| Next changeset 1:79436b3019e9 (2017-08-29) |
|
Commit message:
planemo upload commit 453bb3b44d9f27908cbe2677378da88b9f77b5cf |
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added:
test-data/out_R1.fastq.gz test-data/out_R2.fastq.gz test-data/out_SE.fastq test-data/out_paired.log test-data/out_single.log test-data/t_R1.fastq test-data/t_R1.fastq.gz test-data/t_R2.fastq.gz umi-tools_extract.xml |
| b |
| diff -r 000000000000 -r 418b961e0576 test-data/out_R1.fastq.gz |
| b |
| Binary file test-data/out_R1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 418b961e0576 test-data/out_R2.fastq.gz |
| b |
| Binary file test-data/out_R2.fastq.gz has changed |
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| diff -r 000000000000 -r 418b961e0576 test-data/out_SE.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_SE.fastq Thu Aug 10 06:37:09 2017 -0400 |
| b |
| b"@@ -0,0 +1,288 @@\n+@HISEQ:105:C2UE1ACXX:3:1101:11160:2245_TTA 1:N:0:CAGATC\n+AAAAGTAGTTAATATATTAGATTTGTTTGATAGTGGTAGTATATATTTTTTATTTTAGTATTTAGGAGGTAGAGGTAGATGAATTTTTGAGTTTAAAG\n++\n+BBBFFFFBFFFFFIIIIIIBIIIIBIFFBFIIBBFFFFFFFFIIIIIIIIIIIIIIIBFIIIIIB7BBBFBBFFFF77<F7BFFFFFF7B7BBFFFF7\n+@HISEQ:105:C2UE1ACXX:3:1101:19467:2281_TTT 1:N:0:CATATC\n+TTGGTTAGGGTGAGATGTATAGTTTGGATTTTAGTGATTTTTGTAAAGGGGGAAAAGAATGGAGTTTTGGGTGTAGTGAGAGGTTATAGGAGTAGGGA\n++\n+<B<<FFFBBFFFFFFFFFIFIBFFI<<BFFFIIBBBFFIIIIBFFIIBBF7BBFFFBFFF77BBFBFF777BBBBBB<<<B<7<7BBF77<7<70000\n+@HISEQ:105:C2UE1ACXX:3:1101:7009:2740_TAG 1:N:0:CAGATC\n+AAGTTTTGTTTTTTATTTGGAGGTTATGGAATGTTAAGTAAGGTTTTTTTGGGTTTTGTTATTTATTTGATAATTGTGATTGTAATGTTAATAAGGGA\n++\n+BBBFFFFFFFFFFIIIIIB<FFFFFFIBBFIIFFFIIFIIIFFIFFIIII<0<BBFFBFFFFFFFFFF<BBFFFF<BBBBF7BFFF<BBFFFFF<00<\n+@HISEQ:105:C2UE1ACXX:3:1101:19067:2707_TTT 1:N:0:CAGATC\n+GTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTAGAAAATTTTTTTTAGTAAGATAGATTTTAAAGGGTTTGTTTTTTTTTTTTTTTTTT\n++\n+BBBFFFFFFFFFBBFFFFIIIFIFFIFFIIIIIIIFFFFFB7'0<B0<BBFF'7<0'0<<''0<'0'0<BBB<<B'7'0'0'0<BFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4999:3182_AGG 1:N:0:CAGATC\n+GTTTTATGAGGATTTTAGGGGAGTGATTGTTTAAAGTTTATAAGATTTATGATTTATATATAGTTAGAATAGTATGTGTTAAATAAATATAAAGGGAG\n++\n+<BBFFFFBFFFFFFIIFBBBFFFIIFFIBFFIFIIBFFIIIIIFFIIIIIBFFIIIIIIIIIBFFIBFIII<FFFBFBFFFFFFFFFFFFFFF<07<7\n+@HISEQ:105:C2UE1ACXX:3:1101:2300:3263_GTT 1:N:0:TAGATC\n+TTATTTTTAATAAAATTTTTATTATTTAATTTATTAGTTAATATTTAGGAGTTTTATGTTGTGGTAAAATTTTGTTAGAGAGATAGAGAAAGTATTTA\n++\n+BBBFFFFFFFFBFFIIIIIIBIBBFFI0<FFFBFF70B00<'0<FFFBBBBFF''0B0BB000'7BBFFFFII'<BF0<'<''07'70BBF'7BBBFB\n+@HISEQ:105:C2UE1ACXX:3:1101:5605:3427_AGA 1:N:0:CAGATC\n+AGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAGATAAGAAGTGGTTCGGTTATAGGATTTGTTTTAGATTTTTAGATTTTTTTGTGT\n++\n+BBBFBFFFFFFFFFFBFFFFIIIIIIIBFFFBFFIBFFIIIIIFFIIIFFIBF7BFBFBBFFIFF<<FFFFBBFFBF0<BFFFFF7<BFFFFFF0B7B\n+@HISEQ:105:C2UE1ACXX:3:1101:8129:3589_GAT 1:N:0:CAGATC\n+TTTTAGTTTTTAGTTAGGATTATACGTTTATTGTGATAAAAGAGTTTTTTGATTTATCGGGTTATGTTAGGGTTTATTGATATTAGGGAATTTGAAGA\n++\n+BBBFFBFFFFFFBFFFBBFIIFIIFBFFFFII<BBFFFIIIBFFIFIIIIBBFFIIII<7<FBFF<FBF<7<BBFFFF7<BFFFF700<BBFF0<B'<\n+@HISEQ:105:C2UE1ACXX:3:1101:14304:3866_TAA 1:N:0:CAGATC\n+GTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAATGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAA\n++\n+<BBFFFFFFFFFFFFFFFFII<BBFFFBFFIFBFFBFFFII7FFFFFFFIF<BFIIII<F<BBFIFBFB7<BFFFBBBBBF777<B7BBF7B<BB7BB\n+@HISEQ:105:C2UE1ACXX:3:1101:12720:4398_AGT 1:N:0:CAGATC\n+GTATGTGTGTGTGTGTGTGTATTTAATTGAAGTTGGGTTTGGTGATATATATGTTTAATTTTAGTATTTTAGTGGTAGAGGTAGGTTAATTTTTGTTG\n++\n+<BBFBFFFFFFFFIFIFIFFFFFIIFII0BFBFFB7BFFF<BFFFFIIIIIIBFIIIIFIIII<FIFIIIFBFBBFB7B<<BB7<B<BFFFFFF0<B0\n+@HISEQ:105:C2UE1ACXX:3:1101:14945:4439_ATT 1:N:0:CAGATC\n+AGTGTTGAGTGGAGTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTT\n++\n+BBBBFFBFFFFFFFFFFIIBIFFIFFBFFIIIIBFFIIIIIIBFFIIIBFFBFFFIIIFBFFBFBFFIIIIIFFFBBF77BBFFF7BBFF<BBF<<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:8616:4508_AGG 1:N:0:CAGATC\n+AGAAATTTTGGGGGTGTAGGAGTGGTAGGATAGGAGTGTTGTTTTGTAATAGTTTTTTTTGAGGTTTAATAGGTAGGGTAGTTATTTTTAGTATTGTA\n++\n+BBBFFFFFFBBBFFFIIFFFIFFFIIFFIIFIFBFFFIIF<FBFI<FFIIIBFFFFFFFF077<B<BBBFF<<BBBBBB<7B<BFFFFFF0BBFF0<B\n+@HISEQ:105:C2UE1ACXX:3:1101:18975:4834_GAG 1:N:0:CAGATC\n+TATAAATGGTAATTTTGTAATTTAAAGATTTAAAAGTAATTATTGGTAATAGTTATTTGTGGGAGGTTGAGGTAGGGGGATTTTTGTAGAGATCGGAA\n++\n+BBBFFFFBBFFFFIIIBFIIIIIFIIFFFFIFIIIBFIIIIIIIB<FFIFIBFFFIIIBFFBFFFII<<BFBFFFFIFF<BBBFF0BB7<<<BF707B\n+@HISEQ:105:C2UE1ACXX:3:1101:4984:5374_TTG 1:N:0:CAGATC\n+TGTATCGAGGTTTGAATGAGAGTGGTATTTTTGTTATTTGTTAGTTAATGGTTTTGAGTATTAGTTTGGAAAATGATAATAAGTATTAGTTGAGGTGT\n++\n+B<BFFFBFFFFBF<FFFBFFFFFFFIFFFIII<BFFIIIBFFFFFFIIIBBFFFIBBBFFFIIBFFF<<BFFFFBBFFFFFF<BBFFF<BB7<7<BBB\n+@HISEQ:105:C2UE1ACXX:3:1101:12336:6058_TTT 1:N:0:CAGATC\n+ATTTAGATGATGGTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTTTAAAAAATTTTTTTTATAAAAATAAATTTTAAAGGGTTTTTTTT\n++\n+BBBFFBFFBFFBBFFFIIIIIIIIBFFIIIIIIIIBFFFFIIIIIFFFFFFFFF700<BF0BBFFF0<70''00'0'000'<<'<B<00'0'00007<\n+@HISEQ:105:C2UE1ACXX:3:1101:5999:6265_ATG 1:N:0:CAGATC\n+TATATTGTTATATATTTGTGTTTTTTTTGAA"..b"FFFIBBFFIIIIFIBFFIBBFFFIFIFIIFFIFFIBFIIIFBFFFIIIIIBFBBFFFBFFF<<FFFFI70<7BFF<BFFFFFFBBBF7\n+@HISEQ:105:C2UE1ACXX:3:1101:13060:22287_TGT 1:N:0:CAGATC\n+TAGTGAAGAATAAATTTTTATGTTGTATATTATTTTTTTTTAGTTCGTATATATCGGTATACGTGTTAGGATTTATAAAGATAGTTATTATTTTTTGT\n++\n+BBBFFFFFFFFFFIIIIIIIIBFIFFIIIIIIIIIIIIIIII<FFIBFFIIIIIIB<BFFFFBBBBBF<<BBFFFBFFF<BBF7<BFFFFFFFFFF7B\n+@HISEQ:105:C2UE1ACXX:3:1101:7272:22581_TTA 1:N:0:CAGATC\n+TTAATGATATTAAGAATTTTTTAAAGAATTTTATTTTTTTTAGGAATAGAAGGAGGAGGAGTATTTTGATCGATTTTTTAGGTTTTTTATAGGTGGAG\n++\n+BBBFFBFFFFFFF<BFIIIIIIFIIBFFFFIIFIIIIIIIII<<FFFIBFIBBFFBFFFFFFBBFFF<BBF<BBFFFFFF00<BBFFFFFF000<777\n+@HISEQ:105:C2UE1ACXX:3:1101:10060:23020_TTT 1:N:0:CAGATC\n+TTTTAGATTATTTAAGAAGGTATTAGGTTTTTAAGAGGAAAGGGTAGTCTTATAGTTTTGAGTATTTTTTTTAAAAGGAAGTAAGGATGGTGTTTTTA\n++\n+BBBFFBFFFFFFFIIBFIFFFFFIBBBFFFFIIIBFFFIFIBFFIFFFFIIFFFBFFII7B<FFFIIIIIFFFFBB77<B<BBF<7BB<<BBBBBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:14440:23104_TTT 1:N:0:CAGATC\n+TTTAAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAATTTTTGGTGT\n++\n+BBBFFFFFFFFFFFIIBBIFIBBBFFFFFBFFIIIIBFFIIBFBFFFFFFIIIIFFF7BB<<BBFB<BBBBFFB7<00B<BBFF00<BBFFFF''77B\n+@HISEQ:105:C2UE1ACXX:3:1101:6941:23338_GTT 1:N:0:CAGATC\n+AGAAAGGTTTTAAGTTGGTTGGGAATATAGGGGTTTTTTAGAGTTTTTATTAGGAGTTATAGTGTGTTGAATTTGGTTTTGGGTGTTGATTATAGGTT\n++\n+BBBFFFFFFFFFFBFFBBFFBBBFFFFIIBFFFIFFIIIIBFFFFFIIIIIIB<FFFFFFFBFBFFFF<BBFFF<<BBBB700<BBB0BBFFFF00<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10069:23622_TTT 1:N:0:CAGATC\n+TTTTGTTTTAGGGTTTTATTTTTGTGTTTTATTTTTATTTTCGTATTATTAGTTTTTTTTATACGTTATTTGTAGAAGGTTAGTTTTTTTAATTTAGG\n++\n+BBBFBFFFFFBBBFFFIFIIIIIBFBFFIIBFIIIIIIIIIIBFFFIIIIIFFIIIIIIFFFFF<BFFFFF<BF<<B77BBB7BBFFFFFFFFFFF00\n+@HISEQ:105:C2UE1ACXX:3:1101:14079:24078_AGT 1:N:0:CAGATC\n+TTTAAAGTTTTTAGTTTTGAGTGGAATTTTAAGAATATTAGTGCGTTTTAAGCTTAGGTAGTTTTGGTAGTTTGAAAGTAATAGGGTGTATTTTGTAA\n++\n+BBBFFFFFFFFFFBFFFI<BBFFFFFFIIIIIBFFFIIIIBFFFFFFIIIIBFFIIBBFFFFFFI<7BFBFFF<BBF<BBFFF<07BBBBBFFF<BFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12064:24631_TTT 1:N:0:CCGATC\n+TTATAGTGTATTTATATATATGAAATGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGT\n++\n+BBBFFBFFFFFFFIIIIIIIIBFIFF0BFIIIIIBFFIIIIIIIIIIIIIBFIIFFFIBFFBFFFFFFB<BFF7BBFFFFF<B<BBBFFFFFFF'70<\n+@HISEQ:105:C2UE1ACXX:3:1101:11630:24964_GAT 1:N:0:TAGATC\n+TTAGTTTTTTTAGTGTTTTTTATTTATTTCGTTTTATTATTGGAGTTTGTTAAGAAAATTAGGGTTTGATTTGGATGTTAAGGATTGGTTTTTTTTTT\n++\n+BBBBFFFFFFFFBFFFFIIIIIIIIIIIIIBFFFIFIIIIIB7BFFFFBFFIIBFIIIIIFB<BFBFBFFFF<7BB<BBFF<7<BB77BBFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12594:24878_AAT 1:N:0:CCGATC\n+TTTAATAGGATATGATATTATTTAATTTATAGATTATGGAAATTTTTTATATTTAATGAAGAAAGTTGGAATGTTTTGGGAGGTGTTTAGAATAAATA\n++\n+BBBFFFFB0BFFF<FFIIIFIIFIIIFIFIF<BFFFF<<BFFFIIIIIIIIIIIIIIBFFBFFIBFB7'<FF<<BBF0''77<BFB<BB0<BBBBBFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4483:25030_ATT 1:N:0:CAGATC\n+AGGATGGTGTTTTTATTTTTAGATTTATATTATTTTGTTATATTTGTATTTGAGTAAGTTTATGGGTTTTTTAAAGAGGTAGGAGGAAGTTTTTTGTT\n++\n+B<BFFFFFFFFFFIIIIIIIIBBFIIFIIIIFIIII<BFFIFFIIBFIIII<BBFFIFIFIIIB7<FFFIIIFBF<<77BB00<70<B7BBBFFF0BB\n+@HISEQ:105:C2UE1ACXX:3:1101:12198:25235_TTA 1:N:0:CAGATC\n+ATATATGTAGTTTGTATTATTTTTGTTATAGTATATAAAGGTTAAAGAGTAGTTGTTTTAATTTTAGAGGTGGAGATTGGGTTGTATAGTTTTGGTTT\n++\n+BBBFFFBFFFFFFBFFIIFIIIII0BF<FF0BFFFIFFIBBFBFII<FBFBBFF7FFFIIIIIIII<F7<B'<BB7<B''0<<0<BBB77<BB'0<<B\n+@HISEQ:105:C2UE1ACXX:3:1101:20477:25084_TGT 1:N:0:CATATC\n+AGAGTTTATTGAGAAGTAAAGTATTAATTTTATGGGAGAAATGGGATAGAGGTAGTAGAAGTTGTTATGGAATGGGATTAATTAGGAAGTTAATTAAG\n++\n+BBBFFFFFFF0BBFFBFFIIFFIIIIIIIIIFIBB7FFFFIIFFBFFIFIBFFFFIIFIIFFFBFFFF77BFF<<B<FFFFFFF70<B7BBFFFFFF7\n+@HISEQ:105:C2UE1ACXX:3:1101:5725:25359_TAG 1:N:0:CAGATC\n+GAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATA\n++\n+BBBFFFFFFBFFFIIIIIIIIIIIBIFBFFFFIIBBFFFFFFFIIIIIIFFFBFFBBFFFIIBFFIIBFIIFIFIFFFFF<BF<BBFF7<<FFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:5502:25591_AGA 1:N:0:CAGATC\n+ATATGATTTTATTTTTAGGGATAATATTTTTTAAGTGAATTTTGATTTTTTGGTTAGTTATTTTGATGATGTGTAGAGGGTGTATAGTTTTTGGATAT\n++\n+BBBFBFFFFFFFFIIIIBBBFFFIIIIIIIIIIIBFFFIIIIIBFFIIIII<7BFFBFFFIIII<FF<FFBFFFFFB<<<BFBBBF<<BFFF00<BFB\n" |
| b |
| diff -r 000000000000 -r 418b961e0576 test-data/out_paired.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_paired.log Thu Aug 10 06:37:09 2017 -0400 |
| b |
| @@ -0,0 +1,116 @@ +# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat +# job started at Tue Aug 8 15:14:12 2017 on packer-test -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e +# pid: 32709, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 +# log2stderr : False +# loglevel : 1 +# pattern : NNNXXX +# pattern2 : None +# prime3 : False +# quality_encoding : None +# quality_filter_threshold : None +# random_seed : None +# read2_in : input_read2.gz +# read2_out : out2.gz +# short_help : None +# split : False +# stats : True +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'> +# stdlog : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +Barcode UMI Sample Count +AAAAGT AAA AGT 1 +TTTTTT TTT TTT 1 +TTGGTT TTG GTT 1 +AAGTTT AAG TTT 1 +ATATAA ATA TAA 1 +GTTTTT GTT TTT 4 +GTTTTA GTT TTA 1 +TATAGA TAT AGA 1 +AAGTAT AAG TAT 1 +TTATTT TTA TTT 1 +AGATGA AGA TGA 1 +TTTTAG TTT TAG 2 +GTGTTT GTG TTT 1 +GTATGT GTA TGT 1 +AGTGTT AGT GTT 1 +AGAAAT AGA AAT 1 +TATAAA TAT AAA 1 +TGTATC TGT ATC 1 +TAAAAT TAA AAT 1 +ATTATT ATT ATT 1 +ATTTAG ATT TAG 1 +TATATT TAT ATT 1 +ATTTGG ATT TGG 1 +AAAATA AAA ATA 1 +AAGTTA AAG TTA 1 +GTTGTA GTT GTA 1 +TTTGAA TTT GAA 1 +ATTTGA ATT TGA 1 +TTTATA TTT ATA 2 +ATACGT ATA CGT 1 +GGTTAG GGT TAG 1 +GGTGTT GGT GTT 1 +TGGTTG TGG TTG 1 +AGTTAT AGT TAT 1 +GAGTAG GAG TAG 1 +TGTGTT TGT GTT 1 +TGAATT TGA ATT 1 +TTTAGG TTT AGG 2 +TAGATG TAG ATG 1 +TTGGAT TTG GAT 1 +TTGGAC TTG GAC 1 +TGTATG TGT ATG 1 +AGAGTG AGA GTG 1 +AGAATA AGA ATA 1 +TTGTTT TTG TTT 1 +AATATA AAT ATA 1 +TTATTA TTA TTA 1 +TTAAAG TTA AAG 2 +AGGAGT AGG AGT 1 +ATAAGT ATA AGT 1 +TTGTGG TTG TGG 1 +GTATTA GTA TTA 1 +AGTGGA AGT GGA 1 +TTTGGG TTT GGG 1 +TAAGAG TAA GAG 1 +TTGGGA TTG GGA 1 +TATAGG TAT AGG 1 +TTTTTG TTT TTG 1 +AAGAGG AAG AGG 1 +GAGAGA GAG AGA 1 +TTGGTG TTG GTG 1 +TAGAGG TAG AGG 1 +ATTTTG ATT TTG 1 +TGGATG TGG ATG 1 +ATTTTT ATT TTT 1 +TTATAT TTA TAT 1 +TGTTTG TGT TTG 1 +GTTGGT GTT GGT 1 +TCTTTA TCT TTA 1 +ATTGTT ATT GTT 2 +ATAAGA ATA AGA 1 +TATCGA TAT CGA 1 +TTTGTT TTT GTT 1 +GTGTAT GTG TAT 1 +AGTGAA AGT GAA 1 +GTTGTG GTT GTG 1 +TAGTGA TAG TGA 1 +TATTGA TAT TGA 1 +TTAATG TTA ATG 1 +TTTAAA TTT AAA 2 +AGAAAG AGA AAG 1 +TTTTGT TTT TGT 1 +TTATAG TTA TAG 1 +AGGTGT AGG TGT 1 +TTAGTT TTA GTT 1 +TTTAAT TTT AAT 1 +AGGATG AGG ATG 1 +ATATAT ATA TAT 1 +AGAGTT AGA GTT 1 +GAGAAA GAG AAA 1 +ATATGA ATA TGA 1 +# job finished in 0 seconds at Tue Aug 8 15:14:12 2017 -- 0.41 0.02 0.00 0.00 -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e |
| b |
| diff -r 000000000000 -r 418b961e0576 test-data/out_single.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_single.log Thu Aug 10 06:37:09 2017 -0400 |
| b |
| @@ -0,0 +1,92 @@ +# output generated by extract --bc-pattern=XXXNNN --stdin=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat --stdout /home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat +# job started at Wed Aug 9 09:51:05 2017 on packer-test -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b +# pid: 7652, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 +# log2stderr : False +# loglevel : 1 +# pattern : XXXNNN +# pattern2 : None +# prime3 : True +# quality_encoding : phred33 +# quality_filter_threshold : 10 +# random_seed : None +# read2_in : None +# read2_out : None +# short_help : None +# split : False +# stats : True +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat' mode='r' encoding='UTF-8'> +# stdlog : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat' mode='w' encoding='UTF-8'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +Barcode UMI Sample Count +AAGTTA TTA AAG 1 +GGATTT TTT GGA 1 +GGATAG TAG GGA 1 +TTTTTT TTT TTT 4 +GAGAGG AGG GAG 1 +TTAGTT GTT TTA 1 +TGTAGA AGA TGT 1 +AGAGAT GAT AGA 1 +GAATAA TAA GAA 1 +TTGAGT AGT TTG 1 +TTTATT ATT TTT 1 +GTAAGG AGG GTA 1 +GAAGAG GAG GAA 1 +TGTTTG TTG TGT 1 +ATAATG ATG ATA 1 +TTAGAT GAT TTA 1 +GTCTGA TGA GTC 1 +ATCATC ATC ATC 1 +GTCACC ACC GTC 1 +AACTCC TCC AAC 1 +TTATTA TTA TTA 1 +TGTTGT TGT TGT 2 +GTTTAT TAT GTT 1 +ATGAGT AGT ATG 1 +ATAATT ATT ATA 1 +TTGGTT GTT TTG 1 +GTTTTG TTG GTT 1 +CACGTC GTC CAC 1 +TTGTGT TGT TTG 1 +TGAATT ATT TGA 1 +GGATGT TGT GGA 1 +AGTCAC CAC AGT 1 +GTTTTT TTT GTT 1 +TATAGT AGT TAT 1 +TTTTAT TAT TTT 1 +TAAAAA AAA TAA 1 +ATAGGT GGT ATA 1 +ATTTTA TTA ATT 1 +TGTATA ATA TGT 1 +TGTTTT TTT TGT 2 +AGATTT TTT AGA 1 +TAGAAT AAT TAG 1 +GAAGGA GGA GAA 1 +GTTTGA TGA GTT 1 +TTTTGT TGT TTT 1 +ATTTTT TTT ATT 1 +TGTTAT TAT TGT 1 +CAGGAT GAT CAG 1 +GTATTT TTT GTA 1 +TGGGTA GTA TGG 1 +AAAGTT GTT AAA 1 +GGTGTG GTG GGT 1 +AAGATC ATC AAG 1 +TAGGTT GTT TAG 1 +GAGTTA TTA GAG 1 +TTATTT TTT TTA 1 +GTTGTT GTT GTT 1 +AGGTTT TTT AGG 1 +TAAAGT AGT TAA 1 +AGTTTT TTT AGT 1 +TTTGAT GAT TTT 1 +ATAAAT AAT ATA 1 +GTTATT ATT GTT 1 +TTTTTA TTA TTT 1 +AAGTGT TGT AAG 1 +ATATAG TAG ATA 1 +TATAGA AGA TAT 1 +# job finished in 0 seconds at Wed Aug 9 09:51:05 2017 -- 0.36 0.02 0.00 0.00 -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b |
| b |
| diff -r 000000000000 -r 418b961e0576 test-data/t_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t_R1.fastq Thu Aug 10 06:37:09 2017 -0400 |
| b |
| b"@@ -0,0 +1,400 @@\n+@HISEQ:105:C2UE1ACXX:3:1101:11160:2245 1:N:0:CAGATC\n+AAAAGTAGTTAATATATTAGATTTGTTTGATAGTGGTAGTATATATTTTTTATTTTAGTATTTAGGAGGTAGAGGTAGATGAATTTTTGAGTTTAAAGTTA\n++\n+BBBFFFFBFFFFFIIIIIIBIIIIBIFFBFIIBBFFFFFFFFIIIIIIIIIIIIIIIBFIIIIIB7BBBFBBFFFF77<F7BFFFFFF7B7BBFFFF7<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:19338:2197 1:N:0:CAGATC\n+TTTTTTTTTAGAGGGATTAGTTTTTTTTATTGAGGTTTTTGAAAGTTGTTGTATGTTAATTGTTTTTAGAATGTTGGGTATAAGTAGGATTTAGGTCTATT\n++\n+BBBFFFFFFB0<BF7BBBF7BFFIIIII7BF'0<0BBFFF'<BB'<B7<B07<B7<BFBBF0<BBBBB0<<B0BB<<000<BF00<<'0<BBB0'00BBF#\n+@HISEQ:105:C2UE1ACXX:3:1101:19467:2281 1:N:0:CATATC\n+TTGGTTAGGGTGAGATGTATAGTTTGGATTTTAGTGATTTTTGTAAAGGGGGAAAAGAATGGAGTTTTGGGTGTAGTGAGAGGTTATAGGAGTAGGGATTT\n++\n+<B<<FFFBBFFFFFFFFFIFIBFFI<<BFFFIIBBBFFIIIIBFFIIBBF7BBFFFBFFF77BBFBFF777BBBBBB<<<B<7<7BBF77<7<700007BB\n+@HISEQ:105:C2UE1ACXX:3:1101:7009:2740 1:N:0:CAGATC\n+AAGTTTTGTTTTTTATTTGGAGGTTATGGAATGTTAAGTAAGGTTTTTTTGGGTTTTGTTATTTATTTGATAATTGTGATTGTAATGTTAATAAGGGATAG\n++\n+BBBFFFFFFFFFFIIIIIB<FFFFFFIBBFIIFFFIIFIIIFFIFFIIII<0<BBFFBFFFFFFFFFF<BBFFFF<BBBBF7BFFF<BBFFFFF<00<BB0\n+@HISEQ:105:C2UE1ACXX:3:1101:13708:2613 1:N:0:CAGATC\n+ATATAATAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAAGATAATTAATTTTTAAAATTTTTTTTTTTTTAATAAAA\n++\n+BBBFFFFFBFFFFIIIIIIIIIIIFFFFFB7B007BB0''''''0077BFF7'077BF0''0''''''00''00''''00'<BBBFBBFFFFF########\n+@HISEQ:105:C2UE1ACXX:3:1101:19067:2707 1:N:0:CAGATC\n+GTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTAGAAAATTTTTTTTAGTAAGATAGATTTTAAAGGGTTTGTTTTTTTTTTTTTTTTTTTTT\n++\n+BBBFFFFFFFFFBBFFFFIIIFIFFIFFIIIIIIIFFFFFB7'0<B0<BBFF'7<0'0<<''0<'0'0<BBB<<B'7'0'0'0<BFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4999:3182 1:N:0:CAGATC\n+GTTTTATGAGGATTTTAGGGGAGTGATTGTTTAAAGTTTATAAGATTTATGATTTATATATAGTTAGAATAGTATGTGTTAAATAAATATAAAGGGAGAGG\n++\n+<BBFFFFBFFFFFFIIFBBBFFFIIFFIBFFIFIIBFFIIIIIFFIIIIIBFFIIIIIIIIIBFFIBFIII<FFFBFBFFFFFFFFFFFFFFF<07<7<<7\n+@HISEQ:105:C2UE1ACXX:3:1101:16790:3145 1:N:0:CAGATC\n+TATAGAGGTATTTTGTTATTTTGTTTTAGTTATTGCGGGTTAGAGTAGATGGTTATTTTTAGTAGAGTATTGTTTGTTGTTTTTTATATGTGGTATAGAGG\n++\n+BBBF<BBFFFFFFI<FFFIFIIBBFFIIBFFFFI<BBBFFFF<FFFF7FF70<BFFIFIIF7BFBB<FFBF'BBF'<<0<BFFBBBBBF'<70<<<B####\n+@HISEQ:105:C2UE1ACXX:3:1101:18065:3106 1:N:0:CAGATC\n+AAGTATTTGTTATATATATTTTAAAGTTTTTTTTTTTTTTAGGAATTTTTTTTTATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTTT\n++\n+BBBFFFFFBFFFFIIIIFIIIIIIIFIFIIIIIIIIIIFF''00<<BB'<<'7''000<BFFF77<77BFF77BFBB07<7<BFFFFFFFF##########\n+@HISEQ:105:C2UE1ACXX:3:1101:2300:3263 1:N:0:TAGATC\n+TTATTTTTAATAAAATTTTTATTATTTAATTTATTAGTTAATATTTAGGAGTTTTATGTTGTGGTAAAATTTTGTTAGAGAGATAGAGAAAGTATTTAGTT\n++\n+BBBFFFFFFFFBFFIIIIIIBIBBFFI0<FFFBFF70B00<'0<FFFBBBBFF''0B0BB000'7BBFFFFII'<BF0<'<''07'70BBF'7BBBFB7<B\n+@HISEQ:105:C2UE1ACXX:3:1101:5605:3427 1:N:0:CAGATC\n+AGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAGATAAGAAGTGGTTCGGTTATAGGATTTGTTTTAGATTTTTAGATTTTTTTGTGTAGA\n++\n+BBBFBFFFFFFFFFFBFFFFIIIIIIIBFFFBFFIBFFIIIIIFFIIIFFIBF7BFBFBBFFIFF<<FFFFBBFFBF0<BFFFFF7<BFFFFFF0B7BF0<\n+@HISEQ:105:C2UE1ACXX:3:1101:8129:3589 1:N:0:CAGATC\n+TTTTAGTTTTTAGTTAGGATTATACGTTTATTGTGATAAAAGAGTTTTTTGATTTATCGGGTTATGTTAGGGTTTATTGATATTAGGGAATTTGAAGAGAT\n++\n+BBBFFBFFFFFFBFFFBBFIIFIIFBFFFFII<BBFFFIIIBFFIFIIIIBBFFIIII<7<FBFF<FBF<7<BBFFFF7<BFFFF700<BBFF0<B'<07B\n+@HISEQ:105:C2UE1ACXX:3:1101:14304:3866 1:N:0:CAGATC\n+GTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAATGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAATAA\n++\n+<BBFFFFFFFFFFFFFFFFII<BBFFFBFFIFBFFBFFFII7FFFFFFFIF<BFIIII<F<BBFIFBFB7<BFFFBBBBBF777<B7BBF7B<BB7BBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12720:4398 1:N:0:CAGATC\n+GTATGTGTGTGTGTGTGTGTATTTAATTGAAGTTGGGTTTGGTGATATATATGTTTAATTTTAGTATTTTAGTGGTAGAGGTAGGTTAATTTTTGTTGAGT\n++\n+<BBFBFFFFFFFFIFIFIFFFFFIIFII0BFBFFB7BFFF<BFFFFIIIIIIBFIIIIFIIII<FIFIIIFBFBBFB7B<<BB7<B<BFFFFFF0<B0<7B\n+@HISEQ:105:C2UE1ACXX:3:1101:14945:4439 1:N:0:CAGATC\n+AGTGTTGAGTGGAGTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATT\n++\n+BBBBFFBFFFFFFFFFFIIBIFFIFFBFFIIIIBFFIIIIIIBFFIIIBFFBFFFIIIFBFFBFBFFIIIIIFFFBBF77BBFFF7BBFF<BBF<<BFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:8616:4508 1:N:0:CAGATC\n+AGA"..b"0<BFFBFFFBF7FBFIIFIF7BFFI7<7B<BBFB'<BF'7BBFF7BBBBBBB#######\n+@HISEQ:105:C2UE1ACXX:3:1101:7272:22581 1:N:0:CAGATC\n+TTAATGATATTAAGAATTTTTTAAAGAATTTTATTTTTTTTAGGAATAGAAGGAGGAGGAGTATTTTGATCGATTTTTTAGGTTTTTTATAGGTGGAGTTA\n++\n+BBBFFBFFFFFFF<BFIIIIIIFIIBFFFFIIFIIIIIIIII<<FFFIBFIBBFFBFFFFFFBBFFF<BBF<BBFFFFFF00<BBFFFFFF000<777B<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10060:23020 1:N:0:CAGATC\n+TTTTAGATTATTTAAGAAGGTATTAGGTTTTTAAGAGGAAAGGGTAGTCTTATAGTTTTGAGTATTTTTTTTAAAAGGAAGTAAGGATGGTGTTTTTATTT\n++\n+BBBFFBFFFFFFFIIBFIFFFFFIBBBFFFFIIIBFFFIFIBFFIFFFFIIFFFBFFII7B<FFFIIIIIFFFFBB77<B<BBF<7BB<<BBBBBFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:14440:23104 1:N:0:CAGATC\n+TTTAAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAATTTTTGGTGTTTT\n++\n+BBBFFFFFFFFFFFIIBBIFIBBBFFFFFBFFIIIIBFFIIBFBFFFFFFIIIIFFF7BB<<BBFB<BBBBFFB7<00B<BBFF00<BBFFFF''77BBBF\n+@HISEQ:105:C2UE1ACXX:3:1101:6941:23338 1:N:0:CAGATC\n+AGAAAGGTTTTAAGTTGGTTGGGAATATAGGGGTTTTTTAGAGTTTTTATTAGGAGTTATAGTGTGTTGAATTTGGTTTTGGGTGTTGATTATAGGTTGTT\n++\n+BBBFFFFFFFFFFBFFBBFFBBBFFFFIIBFFFIFFIIIIBFFFFFIIIIIIB<FFFFFFFBFBFFFF<BBFFF<<BBBB700<BBB0BBFFFF00<B7<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10069:23622 1:N:0:CAGATC\n+TTTTGTTTTAGGGTTTTATTTTTGTGTTTTATTTTTATTTTCGTATTATTAGTTTTTTTTATACGTTATTTGTAGAAGGTTAGTTTTTTTAATTTAGGTTT\n++\n+BBBFBFFFFFBBBFFFIFIIIIIBFBFFIIBFIIIIIIIIIIBFFFIIIIIFFIIIIIIFFFFF<BFFFFF<BF<<B77BBB7BBFFFFFFFFFFF00<BB\n+@HISEQ:105:C2UE1ACXX:3:1101:14079:24078 1:N:0:CAGATC\n+TTTAAAGTTTTTAGTTTTGAGTGGAATTTTAAGAATATTAGTGCGTTTTAAGCTTAGGTAGTTTTGGTAGTTTGAAAGTAATAGGGTGTATTTTGTAAAGT\n++\n+BBBFFFFFFFFFFBFFFI<BBFFFFFFIIIIIBFFFIIIIBFFFFFFIIIIBFFIIBBFFFFFFI<7BFBFFF<BBF<BBFFF<07BBBBBFFF<BFFF<B\n+@HISEQ:105:C2UE1ACXX:3:1101:12064:24631 1:N:0:CCGATC\n+TTATAGTGTATTTATATATATGAAATGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGTTTT\n++\n+BBBFFBFFFFFFFIIIIIIIIBFIFF0BFIIIIIBFFIIIIIIIIIIIIIBFIIFFFIBFFBFFFFFFB<BFF7BBFFFFF<B<BBBFFFFFFF'70<<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:6662:24968 1:N:0:CAGATC\n+AGGTGTCGTTTAATTGTTTAGGTTTATGGTATTGTGTTTCGTTTTTTTGGTATTTGTGAGGGTAGAATTGTTTTTGGGTTTTAATTTTTTTAAGTATGGGA\n++\n+BBBFFFFFFFFFFIIBFFIFBBFFFFIB<FFFI<FBFFFFBFFIIIII77BFFIIBFBFBBBFBBFFFF<BBFFF'07BBBBFFFFFFFFFFB0<BF####\n+@HISEQ:105:C2UE1ACXX:3:1101:11630:24964 1:N:0:TAGATC\n+TTAGTTTTTTTAGTGTTTTTTATTTATTTCGTTTTATTATTGGAGTTTGTTAAGAAAATTAGGGTTTGATTTGGATGTTAAGGATTGGTTTTTTTTTTGAT\n++\n+BBBBFFFFFFFFBFFFFIIIIIIIIIIIIIBFFFIFIIIIIB7BFFFFBFFIIBFIIIIIFB<BFBFBFFFF<7BB<BBFF<7<BB77BBFFFFFFFF0<B\n+@HISEQ:105:C2UE1ACXX:3:1101:12594:24878 1:N:0:CCGATC\n+TTTAATAGGATATGATATTATTTAATTTATAGATTATGGAAATTTTTTATATTTAATGAAGAAAGTTGGAATGTTTTGGGAGGTGTTTAGAATAAATAAAT\n++\n+BBBFFFFB0BFFF<FFIIIFIIFIIIFIFIF<BFFFF<<BFFFIIIIIIIIIIIIIIBFFBFFIBFB7'<FF<<BBF0''77<BFB<BB0<BBBBBFFBBF\n+@HISEQ:105:C2UE1ACXX:3:1101:4483:25030 1:N:0:CAGATC\n+AGGATGGTGTTTTTATTTTTAGATTTATATTATTTTGTTATATTTGTATTTGAGTAAGTTTATGGGTTTTTTAAAGAGGTAGGAGGAAGTTTTTTGTTATT\n++\n+B<BFFFFFFFFFFIIIIIIIIBBFIIFIIIIFIIII<BFFIFFIIBFIIII<BBFFIFIFIIIB7<FFFIIIFBF<<77BB00<70<B7BBBFFF0BBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12198:25235 1:N:0:CAGATC\n+ATATATGTAGTTTGTATTATTTTTGTTATAGTATATAAAGGTTAAAGAGTAGTTGTTTTAATTTTAGAGGTGGAGATTGGGTTGTATAGTTTTGGTTTTTA\n++\n+BBBFFFBFFFFFFBFFIIFIIIII0BF<FF0BFFFIFFIBBFBFII<FBFBBFF7FFFIIIIIIII<F7<B'<BB7<B''0<<0<BBB77<BB'0<<BBFB\n+@HISEQ:105:C2UE1ACXX:3:1101:20477:25084 1:N:0:CATATC\n+AGAGTTTATTGAGAAGTAAAGTATTAATTTTATGGGAGAAATGGGATAGAGGTAGTAGAAGTTGTTATGGAATGGGATTAATTAGGAAGTTAATTAAGTGT\n++\n+BBBFFFFFFF0BBFFBFFIIFFIIIIIIIIIFIBB7FFFFIIFFBFFIFIBFFFFIIFIIFFFBFFFF77BFF<<B<FFFFFFF70<B7BBFFFFFF7B<B\n+@HISEQ:105:C2UE1ACXX:3:1101:5725:25359 1:N:0:CAGATC\n+GAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATATAG\n++\n+BBBFFFFFFBFFFIIIIIIIIIIIBIFBFFFFIIBBFFFFFFFIIIIIIFFFBFFBBFFFIIBFFIIBFIIFIFIFFFFF<BF<BBFF7<<FFFFFFFFF0\n+@HISEQ:105:C2UE1ACXX:3:1101:5502:25591 1:N:0:CAGATC\n+ATATGATTTTATTTTTAGGGATAATATTTTTTAAGTGAATTTTGATTTTTTGGTTAGTTATTTTGATGATGTGTAGAGGGTGTATAGTTTTTGGATATAGA\n++\n+BBBFBFFFFFFFFIIIIBBBFFFIIIIIIIIIIIBFFFIIIIIBFFIIIII<7BFFBFFFIIII<FF<FFBFFFFFB<<<BFBBBF<<BFFF00<BFBF7<\n" |
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| diff -r 000000000000 -r 418b961e0576 test-data/t_R1.fastq.gz |
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| Binary file test-data/t_R1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 418b961e0576 test-data/t_R2.fastq.gz |
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| Binary file test-data/t_R2.fastq.gz has changed |
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| diff -r 000000000000 -r 418b961e0576 umi-tools_extract.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/umi-tools_extract.xml Thu Aug 10 06:37:09 2017 -0400 |
| [ |
| b'@@ -0,0 +1,255 @@\n+<tool id="umi_tools_extract" name="UMI-tools extract" version="0.4.4.0">\n+ <description>Extract UMI from fastq files</description>\n+ <requirements>\n+ <requirement type="package" version="0.4.4">umi_tools</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #set $gz = False\n+ #if $input_type.type == \'single\':\n+ #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ ln -s \'$input_type.input_single\' input_single.gz &&\n+ #set $gz = True\n+ #end if\n+ #else\n+ #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ ln -s \'$input_type.input_read1\' input_read1.gz &&\n+ ln -s \'$input_type.input_read2\' input_read2.gz &&\n+ #set $gz = True\n+ #end if\n+ #end if\n+ umi_tools extract\n+ --bc-pattern=\'$bc_pattern\'\n+ #if $input_type.type == \'single\':\n+ #if $gz:\n+ --stdin=input_single.gz\n+ --stdout out.gz\n+ #else\n+ --stdin=\'$input_type.input_single\'\n+ --stdout \'$out\'\n+ #end if\n+ #else:\n+ #if $gz:\n+ --stdin=input_read1.gz\n+ --read2-in=input_read2.gz\n+ --stdout out1.gz\n+ --read2-out=out2.gz\n+ #else:\n+ --stdin=\'$input_type.input_read1\'\n+ --read2-in=\'$input_type.input_read2\'\n+ --stdout \'$out1\'\n+ --read2-out=\'$out2\'\n+ #end if\n+ #if $input_type.barcode.split == "1":\n+ --split-barcode\n+ --bc-pattern2=\'$input_type.barcode.bc_pattern2\'\n+ #end if\n+ #end if\n+ #if not $prime3:\n+ --3prime\n+ #end if\n+ #if $quality.quality_selector ==\'true\':\n+ --quality-filter-threshold \'$quality.quality_filter_threshold\'\n+ --quality-encoding \'$quality.quality_encoding\'\n+ #end if\n+ #if $print_log == "1":\n+ --log=\'$out_log\'\n+ #else\n+ --supress-stats\n+ #end if\n+ #if $gz:\n+ #if $input_type.type == \'single\':\n+ && mv out.gz \'$out\'\n+ #else\n+ && mv out1.gz \'$out1\'\n+ && mv out2.gz \'$out2\'\n+ #end if\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <conditional name="input_type">\n+ <param name="type" type="select" label="Library type">\n+ <option value="single">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ </param>\n+ <when value="single">\n+ <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />\n+ </when>\n+ <when value="paired">\n+ <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />\n+ <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />\n+ <conditional name="barcode">\n+ <param name="split" argument="--split-barcode" type="select" label="Barcode on both reads?">\n+ <option value="0">Barcode on first read only</option>\n+ <option value="1">Barcode on both reads</option>\n+ </param>\n+ <when value="0">\n+ </when>\n+ <when value="1">\n+ <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"\n+ help="Use this option to specify the format of the UMI/barcode for\n+ '..b' </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="type" value="single" />\n+ <param name="input_single" value="t_R1.fastq" ftype="fastq" />\n+ <param name="bc_pattern" value="XXXNNN" />\n+ <param name="prime3" value="0" />\n+ <param name="quality_selector" value="true" />\n+ <param name="quality_filter_threshold" value="10" />\n+ <param name="quality_encoding" value="phred33" />\n+ <output name="out" file="out_SE.fastq" />\n+ <output name="out_log" file="out_single.log" lines_diff="15"/>\n+ </test>\n+ <test>\n+ <param name="type" value="paired" />\n+ <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />\n+ <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />\n+ <param name="bc_pattern" value="NNNXXX" />\n+ <output name="out1" file="out_R1.fastq.gz" decompress="true" />\n+ <output name="out2" file="out_R2.fastq.gz" decompress="true" />\n+ <output name="out_log" file="out_paired.log" lines_diff="10"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+\n+UMI-tools extract.py - Extract UMI from fastq\n+=============================================\n+\n+Purpose\n+-------\n+\n+Extract UMI barcode from a read and add it to the read name, leaving\n+any sample barcode in place. Can deal with paired end reads and UMIs\n+split across the paired ends\n+\n+Options\n+-------\n+\n+--split-barcode\n+ By default the UMI is assumed to be on the first read. Use this\n+ option if the UMI is contained on both reads and specify the\n+ pattern of the barcode/UMI on the second read using the option\n+ ``--bc-pattern2``\n+\n+--bc-pattern\n+ Use this option to specify the format of the UMI/barcode. Use Ns to\n+ represent the random positions and Xs to indicate the bc positions.\n+ Bases with Ns will be extracted and added to the read name. Remaining\n+ bases, marked with an X will be reattached to the read.\n+\n+ E.g. If the pattern is NNXXNN,\n+ Then the read:\n+\n+ @HISEQ:87:00000000 read1\n+ AAGGTTGCTGATTGGATGGGCTAG\n+ DA1AEBFGGCG01DFH00B1FF0B\n+ +\n+\n+ will become:\n+ @HISEQ:87:00000000_AATT read1\n+ GGGCTGATTGGATGGGCTAG\n+ 1AFGGCG01DFH00B1FF0B\n+ +\n+\n+--bc-pattern2\n+ Use this option to specify the format of the UMI/barcode for\n+ the second read pair if required. If --bc-pattern2 is not\n+ supplied, this defaults to the same pattern as --bc-pattern\n+\n+--3prime\n+ By default the barcode is assumed to be on the 5\' end of the read, but\n+ use this option to sepecify that it is on the 3\' end instead\n+\n+-L\n+ Specify a log file to retain logging information and final statistics\n+\n+--split-barcode\n+ barcode is split across read pair\n+\n+--quality-filter-threshold=QUALITY_FILTER_THRESHOLD\n+ Remove reads where any UMI base quality score falls\n+ below this threshold\n+--quality-encoding=QUALITY_ENCODING\n+ Quality score encoding. Choose from phred33[33-77]\n+ phred64 [64-106] or solexa [59-106]\n+\n+Usage:\n+------\n+\n+For single ended reads:\n+ umi_tools extract --bc-pattern=[PATTERN] -L extract.log [OPTIONS]\n+\n+reads from stdin and outputs to stdout.\n+\n+For paired end reads:\n+ umi_tools extract --bc-pattern=[PATTERN] --read2-in=[FASTQIN] --read2-out=[FASTQOUT] -L extract.log [OPTIONS]\n+\n+reads end one from stdin and end two from FASTQIN and outputs end one to stdin\n+and end two to FASTQOUT.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1101/gr.209601.116</citation>\n+ <citation type="bibtex">\n+ @misc{githubUMI-tools,\n+ title = {UMI-tools},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/CGATOxford/UMI-tools},\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |