# HG changeset patch # User devteam # Date 1420821308 18000 # Node ID 76b2f1eee5084f9592a6bdc18b709d8db4ebfb56 Uploaded diff -r 000000000000 -r 76b2f1eee508 bamtools.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools.xml Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,293 @@ + + + BAM datasets and perform other transformations + + bamtools + samtools + + + + ##set up input files + + #for $bam_count, $input_bam in enumerate( $input_bams ): + ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && + ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && + #end for + + #if str( $analysis_type.analysis_type_selector ) == "convert": + #if str( $analysis_type.format_type.format_type_selector ) == "pileup": + #set $reference_fasta_filename = "localref.fa" + #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history": + ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" && + samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 && + #else: + #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path ) + #end if + #end if + #end if + + ##finished setting up inputs + + ##start bamtools commandline + + bamtools + + #if str( $analysis_type.analysis_type_selector ) == "convert": + + convert + + -format ${analysis_type.format_type.format_type_selector} + + #if str( $analysis_type.format_type.format_type_selector ) == "pileup": + + ${analysis_type.format_type.mapqual} + -fasta "${reference_fasta_filename}" + + #elif str( $analysis_type.format_type.format_type_selector ) == "sam": + + ${analysis_type.format_type.noheader} + + #end if + + -out $out_file1 + + #elif str( $analysis_type.analysis_type_selector ) == "count": + + count + > $out_file1 + + #elif str( $analysis_type.analysis_type_selector ) == "coverage": + + coverage + -out $out_file1 + + #elif str( $analysis_type.analysis_type_selector ) == "header": + + header + > $out_file1 + + #elif str( $analysis_type.analysis_type_selector ) == "merge": + + merge + -out $out_file1 + + #elif str( $analysis_type.analysis_type_selector ) == "random": + + random + -n ${analysis_type.count} + -seed ${analysis_type.seed} + -out $out_file1 + + #elif str( $analysis_type.analysis_type_selector ) == "revert": + + revert + ${analysis_type.keepDuplicate} + ${analysis_type.keepQualities} + -out $out_file1 + + #elif str( $analysis_type.analysis_type_selector ) == "sort": + + sort + ${analysis_type.byname} + -out $out_file1 + + #end if + + #for $bam_count, $input_bam in enumerate( $input_bams ): + -in "localbam_${bam_count}.bam" + #end for + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What is does** + +BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). +This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below. + +----- + +**Convert** + +Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either +cashed at this Galaxy instance, or provided by you as a FASTA dataset from History. + +----- + +**Count** + +Counts a number of alignments in a BAM dataset(s). + +----- + +**Coverage** + +Prints per-base coverage for a BAM dataset. + +----- + +**Header** + +Prints header from a BAM dataset(s). + +------ + +**Merge** + +Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button. + +------ + +**Random** + +Grabs a specified number of random lines from BAM dataset(s). + +------ + +**Revert** + +Removes duplicate marks and restores original (non-recalibrated) base qualities. + +----- + +.. class:: infomark + +**More information** + +Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki + + + + 10.1093/bioinformatics/btr174 + + diff -r 000000000000 -r 76b2f1eee508 shed_upload.tar.gz Binary file shed_upload.tar.gz has changed diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-convert-pileup.pu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-convert-pileup.pu Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,239 @@ +phiX174 393 A 1 ^F, h F +phiX174 394 G 1 , < F +phiX174 395 T 1 g ? F +phiX174 396 C 1 , P F +phiX174 397 A 1 , h F +phiX174 398 A 1 , h F +phiX174 399 G 1 , ^ F +phiX174 400 T 1 , H F +phiX174 401 T 1 , h F +phiX174 402 A 1 , V F +phiX174 403 C 1 , h F +phiX174 404 T 1 , E F +phiX174 405 G 1 , P F +phiX174 406 A 1 , h F +phiX174 407 A 1 , h F +phiX174 408 C 1 , h F +phiX174 409 A 1 , h F +phiX174 410 A 1 , h F +phiX174 411 T 1 , h F +phiX174 412 C 1 , h F +phiX174 413 C 1 , h F +phiX174 414 G 1 , O F +phiX174 415 T 1 , G F +phiX174 416 A 1 , ] F +phiX174 417 C 1 , h F +phiX174 418 G 1 , Q F +phiX174 419 T 1 , h F +phiX174 420 T 1 , h F +phiX174 421 T 1 , h F +phiX174 422 C 1 , h F +phiX174 423 C 1 , h F +phiX174 424 A 1 , h F +phiX174 425 G 1 , h F +phiX174 426 A 1 , h F +phiX174 427 C 1 , h F +phiX174 428 C 1 ,$ h F +phiX174 1364 A 1 ^:, h : +phiX174 1365 A 1 , G : +phiX174 1366 G 1 c < : +phiX174 1367 C 1 , h : +phiX174 1368 A 1 , h : +phiX174 1369 T 1 , h : +phiX174 1370 T 1 , S : +phiX174 1371 T 1 , D : +phiX174 1372 G 1 , h : +phiX174 1373 T 1 , H : +phiX174 1374 T 1 , = : +phiX174 1375 T 1 , Q : +phiX174 1376 C 1 , \ : +phiX174 1377 A 1 , h : +phiX174 1378 G 1 , h : +phiX174 1379 G 1 , h : +phiX174 1380 G 1 , h : +phiX174 1381 T 1 , h : +phiX174 1382 T 1 , h : +phiX174 1383 A 1 , h : +phiX174 1384 T 1 , @ : +phiX174 1385 T 1 , J : +phiX174 1386 T 1 g @ : +phiX174 1387 G 1 , R : +phiX174 1388 A 1 , T : +phiX174 1389 A 1 , @ : +phiX174 1390 T 1 , h : +phiX174 1391 A 1 , h : +phiX174 1392 T 1 , h : +phiX174 1393 C 1 , h : +phiX174 1394 T 1 , h : +phiX174 1395 A 1 , h : +phiX174 1396 T 1 , h : +phiX174 1397 A 1 , h : +phiX174 1398 A 1 , h : +phiX174 1399 C 1 ,$ h : +phiX174 2461 G 1 ^:. h : +phiX174 2462 T 1 . h : +phiX174 2463 T 1 . h : +phiX174 2464 A 1 . h : +phiX174 2465 C 1 . h : +phiX174 2466 T 1 . h : +phiX174 2467 C 1 . h : +phiX174 2468 C 1 . h : +phiX174 2469 A 1 . h : +phiX174 2470 G 1 . h : +phiX174 2471 C 1 A ? : +phiX174 2472 T 1 . U : +phiX174 2473 T 1 . [ : +phiX174 2474 C 1 . L : +phiX174 2475 T 1 . W : +phiX174 2476 T 1 . b : +phiX174 2477 C 1 . h : +phiX174 2478 G 1 . h : +phiX174 2479 G 1 . h : +phiX174 2480 C 1 . h : +phiX174 2481 A 1 . h : +phiX174 2482 C 1 . h : +phiX174 2483 C 1 . h : +phiX174 2484 T 1 . L : +phiX174 2485 G 1 . ^ : +phiX174 2486 T 1 . P : +phiX174 2487 T 1 . = : +phiX174 2488 T 1 . h : +phiX174 2489 T 1 . H : +phiX174 2490 A 1 . h : +phiX174 2491 C 1 . h : +phiX174 2492 A 1 . P : +phiX174 2493 G 1 . N : +phiX174 2494 A 1 G = : +phiX174 2495 C 1 . C : +phiX174 2496 A 1 .$ c : +phiX174 4233 G 1 ^:. h : +phiX174 4234 A 1 . \ : +phiX174 4235 T 1 . h : +phiX174 4236 G 1 . h : +phiX174 4237 A 1 . h : +phiX174 4238 G 1 . h : +phiX174 4239 T 1 . h : +phiX174 4240 T 1 . h : +phiX174 4241 T 1 . h : +phiX174 4242 G 1 . h : +phiX174 4243 T 1 C @ : +phiX174 4244 A 1 . N : +phiX174 4245 T 1 . h : +phiX174 4246 C 1 . C : +phiX174 4247 T 1 . Q : +phiX174 4248 G 1 . h : +phiX174 4249 T 1 . h : +phiX174 4250 T 1 . h : +phiX174 4251 A 1 . h : +phiX174 4252 C 1 . h : +phiX174 4253 T 1 . h : +phiX174 4254 G 1 . h : +phiX174 4255 A 1 . h : +phiX174 4256 G 2 .^F. hh :F +phiX174 4257 A 2 G. =V :F +phiX174 4258 A 2 .. CN :F +phiX174 4259 G 2 .. _h :F +phiX174 4260 T 2 .. hh :F +phiX174 4261 T 2 .. Rh :F +phiX174 4262 A 2 .. hh :F +phiX174 4263 A 2 .. hh :F +phiX174 4264 T 2 .. hh :F +phiX174 4265 G 2 .. hh :F +phiX174 4266 G 2 .. UP :F +phiX174 4267 A 2 .. @C :F +phiX174 4268 T 2 .$. hh :F +phiX174 4269 G 1 . [ F +phiX174 4270 A 1 . H F +phiX174 4271 A 1 . N F +phiX174 4272 T 1 . h F +phiX174 4273 T 1 . h F +phiX174 4274 G 1 . h F +phiX174 4275 G 1 . h F +phiX174 4276 C 1 . h F +phiX174 4277 A 1 . h F +phiX174 4278 C 1 . h F +phiX174 4279 A 1 . ? F +phiX174 4280 A 1 . N F +phiX174 4281 T 1 . I F +phiX174 4282 G 1 . c F +phiX174 4283 C 1 . h F +phiX174 4284 T 1 . F F +phiX174 4285 A 1 . ] F +phiX174 4286 C 1 . h F +phiX174 4287 A 1 . g F +phiX174 4288 A 1 . X F +phiX174 4289 T 1 G > F +phiX174 4290 G 1 . V F +phiX174 4291 T 1 .$ h F +phiX174 4724 G 1 ^F. h F +phiX174 4725 T 1 . h F +phiX174 4726 A 1 . E F +phiX174 4727 T 1 . h F +phiX174 4728 T 1 . h F +phiX174 4729 T 1 . h F +phiX174 4730 T 1 . h F +phiX174 4731 T 1 . h F +phiX174 4732 G 1 . h F +phiX174 4733 T 1 . h F +phiX174 4734 G 1 . C F +phiX174 4735 T 1 . R F +phiX174 4736 G 1 . h F +phiX174 4737 C 1 . @ F +phiX174 4738 C 1 . C F +phiX174 4739 T 1 . h F +phiX174 4740 G 1 . h F +phiX174 4741 A 1 . h F +phiX174 4742 G 1 . h F +phiX174 4743 T 1 . h F +phiX174 4744 A 1 . h F +phiX174 4745 T 1 . h F +phiX174 4746 G 1 . h F +phiX174 4747 G 1 . L F +phiX174 4748 T 1 . @ F +phiX174 4749 A 1 . K F +phiX174 4750 C 1 . = F +phiX174 4751 A 1 . G F +phiX174 4752 G 1 . ] F +phiX174 4753 C 1 . h F +phiX174 4754 T 1 . h F +phiX174 4755 A 1 . h F +phiX174 4756 A 1 . J F +phiX174 4757 T 1 . < F +phiX174 4758 G 1 . T F +phiX174 4759 G 1 .$ B F +phiX174 4909 G 1 ^F, K F +phiX174 4910 C 1 , S F +phiX174 4911 T 1 , G F +phiX174 4912 A 1 , R F +phiX174 4913 C 1 , h F +phiX174 4914 A 1 , h F +phiX174 4915 C 1 , W F +phiX174 4916 G 1 , < F +phiX174 4917 C 1 , Q F +phiX174 4918 A 1 , K F +phiX174 4919 G 1 , C F +phiX174 4920 G 1 , = F +phiX174 4921 A 1 , = F +phiX174 4922 C 1 , h F +phiX174 4923 G 1 , h F +phiX174 4924 C 1 , h F +phiX174 4925 T 1 , h F +phiX174 4926 T 1 , h F +phiX174 4927 T 1 , h F +phiX174 4928 T 1 , h F +phiX174 4929 T 1 , P F +phiX174 4930 C 1 , h F +phiX174 4931 A 1 g < F +phiX174 4932 C 1 , h F +phiX174 4933 G 1 , J F +phiX174 4934 T 1 , B F +phiX174 4935 T 1 , h F +phiX174 4936 C 1 , h F +phiX174 4937 T 1 , h F +phiX174 4938 G 1 , h F +phiX174 4939 G 1 , h F +phiX174 4940 T 1 , h F +phiX174 4941 T 1 , h F +phiX174 4942 G 1 , e F +phiX174 4943 G 1 , h F +phiX174 4944 T 1 ,$ h F diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-count.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-count.tab Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,1 @@ +10 diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-coverage.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-coverage.tab Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,4553 @@ +phiX174 392 1 +phiX174 393 1 +phiX174 394 1 +phiX174 395 1 +phiX174 396 1 +phiX174 397 1 +phiX174 398 1 +phiX174 399 1 +phiX174 400 1 +phiX174 401 1 +phiX174 402 1 +phiX174 403 1 +phiX174 404 1 +phiX174 405 1 +phiX174 406 1 +phiX174 407 1 +phiX174 408 1 +phiX174 409 1 +phiX174 410 1 +phiX174 411 1 +phiX174 412 1 +phiX174 413 1 +phiX174 414 1 +phiX174 415 1 +phiX174 416 1 +phiX174 417 1 +phiX174 418 1 +phiX174 419 1 +phiX174 420 1 +phiX174 421 1 +phiX174 422 1 +phiX174 423 1 +phiX174 424 1 +phiX174 425 1 +phiX174 426 1 +phiX174 427 1 +phiX174 428 0 +phiX174 429 0 +phiX174 430 0 +phiX174 431 0 +phiX174 432 0 +phiX174 433 0 +phiX174 434 0 +phiX174 435 0 +phiX174 436 0 +phiX174 437 0 +phiX174 438 0 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+phiX174 4910 1 +phiX174 4911 1 +phiX174 4912 1 +phiX174 4913 1 +phiX174 4914 1 +phiX174 4915 1 +phiX174 4916 1 +phiX174 4917 1 +phiX174 4918 1 +phiX174 4919 1 +phiX174 4920 1 +phiX174 4921 1 +phiX174 4922 1 +phiX174 4923 1 +phiX174 4924 1 +phiX174 4925 1 +phiX174 4926 1 +phiX174 4927 1 +phiX174 4928 1 +phiX174 4929 1 +phiX174 4930 1 +phiX174 4931 1 +phiX174 4932 1 +phiX174 4933 1 +phiX174 4934 1 +phiX174 4935 1 +phiX174 4936 1 +phiX174 4937 1 +phiX174 4938 1 +phiX174 4939 1 +phiX174 4940 1 +phiX174 4941 1 +phiX174 4942 1 +phiX174 4943 1 +phiX174 4944 0 diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-fasta.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-fasta.fa Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-header.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-header.txt Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,3 @@ +@SQ SN:phiX174 LN:5386 +@PG ID:bwa PN:bwa VN:0.5.9-r16 + diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-input1.bam Binary file test-data/bamtools-input1.bam has changed diff -r 000000000000 -r 76b2f1eee508 tool-data/sam_fa_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sam_fa_indices.loc.sample Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a sam_fa_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc +#file has this format (white space characters are TAB characters): +# +#index +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/sam/, +#then the sam_fa_indices.loc entry would look like this: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +# +#and your /depot/data2/galaxy/sam/ directory +#would contain hg18.fa and hg18.fa.fai files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai +# +#Your sam_fa_indices.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa diff -r 000000000000 -r 76b2f1eee508 tool-data/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,8 @@ + + + + + line_type, value, path + +

+ diff -r 000000000000 -r 76b2f1eee508 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jan 09 11:35:08 2015 -0500 @@ -0,0 +1,9 @@ + + + + + + + + +