| Previous changeset 7:4756f7765416 (2018-07-14) Next changeset 9:99aea37a7ff7 (2018-07-20) |
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Commit message:
planemo upload commit f6178c9e071a2158a35b82a3607f6dc8a767675c |
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modified:
umi-tools_extract.xml |
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added:
test-data/out_R1.fastq test-data/out_R2.fastq test-data/read_R1.200.gz test-data/read_R1.200_extracted.fastq.gz test-data/read_R2.200.gz test-data/read_R2.200_extracted.fastq.gz |
| b |
| diff -r 4756f7765416 -r 3cfd8e1073d7 test-data/out_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_R1.fastq Mon Jul 16 17:35:16 2018 -0400 |
| b |
| b"@@ -0,0 +1,400 @@\n+@HISEQ:105:C2UE1ACXX:3:1101:11160:2245_AAA 1:N:0:CAGATC\n+AGTAGTTAATATATTAGATTTGTTTGATAGTGGTAGTATATATTTTTTATTTTAGTATTTAGGAGGTAGAGGTAGATGAATTTTTGAGTTTAAAGTTA\n++\n+FFFFBFFFFFIIIIIIBIIIIBIFFBFIIBBFFFFFFFFIIIIIIIIIIIIIIIBFIIIIIB7BBBFBBFFFF77<F7BFFFFFF7B7BBFFFF7<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:19338:2197_TTT 1:N:0:CAGATC\n+TTTTTTAGAGGGATTAGTTTTTTTTATTGAGGTTTTTGAAAGTTGTTGTATGTTAATTGTTTTTAGAATGTTGGGTATAAGTAGGATTTAGGTCTATT\n++\n+FFFFFFB0<BF7BBBF7BFFIIIII7BF'0<0BBFFF'<BB'<B7<B07<B7<BFBBF0<BBBBB0<<B0BB<<000<BF00<<'0<BBB0'00BBF#\n+@HISEQ:105:C2UE1ACXX:3:1101:19467:2281_TTG 1:N:0:CATATC\n+GTTAGGGTGAGATGTATAGTTTGGATTTTAGTGATTTTTGTAAAGGGGGAAAAGAATGGAGTTTTGGGTGTAGTGAGAGGTTATAGGAGTAGGGATTT\n++\n+<FFFBBFFFFFFFFFIFIBFFI<<BFFFIIBBBFFIIIIBFFIIBBF7BBFFFBFFF77BBFBFF777BBBBBB<<<B<7<7BBF77<7<700007BB\n+@HISEQ:105:C2UE1ACXX:3:1101:7009:2740_AAG 1:N:0:CAGATC\n+TTTTGTTTTTTATTTGGAGGTTATGGAATGTTAAGTAAGGTTTTTTTGGGTTTTGTTATTTATTTGATAATTGTGATTGTAATGTTAATAAGGGATAG\n++\n+FFFFFFFFFFIIIIIB<FFFFFFIBBFIIFFFIIFIIIFFIFFIIII<0<BBFFBFFFFFFFFFF<BBFFFF<BBBBF7BFFF<BBFFFFF<00<BB0\n+@HISEQ:105:C2UE1ACXX:3:1101:13708:2613_ATA 1:N:0:CAGATC\n+TAATAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAAGATAATTAATTTTTAAAATTTTTTTTTTTTTAATAAAA\n++\n+FFFFFBFFFFIIIIIIIIIIIFFFFFB7B007BB0''''''0077BFF7'077BF0''0''''''00''00''''00'<BBBFBBFFFFF########\n+@HISEQ:105:C2UE1ACXX:3:1101:19067:2707_GTT 1:N:0:CAGATC\n+TTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTAGAAAATTTTTTTTAGTAAGATAGATTTTAAAGGGTTTGTTTTTTTTTTTTTTTTTTTTT\n++\n+FFFFFFFFFBBFFFFIIIFIFFIFFIIIIIIIFFFFFB7'0<B0<BBFF'7<0'0<<''0<'0'0<BBB<<B'7'0'0'0<BFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4999:3182_GTT 1:N:0:CAGATC\n+TTATGAGGATTTTAGGGGAGTGATTGTTTAAAGTTTATAAGATTTATGATTTATATATAGTTAGAATAGTATGTGTTAAATAAATATAAAGGGAGAGG\n++\n+FFFFBFFFFFFIIFBBBFFFIIFFIBFFIFIIBFFIIIIIFFIIIIIBFFIIIIIIIIIBFFIBFIII<FFFBFBFFFFFFFFFFFFFFF<07<7<<7\n+@HISEQ:105:C2UE1ACXX:3:1101:16790:3145_TAT 1:N:0:CAGATC\n+AGAGGTATTTTGTTATTTTGTTTTAGTTATTGCGGGTTAGAGTAGATGGTTATTTTTAGTAGAGTATTGTTTGTTGTTTTTTATATGTGGTATAGAGG\n++\n+F<BBFFFFFFI<FFFIFIIBBFFIIBFFFFI<BBBFFFF<FFFF7FF70<BFFIFIIF7BFBB<FFBF'BBF'<<0<BFFBBBBBF'<70<<<B####\n+@HISEQ:105:C2UE1ACXX:3:1101:18065:3106_AAG 1:N:0:CAGATC\n+TATTTGTTATATATATTTTAAAGTTTTTTTTTTTTTTAGGAATTTTTTTTTATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTTT\n++\n+FFFFFBFFFFIIIIFIIIIIIIFIFIIIIIIIIIIFF''00<<BB'<<'7''000<BFFF77<77BFF77BFBB07<7<BFFFFFFFF##########\n+@HISEQ:105:C2UE1ACXX:3:1101:2300:3263_TTA 1:N:0:TAGATC\n+TTTTTAATAAAATTTTTATTATTTAATTTATTAGTTAATATTTAGGAGTTTTATGTTGTGGTAAAATTTTGTTAGAGAGATAGAGAAAGTATTTAGTT\n++\n+FFFFFFFFBFFIIIIIIBIBBFFI0<FFFBFF70B00<'0<FFFBBBBFF''0B0BB000'7BBFFFFII'<BF0<'<''07'70BBF'7BBBFB7<B\n+@HISEQ:105:C2UE1ACXX:3:1101:5605:3427_AGA 1:N:0:CAGATC\n+TGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAGATAAGAAGTGGTTCGGTTATAGGATTTGTTTTAGATTTTTAGATTTTTTTGTGTAGA\n++\n+FBFFFFFFFFFFBFFFFIIIIIIIBFFFBFFIBFFIIIIIFFIIIFFIBF7BFBFBBFFIFF<<FFFFBBFFBF0<BFFFFF7<BFFFFFF0B7BF0<\n+@HISEQ:105:C2UE1ACXX:3:1101:8129:3589_TTT 1:N:0:CAGATC\n+TAGTTTTTAGTTAGGATTATACGTTTATTGTGATAAAAGAGTTTTTTGATTTATCGGGTTATGTTAGGGTTTATTGATATTAGGGAATTTGAAGAGAT\n++\n+FFBFFFFFFBFFFBBFIIFIIFBFFFFII<BBFFFIIIBFFIFIIIIBBFFIIII<7<FBFF<FBF<7<BBFFFF7<BFFFF700<BBFF0<B'<07B\n+@HISEQ:105:C2UE1ACXX:3:1101:14304:3866_GTG 1:N:0:CAGATC\n+TTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAATGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAATAA\n++\n+FFFFFFFFFFFFFFFFII<BBFFFBFFIFBFFBFFFII7FFFFFFFIF<BFIIII<F<BBFIFBFB7<BFFFBBBBBF777<B7BBF7B<BB7BBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12720:4398_GTA 1:N:0:CAGATC\n+TGTGTGTGTGTGTGTGTATTTAATTGAAGTTGGGTTTGGTGATATATATGTTTAATTTTAGTATTTTAGTGGTAGAGGTAGGTTAATTTTTGTTGAGT\n++\n+FBFFFFFFFFIFIFIFFFFFIIFII0BFBFFB7BFFF<BFFFFIIIIIIBFIIIIFIIII<FIFIIIFBFBBFB7B<<BB7<B<BFFFFFF0<B0<7B\n+@HISEQ:105:C2UE1ACXX:3:1101:14945:4439_AGT 1:N:0:CAGATC\n+GTTGAGTGGAGTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATT\n++\n+BFFBFFFFFFFFFFIIBIFFIFFBFFIIIIBFFIIIIIIBFFIIIBFFBFFFIIIFBFFBFBFFIIIIIFFFBBF77BBFFF7BBFF<BBF<<BFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:8616:4508_AGA 1:N:0:CAGATC\n+AATTTTGGGGGTGTAGGAGTGGTAGGATA"..b"0BFFIF<IIIIFFB<FF<FFFFIIIFFFF'0<BFFBFFFBF7FBFIIFIF7BFFI7<7B<BBFB'<BF'7BBFF7BBBBBBB#######\n+@HISEQ:105:C2UE1ACXX:3:1101:7272:22581_TTA 1:N:0:CAGATC\n+ATGATATTAAGAATTTTTTAAAGAATTTTATTTTTTTTAGGAATAGAAGGAGGAGGAGTATTTTGATCGATTTTTTAGGTTTTTTATAGGTGGAGTTA\n++\n+FFBFFFFFFF<BFIIIIIIFIIBFFFFIIFIIIIIIIII<<FFFIBFIBBFFBFFFFFFBBFFF<BBF<BBFFFFFF00<BBFFFFFF000<777B<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10060:23020_TTT 1:N:0:CAGATC\n+TAGATTATTTAAGAAGGTATTAGGTTTTTAAGAGGAAAGGGTAGTCTTATAGTTTTGAGTATTTTTTTTAAAAGGAAGTAAGGATGGTGTTTTTATTT\n++\n+FFBFFFFFFFIIBFIFFFFFIBBBFFFFIIIBFFFIFIBFFIFFFFIIFFFBFFII7B<FFFIIIIIFFFFBB77<B<BBF<7BB<<BBBBBFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:14440:23104_TTT 1:N:0:CAGATC\n+AAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAATTTTTGGTGTTTT\n++\n+FFFFFFFFFFFIIBBIFIBBBFFFFFBFFIIIIBFFIIBFBFFFFFFIIIIFFF7BB<<BBFB<BBBBFFB7<00B<BBFF00<BBFFFF''77BBBF\n+@HISEQ:105:C2UE1ACXX:3:1101:6941:23338_AGA 1:N:0:CAGATC\n+AAGGTTTTAAGTTGGTTGGGAATATAGGGGTTTTTTAGAGTTTTTATTAGGAGTTATAGTGTGTTGAATTTGGTTTTGGGTGTTGATTATAGGTTGTT\n++\n+FFFFFFFFFFBFFBBFFBBBFFFFIIBFFFIFFIIIIBFFFFFIIIIIIB<FFFFFFFBFBFFFF<BBFFF<<BBBB700<BBB0BBFFFF00<B7<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10069:23622_TTT 1:N:0:CAGATC\n+TGTTTTAGGGTTTTATTTTTGTGTTTTATTTTTATTTTCGTATTATTAGTTTTTTTTATACGTTATTTGTAGAAGGTTAGTTTTTTTAATTTAGGTTT\n++\n+FBFFFFFBBBFFFIFIIIIIBFBFFIIBFIIIIIIIIIIBFFFIIIIIFFIIIIIIFFFFF<BFFFFF<BF<<B77BBB7BBFFFFFFFFFFF00<BB\n+@HISEQ:105:C2UE1ACXX:3:1101:14079:24078_TTT 1:N:0:CAGATC\n+AAAGTTTTTAGTTTTGAGTGGAATTTTAAGAATATTAGTGCGTTTTAAGCTTAGGTAGTTTTGGTAGTTTGAAAGTAATAGGGTGTATTTTGTAAAGT\n++\n+FFFFFFFFFFBFFFI<BBFFFFFFIIIIIBFFFIIIIBFFFFFFIIIIBFFIIBBFFFFFFI<7BFBFFF<BBF<BBFFF<07BBBBBFFF<BFFF<B\n+@HISEQ:105:C2UE1ACXX:3:1101:12064:24631_TTA 1:N:0:CCGATC\n+TAGTGTATTTATATATATGAAATGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGTTTT\n++\n+FFBFFFFFFFIIIIIIIIBFIFF0BFIIIIIBFFIIIIIIIIIIIIIBFIIFFFIBFFBFFFFFFB<BFF7BBFFFFF<B<BBBFFFFFFF'70<<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:6662:24968_AGG 1:N:0:CAGATC\n+TGTCGTTTAATTGTTTAGGTTTATGGTATTGTGTTTCGTTTTTTTGGTATTTGTGAGGGTAGAATTGTTTTTGGGTTTTAATTTTTTTAAGTATGGGA\n++\n+FFFFFFFFFFIIBFFIFBBFFFFIB<FFFI<FBFFFFBFFIIIII77BFFIIBFBFBBBFBBFFFF<BBFFF'07BBBBFFFFFFFFFFB0<BF####\n+@HISEQ:105:C2UE1ACXX:3:1101:11630:24964_TTA 1:N:0:TAGATC\n+GTTTTTTTAGTGTTTTTTATTTATTTCGTTTTATTATTGGAGTTTGTTAAGAAAATTAGGGTTTGATTTGGATGTTAAGGATTGGTTTTTTTTTTGAT\n++\n+BFFFFFFFFBFFFFIIIIIIIIIIIIIBFFFIFIIIIIB7BFFFFBFFIIBFIIIIIFB<BFBFBFFFF<7BB<BBFF<7<BB77BBFFFFFFFF0<B\n+@HISEQ:105:C2UE1ACXX:3:1101:12594:24878_TTT 1:N:0:CCGATC\n+AATAGGATATGATATTATTTAATTTATAGATTATGGAAATTTTTTATATTTAATGAAGAAAGTTGGAATGTTTTGGGAGGTGTTTAGAATAAATAAAT\n++\n+FFFFB0BFFF<FFIIIFIIFIIIFIFIF<BFFFF<<BFFFIIIIIIIIIIIIIIBFFBFFIBFB7'<FF<<BBF0''77<BFB<BB0<BBBBBFFBBF\n+@HISEQ:105:C2UE1ACXX:3:1101:4483:25030_AGG 1:N:0:CAGATC\n+ATGGTGTTTTTATTTTTAGATTTATATTATTTTGTTATATTTGTATTTGAGTAAGTTTATGGGTTTTTTAAAGAGGTAGGAGGAAGTTTTTTGTTATT\n++\n+FFFFFFFFFFIIIIIIIIBBFIIFIIIIFIIII<BFFIFFIIBFIIII<BBFFIFIFIIIB7<FFFIIIFBF<<77BB00<70<B7BBBFFF0BBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12198:25235_ATA 1:N:0:CAGATC\n+TATGTAGTTTGTATTATTTTTGTTATAGTATATAAAGGTTAAAGAGTAGTTGTTTTAATTTTAGAGGTGGAGATTGGGTTGTATAGTTTTGGTTTTTA\n++\n+FFFBFFFFFFBFFIIFIIIII0BF<FF0BFFFIFFIBBFBFII<FBFBBFF7FFFIIIIIIII<F7<B'<BB7<B''0<<0<BBB77<BB'0<<BBFB\n+@HISEQ:105:C2UE1ACXX:3:1101:20477:25084_AGA 1:N:0:CATATC\n+GTTTATTGAGAAGTAAAGTATTAATTTTATGGGAGAAATGGGATAGAGGTAGTAGAAGTTGTTATGGAATGGGATTAATTAGGAAGTTAATTAAGTGT\n++\n+FFFFFFF0BBFFBFFIIFFIIIIIIIIIFIBB7FFFFIIFFBFFIFIBFFFFIIFIIFFFBFFFF77BFF<<B<FFFFFFF70<B7BBFFFFFF7B<B\n+@HISEQ:105:C2UE1ACXX:3:1101:5725:25359_GAG 1:N:0:CAGATC\n+AAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATATAG\n++\n+FFFFFFBFFFIIIIIIIIIIIBIFBFFFFIIBBFFFFFFFIIIIIIFFFBFFBBFFFIIBFFIIBFIIFIFIFFFFF<BF<BBFF7<<FFFFFFFFF0\n+@HISEQ:105:C2UE1ACXX:3:1101:5502:25591_ATA 1:N:0:CAGATC\n+TGATTTTATTTTTAGGGATAATATTTTTTAAGTGAATTTTGATTTTTTGGTTAGTTATTTTGATGATGTGTAGAGGGTGTATAGTTTTTGGATATAGA\n++\n+FBFFFFFFFFIIIIBBBFFFIIIIIIIIIIIBFFFIIIIIBFFIIIII<7BFFBFFFIIII<FF<FFBFFFFFB<<<BFBBBF<<BFFF00<BFBF7<\n" |
| b |
| diff -r 4756f7765416 -r 3cfd8e1073d7 test-data/out_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_R2.fastq Mon Jul 16 17:35:16 2018 -0400 |
| b |
| b"@@ -0,0 +1,400 @@\n+@HISEQ:105:C2UE1ACXX:3:1101:11160:2245_AAA 2:N:0:CAGATC\n+CATAAAAACCAAAACTAACTAAACCCCAAATAAAAAACAACCTAACCTCTAACAAAAACAACAACAACTAACACCTCAAAATCAACTCTAAATAAAAACTA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:19338:2197_TTT 2:N:0:CAGATC\n+CTAATTTCTATTACCTACCTAACAACTATAACTATAATACTAACAAAAAACAAACAACATAGACCTAAATCCTACTTATACCCAACATTCTAAAAACAATT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII0<BFFIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:19467:2281_TTG 2:N:0:CATATC\n+ACACAACAAAATCCCTACTCCTATAACCTCTCACTACACCCAAAACTCCATTCTTTTCCCCCTTTACAAAAATCACTAAAATCCAAACTATACATCTCACC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIFFIIIIFFFFBBFFFFFFFBBFFFFFBBBFFFBFFFFBF\n+@HISEQ:105:C2UE1ACXX:3:1101:7009:2740_AAG 2:N:0:CAGATC\n+TAAATAAAACCCAAACCCACACTATCTATCCCTTATTAACATTACAATCACAATTATCAAATAAATAACAAAACCCAAAAAAACCTTACTTAACATTCCAT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:13708:2613_ATA 2:N:0:CAGATC\n+TTCAAAAACTCCATAACAAACACAAATAAAAAATAAAAAACTCCTAAATCTCACCTTAAAAACTTATCTAACTGCAACTATTATCTTACTTAAAAAAAAAC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:19067:2707_GTT 2:N:0:CAGATC\n+ATCACTCTTCCAAAAATCACTCGAATCCACAAATACAAAAACTTTCTAACCACACACCTAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCTTTAAAACCT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIFFIIIIIIIIIIIIIIIFIIIIIIIIIFIIIIIIIFIIIIIFFFFFFFFFFFFFFFBB####################\n+@HISEQ:105:C2UE1ACXX:3:1101:4999:3182_GTT 2:N:0:CAGATC\n+CTTATAATTCAAATTTCTAAACTCCTACTCCCTCTCCCTTTATATTTATTTAACACATACTATTCTAACTATATATAAATCATAAATCTTATAAACTTTAA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:16790:3145_TAT 2:N:0:CAGATC\n+AACATACCTATAAAAACGCACTACTTTTATATACAAAATCCGTCTCTACTAATACCATAACCAACCTCTATACCACATATAAAAAACAACAAACAATACTC\n++\n+BBBFFFFFFFFBFIIIIF<FFFFFIIIIIFFFIIIIIFIFFFIIIIIIFIFFFFIIIIIIIIIIIIFBBBBFFFFFFBBFFFFFFFFFFBBFFFFFFFFBB\n+@HISEQ:105:C2UE1ACXX:3:1101:18065:3106_AAG 2:N:0:CAGATC\n+AAAAACTAAACCCAAAAAAAAAACAATAAAAATAAAATAATAAAAATTATCATAATAAATTCCTAAAAAAAAAAAAAACTTTAAAAAAAAAAAAAAAAAAA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIFIIIIIBFIIIFFFFFIIIFFFFFFFBFFFFFFFFFFBFFFFFFFFFFFFFF'0<<<BFB###############\n+@HISEQ:105:C2UE1ACXX:3:1101:2300:3263_TTA 2:N:0:TAGATC\n+AAAAATACAAAAAATAAAAAAAAAAAAAAACATTAAATTTAAAAAAAATTTATTTTTTATTTTATTTTATTTTTATTTTTTTAAATTAAAATAAAAAAAAA\n++\n+BBBFFFFBFFFFFIFFIIIIIIIIIIIFF<'<<<BBBFF0<FFBBBBFB7'0<BB000<'<F<0BBFB'<<BBB0<B<B<B7B<<0'<B'00BBFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:5605:3427_AGA 2:N:0:CAGATC\n+AACCTCTACACAAAAAAATCTAAAAATCTAAAACAAATCCTATAACCGAACCACTTCTTATCTATAAATCTTACTAAAACTCCCCACATCCTATACCTCTC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFIFIIFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:8129:3589_TTT 2:N:0:CAGATC\n+TCTTATCTCTTCAAATTCCCTAATATCAATAAACCCTAACATAACCCGATAAATCAAAAAACTCTTTTATCACAATAAACGTATAATCCTAACTAAAAACT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIFFFFFFFFFFFFFFFFFFFFBBBFFFFFFFFFFFFFFFF<\n+@HISEQ:105:C2UE1ACXX:3:1101:14304:3866_GTG 2:N:0:CAGATC\n+AATTTATTCTTCACTAAAACCCCTTAACCAATACCAACATTTCCACAAAATTCTACCCTCTACAAAAACAACCTATCAAACTCAAAAATCCCCTATATAAA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFBBBFFBFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12720:4398_GTA 2:N:0:CAGATC\n+CTAATTTAACCTTTAAACTCAACAAAAATTAACCTACCTCTACCACTAAAATACTAAAATTAAACATATATATCACCAAACCCAACTTCAATTAAATACAC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFBFFFFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:14945:4439_AGT 2:N:0:CAGATC\n+ACTCTCTCCTATATTCTTTACCAACATATATAACTTAACTCTCTAATAACCTTAACTATTCCTCACCCTAACCTCCACAAATACTATATATAATACTATAC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIBFIIIIIFIIFFFFFFFFFFFFFFFFFFFF"..b'+@HISEQ:105:C2UE1ACXX:3:1101:7272:22581_TTA 2:N:0:CAGATC\n+CTAACTCCACCTATAAAAAACCTAAAAAATCGATCAAAATACTCCTCCTCCTTCTATTCCTAAAAAAAATAAAATTCTTTAAAAAATTCTTAATATCATTA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIFFIIFIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:10060:23020_TTT 2:N:0:CAGATC\n+CAAAATAATATAAATCTAAAAATAAAAACACCATCCTTACTTCCTTTTAAAAAAAATACTCAAAACTATAAGACTACCCTTTCCTCTTAAAAACCTAATAC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFBFFBFF\n+@HISEQ:105:C2UE1ACXX:3:1101:14440:23104_TTT 2:N:0:CAGATC\n+ATATTCTATAAAACACCAAAAATTCCTAAAAACCTCTAAAAACCAACTCCTACAAAAAAAACAACCCACAAAACAAAAATCAACTCCCCAAACCTTAACTT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:6941:23338_AGA 2:N:0:CAGATC\n+CTTATTCATTCCATCGCCTATAACATAAAAACAAAAATAAACATTATCATAACAACCTATAATCAACACCCAAAACCAAATTCAACACACTATAACTCCTA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:10069:23622_TTT 2:N:0:CAGATC\n+CTTAAAATTCACTTCACATTAACTTTTAAATATTATTCCAATATATTTAAAATAACACTTTAAAAAAAACCTAAATTAAAAAAACTAACCTTCTACAAATA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:14079:24078_TTT 2:N:0:CAGATC\n+ATAAAACTAAACTTTCATATATTACTCTTAAATTTTTTTCCTAACTATAAAAAACTTTACAAAATACACCCTATTACTTTCAAACTACCAAAACTACCTAA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12064:24631_TTA 2:N:0:CCGATC\n+AAAAAAACCACCATTCTACAATCCCTTAAAAAAACCCCCAATAAAAAATAAACCCAAACCTAAACAAACAAAAAAACTCAAAAAATTAACTCTAAATATCA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFBBBFFBFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:6662:24968_AGG 2:N:0:CAGATC\n+CTCCCATACTTAAAAAAATTAAAACCCAAAAACAATTCTACCCTCACAAATACCAAAAAAACGAAACACAATACCATAAACCTAAACAATTAAACGACACC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFBFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:11630:24964_TTA 2:N:0:TAGATC\n+AAAAAAACATACCAACAACCTTTCAAATACAAAACTCCGTAAAATCTATACTATCTAACAATACCCTAAATCAAAAAAAAAACCAATCCTTAACATCCAAA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFBFBFBBFBFFFFFBFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12594:24878_TTT 2:N:0:CCGATC\n+ATATAATATTACCTATTTATTTTTATTATTATTATTATTATTATTTATTTATTTATTCTAAACACCTCCCAAAACATTCCAACTTTCTTCATTAAATATAA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIFFFFFFIIIFFIFIIIFIIIIIIIIIIIFFFFIIIFFFFIIIIIIIIIIFFIIIIFIIFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4483:25030_AGG 2:N:0:CAGATC\n+CCTAATACTCTATACTAAACAAATAACAAAAAACTTCCTCCTACCTCTTTAAAAAACCCATAAACTTACTCAAATACAAATATAACAAAATAATATAAATC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIFIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:12198:25235_ATA 2:N:0:CAGATC\n+CACAAAAACAACATACCTCTTAATAATCTTTCAAACTTACACCAAATCTATTTCTATCCTCATCTTCCATTTATAAAAACCAAAACTATACAACCCAATCT\n++\n+BBBFFFFFFFFFFFIFFFFFFBFBFFBBFF<FIBFFIF<BFIIIIIIIIFFFFFBFBFBBFF<B<BFFFBBFIIIIFIIFFFFFFFFFBFBFFBBBBBBB<\n+@HISEQ:105:C2UE1ACXX:3:1101:20477:25084_AGA 2:N:0:CATATC\n+AAAACCCAACTCTTCCACCAAAAAAATTACTTTATCTCTAATACTCTTAAAATACCCTATATTATCCTTATACAAAAACACTTAATTAACTTCCTAATTAA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIFIIFIIIIIIIIFIIIIIIIIIIIIIF0<BFFFFFFFFFFFFBBBFFFFFFFFFBBB<<BB70\n+@HISEQ:105:C2UE1ACXX:3:1101:5725:25359_GAG 2:N:0:CAGATC\n+ATAACTTAACTCTCTAATAACCTTAACTATTCCTCTCCCTAACCTCCACAAATACTATATATAATACTATACTTCTTAATAAACTTACTTAACATAAACCA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:5502:25591_ATA 2:N:0:CAGATC\n+TTCTTAATTCCATCTTTAAACAATAATATTAAAATATTACTTCCCAAAATACAAACCCATATCCATATCCAAAAACTAAACAACCTCTACACCTCAACAAA\n++\n+<<<BBBBBBBBBBBBBBBBB70B00B000<0BBB###################################################################\n' |
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| diff -r 4756f7765416 -r 3cfd8e1073d7 umi-tools_extract.xml --- a/umi-tools_extract.xml Sat Jul 14 06:14:14 2018 -0400 +++ b/umi-tools_extract.xml Mon Jul 16 17:35:16 2018 -0400 |
| [ |
| @@ -1,7 +1,23 @@ -<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1"> +<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.2"> <description>Extract UMI from fastq files</description> <macros> <import>macros.xml</import> + <macro name="out_conditional"> + <actions> + <conditional name="input_type.type"> + <when value="paired_collection" > + <action type="format"> + <option type="from_param" name="input_type.input_readpair" param_attribute="forward.ext" /> + </action> + </when> + <when value="paired" > + <action type="format"> + <option type="from_param" name="input_type.input_read1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions> + </macro> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -137,15 +153,18 @@ </conditional> </inputs> <outputs> - <data name="out" format_source="input_single"> + <data name="out" format_source="input_single" label="Reads: ${tool.name} on ${on_string}" > <filter>input_type['type'] == "single"</filter> </data> - <data name="out1" format_source="input_read1"> - <filter>input_type['type'] !== "single"</filter> + <data name="out1" format_source="input_read1" label="Reads1: ${tool.name} on ${on_string}" > + <filter>input_type['type'] != "single"</filter> + <expand macro="out_conditional" /> </data> - <data name="out2" format_source="input_read2"> - <filter>input_type['type'] !== "single"</filter> + <data name="out2" format_source="input_read2" label="Reads2: ${tool.name} on ${on_string}" > + <filter>input_type['type'] != "single"</filter> + <expand macro="out_conditional" /> </data> + <data name="out_log" format="txt"> <filter>print_log == True</filter> </data> @@ -159,30 +178,47 @@ <param name="quality_selector" value="true" /> <param name="quality_filter_threshold" value="10" /> <param name="quality_encoding" value="phred33" /> - <output name="out" file="out_SE.fastq" /> - <output name="out_log" file="out_single.log" lines_diff="22"/> + <output name="out" file="out_SE.fastq" ftype="fastq" /> + <output name="out_log" > + <assert_contents> + <has_text text="Input Reads: 100" /> + <has_text text="umi quality: 28" /> + <has_text text="Reads output: 72" /> + </assert_contents> + </output> </test> <test> <param name="type" value="paired" /> <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" /> <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" /> <param name="bc_pattern" value="NNNXXX" /> - <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out_log" file="out_paired.log" lines_diff="16"/> + <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> + <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> + <output name="out_log" > + <assert_contents> + <has_text text="Input Reads: 100" /> + <has_text text="Reads output: 100" /> + </assert_contents> + </output> </test> <test> <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed --> + <param name="paired_type" value="no" /> <param name="input_readpair" > - <collection type="paired"> + <collection type="paired" > <element name="forward" ftype="fastq" value="t_R1.fastq" /> <element name="reverse" ftype="fastq" value="t_R2.fastq" /> </collection> </param> <param name="bc_pattern" value="NNNXXX" /> - <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out_log" file="out_paired.log" lines_diff="25" /> + <output name="out1" file="out_R1.fastq" ftype="fastq" /> + <output name="out2" file="out_R2.fastq" ftype="fastq" /> + <output name="out_log" > + <assert_contents> + <has_text text="Input Reads: 100" /> + <has_text text="Reads output: 100" /> + </assert_contents> + </output> </test> <test> <param name="type" value="paired" /> @@ -192,7 +228,7 @@ <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" /> <param name="use_barcodes" value="yes" /> <param name="filter_barcode_file" value="scrb_seq_barcodes" /> - <output name="out2" file="scrb_extract.fastq.gz" decompress="true" /> + <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> </test> <test><!-- same as above but with regex barcode--> <param name="type" value="paired" /> @@ -202,7 +238,16 @@ <param name="bc_pattern" value="^(?P<cell_1>.{6})(?P<umi_1>.{10})" /> <param name="use_barcodes" value="yes" /> <param name="filter_barcode_file" value="scrb_seq_barcodes" /> - <output name="out2" file="scrb_extract.fastq.gz" decompress="true" /> + <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> + </test> + <test><!-- CelSeq2 example --> + <param name="type" value="paired" /> + <param name="input_read1" value="read_R1.200.gz" ftype="fastq.gz" /> + <param name="input_read2" value="read_R2.200.gz" ftype="fastq.gz" /> + <param name="extract_method" value="string" /> + <param name="bc_pattern" value="NNNNNNCCCCCC" /> + <output name="out1" file="read_R1.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> + <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> </test> </tests> <help><![CDATA[ |