Mercurial > repos > devteam > fastq_manipulation
comparison fastq_manipulation.xml @ 6:e06d41f3ed3e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
| author | iuc |
|---|---|
| date | Sun, 23 Nov 2025 17:50:28 +0000 |
| parents | e30352e889fe |
| children |
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| 5:e30352e889fe | 6:e06d41f3ed3e |
|---|---|
| 18 <configfiles> | 18 <configfiles> |
| 19 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module | 19 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module |
| 20 #import binascii | 20 #import binascii |
| 21 import binascii | 21 import binascii |
| 22 import re | 22 import re |
| 23 import six | 23 |
| 24 | 24 maketrans = str.maketrans |
| 25 if six.PY2: | |
| 26 from string import maketrans | |
| 27 else: | |
| 28 maketrans = str.maketrans | |
| 29 | |
| 30 | 25 |
| 31 ##does read match | 26 ##does read match |
| 32 def match_read(fastq_read): | 27 def match_read(fastq_read): |
| 33 #for $match_block in $match_blocks: | 28 #for $match_block in $match_blocks: |
| 34 #if $match_block['match_type']['match_type_selector'] == 'identifier': | 29 #if $match_block['match_type']['match_type_selector'] == 'identifier': |
| 251 </outputs> | 246 </outputs> |
| 252 <tests> | 247 <tests> |
| 253 <!-- match all and do nothing --> | 248 <!-- match all and do nothing --> |
| 254 <test> | 249 <test> |
| 255 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 250 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 256 <param name="match_type_selector" value="identifier" /> | 251 <repeat name="match_blocks"> |
| 257 <param name="match_selector" value="regex" /> | 252 <conditional name="match_type"> |
| 258 <param name="match_by" value=".*" /> | 253 <param name="match_type_selector" value="identifier" /> |
| 259 <param name="manipulation_type_selector" value="identifier" /> | 254 <conditional name="match"> |
| 260 <param name="manipulation_selector" value="translate" /> | 255 <param name="match_selector" value="regex" /> |
| 261 <param name="from" value="" /> | 256 <param name="match_by" value=".*" /> |
| 262 <param name="to" value="" /> | 257 </conditional> |
| 258 </conditional> | |
| 259 </repeat> | |
| 260 <repeat name="manipulate_blocks"> | |
| 261 <conditional name="manipulation_type"> | |
| 262 <param name="manipulation_type_selector" value="identifier" /> | |
| 263 <conditional name="manipulation"> | |
| 264 <param name="manipulation_selector" value="translate" /> | |
| 265 <param name="from" value="" /> | |
| 266 <param name="to" value="" /> | |
| 267 </conditional> | |
| 268 </conditional> | |
| 269 </repeat> | |
| 263 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 270 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 264 </test> | 271 </test> |
| 265 <!-- match None and do nothing --> | 272 <!-- match None and do nothing --> |
| 266 <test> | 273 <test> |
| 267 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 274 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 268 <param name="match_type_selector" value="identifier" /> | 275 <repeat name="match_blocks"> |
| 269 <param name="match_selector" value="regex" /> | 276 <conditional name="match_type"> |
| 270 <param name="match_by" value="STRINGDOESNOTEXIST" /> | 277 <param name="match_type_selector" value="identifier" /> |
| 271 <param name="manipulation_type_selector" value="identifier" /> | 278 <conditional name="match"> |
| 272 <param name="manipulation_selector" value="translate" /> | 279 <param name="match_selector" value="regex" /> |
| 273 <param name="from" value="" /> | 280 <param name="match_by" value="STRINGDOESNOTEXIST" /> |
| 274 <param name="to" value="" /> | 281 </conditional> |
| 282 </conditional> | |
| 283 </repeat> | |
| 284 <repeat name="manipulate_blocks"> | |
| 285 <conditional name="manipulation_type"> | |
| 286 <param name="manipulation_type_selector" value="identifier" /> | |
| 287 <conditional name="manipulation"> | |
| 288 <param name="manipulation_selector" value="translate" /> | |
| 289 <param name="from" value="" /> | |
| 290 <param name="to" value="" /> | |
| 291 </conditional> | |
| 292 </conditional> | |
| 293 </repeat> | |
| 275 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 294 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 276 </test> | 295 </test> |
| 277 <!-- match all and remove --> | 296 <!-- match all and remove --> |
| 278 <test> | 297 <test> |
| 279 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 298 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 280 <param name="match_type_selector" value="identifier" /> | 299 <repeat name="match_blocks"> |
| 281 <param name="match_selector" value="regex" /> | 300 <conditional name="match_type"> |
| 282 <param name="match_by" value=".*" /> | 301 <param name="match_type_selector" value="identifier" /> |
| 283 <param name="manipulation_type_selector" value="miscellaneous" /> | 302 <conditional name="match"> |
| 284 <param name="manipulation_selector" value="remove" /> | 303 <param name="match_selector" value="regex" /> |
| 304 <param name="match_by" value=".*" /> | |
| 305 </conditional> | |
| 306 </conditional> | |
| 307 </repeat> | |
| 308 <repeat name="manipulate_blocks"> | |
| 309 <conditional name="manipulation_type"> | |
| 310 <param name="manipulation_type_selector" value="miscellaneous" /> | |
| 311 <conditional name="manipulation"> | |
| 312 <param name="manipulation_selector" value="remove" /> | |
| 313 </conditional> | |
| 314 </conditional> | |
| 315 </repeat> | |
| 285 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> | 316 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> |
| 286 </test> | 317 </test> |
| 287 <!-- match None and remove --> | 318 <!-- match None and remove --> |
| 288 <test> | 319 <test> |
| 289 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 320 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 290 <param name="match_type_selector" value="identifier" /> | 321 <repeat name="match_blocks"> |
| 291 <param name="match_selector" value="regex" /> | 322 <conditional name="match_type"> |
| 292 <param name="match_by" value="STRINGDOESNOTEXIST" /> | 323 <param name="match_type_selector" value="identifier" /> |
| 293 <param name="manipulation_type_selector" value="miscellaneous" /> | 324 <conditional name="match"> |
| 294 <param name="manipulation_selector" value="remove" /> | 325 <param name="match_selector" value="regex" /> |
| 326 <param name="match_by" value="STRINGDOESNOTEXIST" /> | |
| 327 </conditional> | |
| 328 </conditional> | |
| 329 </repeat> | |
| 330 <repeat name="manipulate_blocks"> | |
| 331 <conditional name="manipulation_type"> | |
| 332 <param name="manipulation_type_selector" value="miscellaneous" /> | |
| 333 <conditional name="manipulation"> | |
| 334 <param name="manipulation_selector" value="remove" /> | |
| 335 </conditional> | |
| 336 </conditional> | |
| 337 </repeat> | |
| 295 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 338 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 296 </test> | 339 </test> |
| 297 <!-- match all and trim to 4 inner-most bases --> | 340 <!-- match all and trim to 4 inner-most bases --> |
| 298 <test> | 341 <test> |
| 299 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 342 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 300 <param name="match_type_selector" value="identifier" /> | 343 <repeat name="match_blocks"> |
| 301 <param name="match_selector" value="regex" /> | 344 <conditional name="match_type"> |
| 302 <param name="match_by" value=".*" /> | 345 <param name="match_type_selector" value="identifier" /> |
| 303 <param name="manipulation_type_selector" value="sequence" /> | 346 <conditional name="match"> |
| 304 <param name="manipulation_selector" value="trim" /> | 347 <param name="match_selector" value="regex" /> |
| 305 <param name="base_offset_type" value="offsets_absolute"/> | 348 <param name="match_by" value=".*" /> |
| 306 <param name="left_column_offset" value="45"/> | 349 </conditional> |
| 307 <param name="right_column_offset" value="45"/> | 350 </conditional> |
| 308 <param name="keep_zero_length" value="true" /> | 351 </repeat> |
| 352 <repeat name="manipulate_blocks"> | |
| 353 <conditional name="manipulation_type"> | |
| 354 <param name="manipulation_type_selector" value="sequence" /> | |
| 355 <conditional name="manipulation"> | |
| 356 <param name="manipulation_selector" value="trim" /> | |
| 357 <conditional name="offset_type"> | |
| 358 <param name="base_offset_type" value="offsets_absolute"/> | |
| 359 <param name="left_column_offset" value="45"/> | |
| 360 <param name="right_column_offset" value="45"/> | |
| 361 </conditional> | |
| 362 <param name="keep_zero_length" value="true" /> | |
| 363 </conditional> | |
| 364 </conditional> | |
| 365 </repeat> | |
| 309 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> | 366 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
| 310 </test> | 367 </test> |
| 311 <test> | 368 <test> |
| 312 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 369 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 313 <param name="match_type_selector" value="identifier" /> | 370 <repeat name="match_blocks"> |
| 314 <param name="match_selector" value="regex" /> | 371 <conditional name="match_type"> |
| 315 <param name="match_by" value=".*" /> | 372 <param name="match_type_selector" value="identifier" /> |
| 316 <param name="manipulation_type_selector" value="sequence" /> | 373 <conditional name="match"> |
| 317 <param name="manipulation_selector" value="trim" /> | 374 <param name="match_selector" value="regex" /> |
| 318 <param name="base_offset_type" value="offsets_percent"/> | 375 <param name="match_by" value=".*" /> |
| 319 <param name="left_column_offset" value="47.87"/> | 376 </conditional> |
| 320 <param name="right_column_offset" value="47.87"/> | 377 </conditional> |
| 321 <param name="keep_zero_length" value="true" /> | 378 </repeat> |
| 379 <repeat name="manipulate_blocks"> | |
| 380 <conditional name="manipulation_type"> | |
| 381 <param name="manipulation_type_selector" value="sequence" /> | |
| 382 <conditional name="manipulation"> | |
| 383 <param name="manipulation_selector" value="trim" /> | |
| 384 <conditional name="offset_type"> | |
| 385 <param name="base_offset_type" value="offsets_percent"/> | |
| 386 <param name="left_column_offset" value="47.87"/> | |
| 387 <param name="right_column_offset" value="47.87"/> | |
| 388 </conditional> | |
| 389 <param name="keep_zero_length" value="true" /> | |
| 390 </conditional> | |
| 391 </conditional> | |
| 392 </repeat> | |
| 322 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> | 393 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
| 323 </test> | 394 </test> |
| 324 <!-- match all and rev comp --> | 395 <!-- match all and rev comp --> |
| 325 <test> | 396 <test> |
| 326 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 397 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 327 <param name="match_type_selector" value="identifier" /> | 398 <repeat name="match_blocks"> |
| 328 <param name="match_selector" value="regex" /> | 399 <conditional name="match_type"> |
| 329 <param name="match_by" value=".*" /> | 400 <param name="match_type_selector" value="identifier" /> |
| 330 <param name="manipulation_type_selector" value="sequence" /> | 401 <conditional name="match"> |
| 331 <param name="manipulation_selector" value="rev_comp" /> | 402 <param name="match_selector" value="regex" /> |
| 403 <param name="match_by" value=".*" /> | |
| 404 </conditional> | |
| 405 </conditional> | |
| 406 </repeat> | |
| 407 <repeat name="manipulate_blocks"> | |
| 408 <conditional name="manipulation_type"> | |
| 409 <param name="manipulation_type_selector" value="sequence" /> | |
| 410 <conditional name="manipulation"> | |
| 411 <param name="manipulation_selector" value="rev_comp" /> | |
| 412 </conditional> | |
| 413 </conditional> | |
| 414 </repeat> | |
| 332 <output name="output_file" file="sanger_full_range_rev_comp.fastqsanger" ftype="fastqsanger" /> | 415 <output name="output_file" file="sanger_full_range_rev_comp.fastqsanger" ftype="fastqsanger" /> |
| 333 </test> | 416 </test> |
| 334 <!-- match all and rev comp, with ambiguous DNA --> | 417 <!-- match all and rev comp, with ambiguous DNA --> |
| 335 <test> | 418 <test> |
| 336 <param name="input_file" value="misc_dna_original_sanger.fastqsanger" ftype="fastqsanger" /> | 419 <param name="input_file" value="misc_dna_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 337 <param name="match_type_selector" value="identifier" /> | 420 <repeat name="match_blocks"> |
| 338 <param name="match_selector" value="regex" /> | 421 <conditional name="match_type"> |
| 339 <param name="match_by" value=".*" /> | 422 <param name="match_type_selector" value="identifier" /> |
| 340 <param name="manipulation_type_selector" value="sequence" /> | 423 <conditional name="match"> |
| 341 <param name="manipulation_selector" value="rev_comp" /> | 424 <param name="match_selector" value="regex" /> |
| 425 <param name="match_by" value=".*" /> | |
| 426 </conditional> | |
| 427 </conditional> | |
| 428 </repeat> | |
| 429 <repeat name="manipulate_blocks"> | |
| 430 <conditional name="manipulation_type"> | |
| 431 <param name="manipulation_type_selector" value="sequence" /> | |
| 432 <conditional name="manipulation"> | |
| 433 <param name="manipulation_selector" value="rev_comp" /> | |
| 434 </conditional> | |
| 435 </conditional> | |
| 436 </repeat> | |
| 342 <output name="output_file" file="misc_dna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" /> | 437 <output name="output_file" file="misc_dna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" /> |
| 343 </test> | 438 </test> |
| 344 <!-- match all and rev comp, with ambiguous RNA --> | 439 <!-- match all and rev comp, with ambiguous RNA --> |
| 345 <test> | 440 <test> |
| 346 <param name="input_file" value="misc_rna_original_sanger.fastqsanger" ftype="fastqsanger" /> | 441 <param name="input_file" value="misc_rna_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 347 <param name="match_type_selector" value="identifier" /> | 442 <repeat name="match_blocks"> |
| 348 <param name="match_selector" value="regex" /> | 443 <conditional name="match_type"> |
| 349 <param name="match_by" value=".*" /> | 444 <param name="match_type_selector" value="identifier" /> |
| 350 <param name="manipulation_type_selector" value="sequence" /> | 445 <conditional name="match"> |
| 351 <param name="manipulation_selector" value="rev_comp" /> | 446 <param name="match_selector" value="regex" /> |
| 447 <param name="match_by" value=".*" /> | |
| 448 </conditional> | |
| 449 </conditional> | |
| 450 </repeat> | |
| 451 <repeat name="manipulate_blocks"> | |
| 452 <conditional name="manipulation_type"> | |
| 453 <param name="manipulation_type_selector" value="sequence" /> | |
| 454 <conditional name="manipulation"> | |
| 455 <param name="manipulation_selector" value="rev_comp" /> | |
| 456 </conditional> | |
| 457 </conditional> | |
| 458 </repeat> | |
| 352 <output name="output_file" file="misc_rna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" /> | 459 <output name="output_file" file="misc_rna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" /> |
| 353 </test> | 460 </test> |
| 354 <!-- match first seq and rev comp --> | 461 <!-- match first seq and rev comp --> |
| 355 <test> | 462 <test> |
| 356 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 463 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 357 <param name="match_type_selector" value="identifier" /> | 464 <repeat name="match_blocks"> |
| 358 <param name="match_selector" value="regex" /> | 465 <conditional name="match_type"> |
| 359 <param name="match_by" value="FAKE0001" /> | 466 <param name="match_type_selector" value="identifier" /> |
| 360 <param name="manipulation_type_selector" value="sequence" /> | 467 <conditional name="match"> |
| 361 <param name="manipulation_selector" value="rev_comp" /> | 468 <param name="match_selector" value="regex" /> |
| 469 <param name="match_by" value="FAKE0001" /> | |
| 470 </conditional> | |
| 471 </conditional> | |
| 472 </repeat> | |
| 473 <repeat name="manipulate_blocks"> | |
| 474 <conditional name="manipulation_type"> | |
| 475 <param name="manipulation_type_selector" value="sequence" /> | |
| 476 <conditional name="manipulation"> | |
| 477 <param name="manipulation_selector" value="rev_comp" /> | |
| 478 </conditional> | |
| 479 </conditional> | |
| 480 </repeat> | |
| 362 <output name="output_file" file="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" /> | 481 <output name="output_file" file="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" /> |
| 363 </test> | 482 </test> |
| 364 <!-- match first seq and rev comp: i.e. undo above --> | 483 <!-- match first seq and rev comp: i.e. undo above --> |
| 365 <test> | 484 <test> |
| 366 <param name="input_file" value="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" /> | 485 <param name="input_file" value="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" /> |
| 367 <param name="match_type_selector" value="identifier" /> | 486 <repeat name="match_blocks"> |
| 368 <param name="match_selector" value="regex" /> | 487 <conditional name="match_type"> |
| 369 <param name="match_by" value="FAKE0001" /> | 488 <param name="match_type_selector" value="identifier" /> |
| 370 <param name="manipulation_type_selector" value="sequence" /> | 489 <conditional name="match"> |
| 371 <param name="manipulation_selector" value="rev_comp" /> | 490 <param name="match_selector" value="regex" /> |
| 491 <param name="match_by" value="FAKE0001" /> | |
| 492 </conditional> | |
| 493 </conditional> | |
| 494 </repeat> | |
| 495 <repeat name="manipulate_blocks"> | |
| 496 <conditional name="manipulation_type"> | |
| 497 <param name="manipulation_type_selector" value="sequence" /> | |
| 498 <conditional name="manipulation"> | |
| 499 <param name="manipulation_selector" value="rev_comp" /> | |
| 500 </conditional> | |
| 501 </conditional> | |
| 502 </repeat> | |
| 372 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 503 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 373 </test> | 504 </test> |
| 374 <!-- match all and DNA to RNA --> | 505 <!-- match all and DNA to RNA --> |
| 375 <test> | 506 <test> |
| 376 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 507 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 377 <param name="match_type_selector" value="identifier" /> | 508 <repeat name="match_blocks"> |
| 378 <param name="match_selector" value="regex" /> | 509 <conditional name="match_type"> |
| 379 <param name="match_by" value=".*" /> | 510 <param name="match_type_selector" value="identifier" /> |
| 380 <param name="manipulation_type_selector" value="sequence" /> | 511 <conditional name="match"> |
| 381 <param name="manipulation_selector" value="dna_to_rna" /> | 512 <param name="match_selector" value="regex" /> |
| 513 <param name="match_by" value=".*" /> | |
| 514 </conditional> | |
| 515 </conditional> | |
| 516 </repeat> | |
| 517 <repeat name="manipulate_blocks"> | |
| 518 <conditional name="manipulation_type"> | |
| 519 <param name="manipulation_type_selector" value="sequence" /> | |
| 520 <conditional name="manipulation"> | |
| 521 <param name="manipulation_selector" value="dna_to_rna" /> | |
| 522 </conditional> | |
| 523 </conditional> | |
| 524 </repeat> | |
| 382 <output name="output_file" file="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" /> | 525 <output name="output_file" file="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" /> |
| 383 </test> | 526 </test> |
| 384 <!-- match all and RNA to DNA--> | 527 <!-- match all and RNA to DNA--> |
| 385 <test> | 528 <test> |
| 386 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" /> | 529 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" /> |
| 387 <param name="match_type_selector" value="identifier" /> | 530 <repeat name="match_blocks"> |
| 388 <param name="match_selector" value="regex" /> | 531 <conditional name="match_type"> |
| 389 <param name="match_by" value=".*" /> | 532 <param name="match_type_selector" value="identifier" /> |
| 390 <param name="manipulation_type_selector" value="sequence" /> | 533 <conditional name="match"> |
| 391 <param name="manipulation_selector" value="rna_to_dna" /> | 534 <param name="match_selector" value="regex" /> |
| 535 <param name="match_by" value=".*" /> | |
| 536 </conditional> | |
| 537 </conditional> | |
| 538 </repeat> | |
| 539 <repeat name="manipulate_blocks"> | |
| 540 <conditional name="manipulation_type"> | |
| 541 <param name="manipulation_type_selector" value="sequence" /> | |
| 542 <conditional name="manipulation"> | |
| 543 <param name="manipulation_selector" value="rna_to_dna" /> | |
| 544 </conditional> | |
| 545 </conditional> | |
| 546 </repeat> | |
| 392 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 547 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
| 393 </test> | 548 </test> |
| 394 <!-- match all and RNA to DNA (gz compressed) --> | 549 <!-- match all and RNA to DNA (gz compressed) --> |
| 395 <test> | 550 <test> |
| 396 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" /> | 551 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" /> |
| 397 <param name="match_type_selector" value="identifier" /> | 552 <repeat name="match_blocks"> |
| 398 <param name="match_selector" value="regex" /> | 553 <conditional name="match_type"> |
| 399 <param name="match_by" value=".*" /> | 554 <param name="match_type_selector" value="identifier" /> |
| 400 <param name="manipulation_type_selector" value="sequence" /> | 555 <conditional name="match"> |
| 401 <param name="manipulation_selector" value="rna_to_dna" /> | 556 <param name="match_selector" value="regex" /> |
| 557 <param name="match_by" value=".*" /> | |
| 558 </conditional> | |
| 559 </conditional> | |
| 560 </repeat> | |
| 561 <repeat name="manipulate_blocks"> | |
| 562 <conditional name="manipulation_type"> | |
| 563 <param name="manipulation_type_selector" value="sequence" /> | |
| 564 <conditional name="manipulation"> | |
| 565 <param name="manipulation_selector" value="rna_to_dna" /> | |
| 566 </conditional> | |
| 567 </conditional> | |
| 568 </repeat> | |
| 402 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> | 569 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> |
| 403 </test> | 570 </test> |
| 404 <!-- match all and RNA to DNA (bz2 compressed) --> | 571 <!-- match all and RNA to DNA (bz2 compressed) --> |
| 405 <test> | 572 <test> |
| 406 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" /> | 573 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" /> |
| 407 <param name="match_type_selector" value="identifier" /> | 574 <repeat name="match_blocks"> |
| 408 <param name="match_selector" value="regex" /> | 575 <conditional name="match_type"> |
| 409 <param name="match_by" value=".*" /> | 576 <param name="match_type_selector" value="identifier" /> |
| 410 <param name="manipulation_type_selector" value="sequence" /> | 577 <conditional name="match"> |
| 411 <param name="manipulation_selector" value="rna_to_dna" /> | 578 <param name="match_selector" value="regex" /> |
| 579 <param name="match_by" value=".*" /> | |
| 580 </conditional> | |
| 581 </conditional> | |
| 582 </repeat> | |
| 583 <repeat name="manipulate_blocks"> | |
| 584 <conditional name="manipulation_type"> | |
| 585 <param name="manipulation_type_selector" value="sequence" /> | |
| 586 <conditional name="manipulation"> | |
| 587 <param name="manipulation_selector" value="rna_to_dna" /> | |
| 588 </conditional> | |
| 589 </conditional> | |
| 590 </repeat> | |
| 412 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> | 591 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> |
| 413 </test> | 592 </test> |
| 414 </tests> | 593 </tests> |
| 415 <help><![CDATA[ | 594 <help><![CDATA[ |
| 416 This tool allows you to build complex manipulations to be applied to each matching read in a FASTQ file. A read must match all matching directives in order for it to be manipulated; if a read does not match, it is output in a non-modified manner. All reads matching will have each of the specified manipulations performed upon them, in the order specified. | 595 This tool allows you to build complex manipulations to be applied to each matching read in a FASTQ file. A read must match all matching directives in order for it to be manipulated; if a read does not match, it is output in a non-modified manner. All reads matching will have each of the specified manipulations performed upon them, in the order specified. |