name>symbolColumnMapping</name> 489 <label>Gene symbol</label> 490 <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description> 491 <class /> 492 <value /> 493 </parameter> 494 <parameter> 495 <name>headerRegexp</name> 496 <label>Header</label> 497 <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description> 498 <class /> 499 <value /> 500 </parameter> 501 <parameter> 502 <name>scoreColumnMapping</name> 503 <label>Score</label> 504 <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description> 505 <class /> 506 <value /> 507 </parameter> 508 <parameter> 509 <name>dataHeaderRegexp</name> 510 <label>Data header</label> 511 <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description> 512 <class>java.lang.String</class> 513 <value>^SYMBOL.+Probe_Id.+Array_Address_Id.*</value> 514 </parameter> 515 <parameter> 516 <name>extendedColumnMapping.controlCompositeMap</name> 517 <label>Control composite map</label> 518 <description /> 519 <class /> 520 <value /> 521 </parameter> 522 <parameter> 523 <name>reporterType</name> 524 <label>Reporter type</label> 525 <description>The reporter type assigned to the imported reporters</description> 526 <class /> 527 <value /> 528 </parameter> 529 <parameter> 530 <name>extendedColumnMapping.length</name> 531 <label>Length</label> 532 <description>The length of the sequence</description> 533 <class /> 534 <value /> 535 </parameter> 536 <parameter> 537 <name>extendedColumnMapping.probeChrOrientation</name> 538 <label>Probe chr orientation</label> 539 <description /> 540 <class>java.lang.String</class> 541 <value>\Probe_Chr_Orientation\</value> 542 </parameter> 543 <parameter> 544 <name>extendedColumnMapping.startPosition</name> 545 <label>Start position</label> 546 <description /> 547 <class /> 548 <value /> 549 </parameter> 550 <parameter> 551 <name>complexExpressions</name> 552 <label>Complex column mappings</label> 553 <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\' 554 allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description> 555 <class>java.lang.String</class> 556 <value>disallow</value> 557 </parameter> 558 <parameter> 559 <name>reporterTypeColumnMapping</name> 560 <label>Reporter type</label> 561 <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description> 562 <class /> 563 <value /> 564 </parameter> 565 <parameter> 566 <name>charset</name> 567 <label>Character set</label> 568 <description>The character set to use when reading the file. This setting overrides the character set specified by the file. If neither this parameter nor the file specifies a character set, the system default is used (ISO-8859-1).</description> 569 <class>java.lang.String</class> 570 <value>ISO-8859-1</value> 571 </parameter> 572 <parameter> 573 <name>extendedColumnMapping.controlGroupName</name> 574 <label>Control group name</label> 575 <description /> 576 <class /> 577 <value /> 578 </parameter> 579 <parameter> 580 <name>extendedColumnMapping.probeCoordinates</name> 581 <label>Probe coordinates</label> 582 <description /> 583 <class>java.lang.String</class> 584 <value>\Probe_Coordinates\</value> 585 </parameter> 586 <parameter> 587 <name>extendedColumnMapping.controlGroupId</name> 588 <label>Control group id</label> 589 <description /> 590 <class /> 591 <value /> 592 </parameter> 593 <parameter> 594 <name>dataSplitterRegexp</name> 595 <label>Data splitter</label> 596 <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description> 597 <class>java.lang.String</class> 598 <value>\t</value> 599 </parameter> 600 <parameter> 601 <name>extendedColumnMapping.antibiotics</name> 602 <label>Antibiotics</label> 603 <description /> 604 <class /> 605 <value /> 606 </parameter> 607 <parameter> 608 <name>reporterIdColumnMapping</name> 609 <label>External ID</label> 610 <description>Mapping that picks the reporter's external ID from the data columns. For example: \ID\</description> 611 <class>java.lang.String</class> 612 <value>\Probe_Id\</value> 613 </parameter> 614 <parameter> 615 <name>extendedColumnMapping.species</name> 616 <label>Species</label> 617 <description>The organism from which the reporter is derived</description> 618 <class>java.lang.String</class> 619 <value>\Species\</value> 620 </parameter> 621 <parameter> 622 <name>extendedColumnMapping.sequence</name> 623 <label>Sequence</label> 624 <description>The nucleotide sequence of the reporter</description> 625 <class>java.lang.String</class> 626 <value>\ProbeSeq\</value> 293 627 </parameter> 294 628 <parameter>
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