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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d |
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added:
test-data/SP1_f.fastq test-data/SP1_f.fastq.gz test-data/SP1_f.trimmed.fastq.gz test-data/SP1_r.fastq test-data/SP1_r.fastq.gz test-data/SP1_r.trimmed.fastq.gz trim_adapters.xml |
| b |
| diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SP1_f.fastq Wed Jun 20 15:48:09 2018 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+@cluster_2:UMI_ATTCCG\n+TTTCCGGGGCACATAATCTTCAGCCGGGCGC\n++\n+9C;=;=<9@4868>9:67AA<9>65<=>591\n+@cluster_12:UMI_GGTCAA\n+GCAGTTTAAGATCATTTTATTGAAGAGCAAG\n++\n+?7?AEEC@>=1?A?EEEB9ECB?==:B.A?A\n+@cluster_29:UMI_GCAGGA\n+CCCCCTTAAATAGCTGTTTATTTGGCCCCAG\n++\n+8;;;>DC@DAC=B?C@9?B?CDCB@><<??A\n+@cluster_36:UMI_AACAGA\n+TCCCCCCCCCAAATCGGAAAAACACACCCCC\n++\n+5?:5;<02:@977=:<0=9>@5>7>;>*3,-\n+@cluster_39:UMI_GAACCG\n+CCTTCCATCACCAGATCGGAAAAACACACGC\n++\n+00>7;8@5<192?/8;0;;>=3=/3239713\n+@cluster_53:UMI_GTGGGG\n+GGAAAATGAAAATGTTGGATGAGAACAATTA\n++\n+<>=CCA@A8>?=86AB@>0?76<993=@=7.\n+@cluster_58:UMI_GTTTTG\n+AAAGCAATCCACAGAAGGGCATTTCTACCGA\n++\n+@D?B:AA??=;>?=@?A=@:@EEB?A=@<@<\n+@cluster_63:UMI_TTTCCC\n+GCAACCATACTCCCCCCGGAACCCAAAGACT\n++\n+@:A@@A@C<?D?;;98<=>=@;<AAD?==?D\n+@cluster_70:UMI_CCGGGA\n+CTTTTTCTTCTAAAATTTTTTCTTCTCTGGC\n++\n+?DEEEB?DB?A@DD?EEEEEB?DB?D9CB/.\n+@cluster_82:UMI_TTTTTG\n+GCTTATGTTTTATAAAAATAAGTTGCCCCAG\n++\n+75;6>>>>DEC7?6CC>A=9=>@C1<<9>12\n+@cluster_87:UMI_TGACAC\n+GGTTGAGCACAGGGTACTTTATTGATGGTAC\n++\n+=@E@B=B::;;A=?A=9DEB9ECB8?B@@97\n+@cluster_90:UMI_ACGGGG\n+TTTTTTTGTGAAGGAGTCTTTCCCCCCAGAC\n++\n+CEEEEDB96203:8+01.3353/897?.+,0\n+@cluster_96:UMI_ACTAGG\n+GGAATGCAACAACTTTATTGAAAGGAAAGTG\n++\n+=>@AB::A??A@?DEC?ECB@D?A>=C?A;9\n+@cluster_99:UMI_CAACAA\n+TTTGTTTTTTTTTTTTCCACCCCCACATGGA\n++\n+<DB1BD:5?9BB:=63<5+56721--/11;3\n+@cluster_107:UMI_TCCATG\n+ATCGGAAGAGCACACGTCTGAACTCCAGTCA\n++\n+<?;=>?<=9;59:6<@?>C<99=D79<?354\n+@cluster_114:UMI_TTTATG\n+TCTTTTTTTCTTTTCTTTTTTTTTTTTTTTA\n++\n+B?DEEEEEB?DEEB?DEEEEEEEEEEEEE<.\n+@cluster_124:UMI_CGGCGC\n+GAGACGGAGTTTCACTCTTATTGCCCCCCAG\n++\n+2///1:>7A7;B3.8C?@>.4C5><;;9A23\n+@cluster_130:UMI_GTAGGG\n+GGTAGAGATAGGGTCTTGCTATGTAGCCCAG\n++\n+4@:<=8=;B69;@9<9=:?87@:B:8.293;\n+@cluster_134:UMI_TAGTGA\n+TGTTAGACAAAATAAATGTATTTTTTCACTC\n++\n+1/32++,2668/1/5/<14/69A=@62*-40\n+@cluster_140:UMI_TTACTC\n+GGACCCCCCCCAAAGTCGGAAAACACACCCC\n++\n+9//865/-71336003/2-566620433.2+\n+@cluster_148:UMI_GCCTGG\n+CATACCCCCCCCAGATCGGAAAAACACACGC\n++\n+9@C=@47;;9<A?,<?==>?C;D3><:=?32\n+@cluster_152:UMI_TCGAAA\n+GCTGTCTAGTCATCCTCGTCGGTCTTCTGCT\n++\n+B?C@B?A=ABA@??>D=@B==@B?DB?C:?D\n+@cluster_159:UMI_CGGGGG\n+GTCTGCACAGATAAATCTTTCTTCTCATTAC\n++\n+4:7<+*-/0.,3@B300=;41=3=20=9;-2\n+@cluster_164:UMI_GCTGAG\n+TATTTTTTTTTTTTTTTTTTTTTTTTGTGTG\n++\n+??E7EEECEEDEEEECEEEEEEEED20101*\n+@cluster_169:UMI_TGAGCC\n+AAAAATGCCTGGAAATCACTTGCTAGTTACA\n++\n+ADCB<B:>>CB>@DA?A9?DB:?A=AEC=>3\n+@cluster_176:UMI_TGGGCG\n+GGGTTCAAACCCCCAGATCGGAAAAGACACA\n++\n+<=@BB;AD?96:;@?=:?<=>:>9</,-+-+\n+@cluster_182:UMI_TATCAG\n+AATGTTCTTTCCTCTGTTGGCTTTGGCCATT\n++\n+@@41EB05E1>.6140DC5@68EC70=65E3\n+@cluster_189:UMI_GCCTTG\n+TTGGTATATAAACTATTTATTAACAGACAAG\n++\n+ECB@C?C?C@D??@?EEC9EC@@>?==>A=B\n+@cluster_197:UMI_AGGATG\n+GGCATATGAAAATTTATTACTACAGTGTTTT\n++\n+=@:@C?BB@DDAEEC?@C=?A=??AA@DEE=\n+@cluster_211:UMI_ACTGGC\n+CCCCCCCCAAATCGGAAAAACACACCCCTAA\n++\n+<<<<<<<AADA?==>@DDC??=?=@<;>@@?\n+@cluster_216:UMI_TATTCC\n+GCTTTGCAACCATACTCCCCCCAAGATCGGA\n++\n+<>D87:-A9@::>;;9?;;<<@14;2;/=.9\n+@cluster_218:UMI_TGCTCC\n+CCCCCCCAAAATCGGAAAAACACACCCCTAA\n++\n+;;;<<;1/7>=?2=;@D<C=<797@7235@<\n+@cluster_222:UMI_TTTGTG\n+TGAGACAGGGTTCGCCAGCGTGGACCCTTTA\n++\n+4:/4+5275/34,4-060./54.+0*0472,\n+@cluster_228:UMI_GCCTTC\n+CAGGTGTTTTTTCTCCCAGATCGGAAGAGCA\n++\n+@?A@A@EEEEEB?D?<A?=<?==>@?==B58\n+@cluster_232:UMI_TGTTCC\n+TCCCCCCCCCAAATCGGAAAAACACACCCCC\n++\n+D?<<<<<<<AADA?==>@DDD@?=?=@:<5+\n+@cluster_241:UMI_CTCTCA\n+CAACTTTCCCTTACCCCAGATCGGAAGAGCA\n++\n+?A@?DEB?<>DC=@<<A?=<?==>@?==B:<\n+@cluster_252:UMI_CAAAAG\n+TACCTTTGAGACAGAGTCTCGCTCTGTCACC\n++\n+B=@>DECB==:=;==AB?D=B?D?C@BA=@;\n+@cluster_254:UMI_TGTGCC\n+TAATGTGCTACTTTTAATTTATTAAAATCCC\n++\n+A@AB@A:?A=?DEEC@AEEC?E;@DDA??<<\n+@cluster_258:UMI_TGCGGC\n+GTTTGTTTTTTTTTTTTTCCCAGATCGGAAG\n++\n+>BEC;EEEEEEEEDEEC48-543197=>?.2\n+@cluster_272:UMI_ACTCGA\n+AACTTGACACCTTTAAAATAGCATTAAACAG\n++\n+D72D>?<==1=4EC3DD24/4.@8C1D0/48\n+@cluster_281:UMI_CCGATA\n+TAGTCTTAGCATTTACTTTCCCCCCAGATCG\n++\n+B=A>?DC=B:@EE@=>DEB?<;<<@?=<=8B\n+@cluster_287:UMI_GGATGC\n+GGACATAATAATAACAATTGAATGTCTGCAC\n++\n+=>=?@C@AC@AC@@?AAECB@AB@B?C::<?\n+@cluster_290:UMI_TTCCCC\n+ACTTTTGAGACAGGGTCTTGCT'..b'TTTATTAGCCACAG\n++\n+7;651C=9<8:D78?D>DE4855<396;1;1\n+@cluster_545:UMI_ACGATC\n+CTTGCTTCAGTTTTATTTGTACAAATATCAC\n++\n+79A6?66@;A;EE52EE41?=:A56B<.547\n+@cluster_563:UMI_GCCTCG\n+CCCCCCCCCCAAATCGGAAAAACACACCCCC\n++\n+0;;71;;;<@3:??=8>:@;?=>8>9453;/\n+@cluster_566:UMI_CGCATA\n+GACGGATGAGTCTTTTAATAGAAAAACACAC\n++\n+==?=><BB=AB?DEEC<AC==@DBC@>=?;7\n+@cluster_572:UMI_AAGACC\n+GCAACCATACTCCCCCAGATCGGAAAAGCAC\n++\n+B:A@@A@C=?D?<<<A?=<?==>@D6?B:=@\n+@cluster_586:UMI_AATTCA\n+CTGCTCAGCTCTTTATTGATTGGTGTGCCCA\n++\n+??:?>A?@2><<59=E?@<B?5?9@7:8:?6\n+@cluster_588:UMI_ACATGG\n+AGTTAGAGTCTCAGTCACCCAGGCTGGAATA\n++\n+=AE?===A@=D@4AA@=?855A@>;B<@;=5\n+@cluster_592:UMI_GCCGTC\n+TGTGTCTCTCTGTCCCCAGATCGGAAGAGCA\n++\n+C?@7B?@?C1@;<;598?883846@?0792@\n+@cluster_602:UMI_CTCTCA\n+GGTTTCCGCCCCCCAGATCGGAAGAGCACAC\n++\n+A@DEB<;:>695:@?=<?=//:6+790<<=:\n+@cluster_607:UMI_TCCGAC\n+GATTAATGAAAACATTCTTGGCAAATGCTTT\n++\n+@<EC@ABB?CB?>@DB?DCB;:ADAB::>?6\n+@cluster_615:UMI_TGGGAC\n+TCTAAACCTGGAAATTTATCTGGAGTCTTCC\n++\n+611@D@0>651@DA6E2.?377>-0?:>B/;\n+@cluster_621:UMI_TTCGTC\n+GTTTTTTACCCCCTCCCCAGATCGGAAGAGC\n++\n+@EEEEEC=@:<<>C><<A7<:?=7>@?7=@8\n+@cluster_626:UMI_CGCGCA\n+CTTTTTTTTTTTAAAAACCCCCAGATCGGAA\n++\n+?DEEEEEEEEEC@DDD?@<<<A==<?4=>@<\n+@cluster_634:UMI_AGATCA\n+GTTTTTTTTTTTTCTCTCCTAACACCCCAGA\n++\n+?EEEEEEEEEEEB?D?D?>@@@?=@<<A;69\n+@cluster_648:UMI_CCTATG\n+TTTTTTCCCCCCAAGATCGGAAAAACACACC\n++\n+EEEEEB?<<<<A1?=<?9=:@DDD32121@9\n+@cluster_663:UMI_CAAAGG\n+TAAGACCCTCATCAATAGATGGAGATATACA\n++\n+B@?==@<>DA@?AA@C==<BB>==<C?C=?5\n+@cluster_672:UMI_GGACGA\n+ATTTTGTCTTTTGTTTTCATTTTTTCTTGCT\n++\n+AEEDB@A?DEEC@BEEBA;EEEEEB?DC:?D\n+@cluster_675:UMI_GTATTG\n+CAGTTGTCAAATGATCCTTTATTGAAATGTT\n++\n+:?AEC@BAADABB<??>DEC?ECB@DAB@DB\n+@cluster_677:UMI_CCTGGA\n+GCACCCCCTCCCAGATCGGAAAAACACACCC\n++\n+B:=@<<<>D?<A?,<?==>@DDD>?=?=@:>\n+@cluster_681:UMI_GGACCC\n+AGCTTTGCAACCATACTCCCCCCCCAGATCG\n++\n+?B?DEC::A@@A@C=?D?<<<<<<A?=<?=B\n+@cluster_684:UMI_GTTCAC\n+TGCAACCATACTCCCCCCCCCAGATCGGAAT\n++\n+C::A@=A@C=?D?<3<<<<<A?=;?4.>@A/\n+@cluster_689:UMI_CCTTCA\n+AAAGAAGTAAGCCTTTATTTCCTTGTTTTGC\n++\n+DD?=@?AC@?B>>DEC?EEB?>DC@EEEC:;\n+@cluster_692:UMI_GCGTCC\n+GAGGTGAAGTTTCACTTTGTCCCCAGATCGA\n++\n+@=@@:?<3@D=A@27DDC7>?<;A?14;2<,\n+@cluster_699:UMI_TGTTTC\n+CTTTCTTTCTTTCTTTTGTTTCTTTCTTGCT\n++\n+>DEB?DEB?DEB?DEEC@EEB?DEB?DC:?D\n+@cluster_706:UMI_CCACGG\n+GCCCTTCTGCTCCCCCAGATCGGAAGAGCAC\n++\n+@><>DB?C:?D?<<<A?=<?==>@?1=B:=@\n+@cluster_714:UMI_ACGCGA\n+TTTTTCCCCCCCCCAGATCGAAAAAGCACAC\n++\n+EEEEA?<<<<<<;8?=<?=@8DD4?:8<><@\n+@cluster_716:UMI_GGGGTC\n+CCCCCCCCAAAATCGAAAAAACACACCCCTA\n++\n+<<<<<<;<1C?0.4@/DDA:;>3>8=;626<\n+@cluster_719:UMI_GAGAAA\n+GGGAGTAGTGTCTTTATTCATTAAAGCCTGA\n++\n+A=>=AC=AA@B?DEC?EBA@EC@D?B>>CB=\n+@cluster_722:UMI_TCCATA\n+GTTTTTTTTTTTTTTTTCAGTAAGCACAGGT\n++\n+AEEEEEEEEEEEEEEEBA?@:@?B:=??A@4\n+@cluster_730:UMI_ACCTTG\n+TCCCCCCCCCCAAATCGGAAAAACACACCCC\n++\n+B?<<<<<;<76AB@?=<5@DCD??=>2@;;6\n+@cluster_732:UMI_AGGAAG\n+CCCCCCCCCAAATCGGAAAAACACACCCCTA\n++\n+6<<<<<<<AADA?==>@DAD?><?=@:;>@0\n+@cluster_756:UMI_TCGATA\n+CTTTGTTTCAAGTTTTAATCAAAGCTTGTAT\n++\n+?DEC@EEBAA?AEEEC@A?AAD?B?DC@C??\n+@cluster_764:UMI_ACGACC\n+CACGCTTAATTCACTTTATTTTTCCCCAGAT\n++\n+>=?B?DC@AEBA=?DEC?EEEEB?<<A<=<9\n+@cluster_772:UMI_AGGAAA\n+AAGACCACAAAGATTTAATTTAAAATCACAG\n++\n+D?==@A=?AD?=<EEC@AEEC@DDA?A=??B\n+@cluster_778:UMI_TTGGGC\n+ATTTAACATGAGGAAACCCCAGATCGGAAGA\n++\n+@EEA@?>@BB;A>@D<@;:64=8?==>@?<6\n+@cluster_787:UMI_GCAGTC\n+TGATAGCATTGCGAGACGCTGGAGCCGGAGC\n++\n+CB<C=B:;EC:?@===?B?CB><@>==>6A9\n+@cluster_794:UMI_GCATCC\n+CCCCCCCAGATCGGAAAAGCACACGCCTGAA\n++\n+;;9<<<A?=8>===@D;?B:=<=?B:>C><8\n+@cluster_799:UMI_CGTGCA\n+GCTCGTCTTTCTCCCCCAGATCGGAACAGTA\n++\n+=.B10486=:2989;58/-4=255::.=684\n+@cluster_807:UMI_GATATG\n+TTTTTCCACACGTAAAATTTATAAACATTTA\n++\n+83EEA3:620725;DD5CAB:53C3=/472-\n+@cluster_810:UMI_TCTCGC\n+GAAGAGCACACGTCTGAACTCCAGTCACCGT\n++\n+9?<9;@23538<88>@348<396;;365/=4\n+@cluster_816:UMI_ATGTAG\n+TGAGACAACATCTCACTCTGTTACCCCCCAA\n++\n+AA===>A?:@>?C@=?C?C@BC3/;<;<A1.\n+@cluster_823:UMI_TTTTTA\n+CCATTATAATAGCCATCTTTATTTGTAAAAA\n++\n+?A@EC?C@AC=B>A@??DEC?EEC@C@DDD:\n+@cluster_828:UMI_CTCGTA\n+GCCCCCCCCCAAATCGGAAAAACACACCCCC\n++\n+B><<<<<<<AADA?==>@DDD?>=>=@;<<3\n' |
| b |
| diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_f.fastq.gz |
| b |
| Binary file test-data/SP1_f.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_f.trimmed.fastq.gz |
| b |
| Binary file test-data/SP1_f.trimmed.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SP1_r.fastq Wed Jun 20 15:48:09 2018 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+@cluster_8:UMI_CTTTGA\n+TATCCTTGCAATACTCTCCGAACGGGAGAGC\n++\n+1/04.72,(003,-2-22+00-12./.-.4-\n+@cluster_21:UMI_AGAACA\n+GGCATTGCAAAATTTATTACACCCCCAGATC\n++\n+>=2.660/?:36AD;0<14703640334-//\n+@cluster_34:UMI_AGCTCA\n+TCTTGCAAAAACTCCTAGATCGGAAGAGCAC\n++\n+-/CA:+<599803./2065?6=<>90;?150\n+@cluster_37:UMI_GAGGAG\n+GTCTTTGTACAAAATTTTATTAAAGGTCTTT\n++\n+?B?DEC@A=?ADDAEEEC?EC@D6A@@>DE4\n+@cluster_43:UMI_GGATTG\n+GAGTTATAATCCAATCTTTATTTAAAAATCT\n++\n+>=AEC?C@;??0A>?0DEB9EEB@DDC1?=6\n+@cluster_55:UMI_CTAATG\n+AGACAAAAGGATTTATTTGGAAATTTCCAAA\n++\n+===>7DD?A>;EEC?EECB>?DAEEB?AAC3\n+@cluster_62:UMI_CCTTGC\n+GAGTTGCGACAATACTCTCCCCCGAGACCCA\n++\n+9/96C1954/12?=7=?5::94,40125442\n+@cluster_66:UMI_TTGGGG\n+CCAACTAACTTTTATTTTAAGTTCAGGGGGT\n++\n+<AA@?A@@?DEEC?EEEC@?AEBA?A===@9\n+@cluster_71:UMI_CCAATA\n+CAGCTTTGCAACCATACTCCCCCCGGAACCC\n++\n+<?B?DEB::9>@?@C=?:=<<<:===@?=83\n+@cluster_83:UMI_CCAGTC\n+CTCCCACAGTTCTGCGCCAGAGCGGAAGAGC\n++\n+=:?*>4>;>66;C:612661<2322141=:-\n+@cluster_88:UMI_TGCCGA\n+TCACTACCTCCCCGGGTCGGGAGTGGGGTAT\n++\n+/@=>@=@<D;;;<==@B9==>,75<:593=7\n+@cluster_93:UMI_ATTGTA\n+TCCTCACTATCTGATTCCTCCCCAGATCGGA\n++\n+;9=BA=?@<??CB;EB?=C?;8@:=:=88:7\n+@cluster_98:UMI_CTTTGG\n+AGTTCCCCCCCCTATATCGAAAAACACACCC\n++\n++670.98;.+460.1533=09;3481/14*3\n+@cluster_105:UMI_TCGCGC\n+GATTGAGACAGAGTCTGCTGTGTTGCCCCCC\n++\n+?<E=====>?==A@?C:?C@A=EC7>;;<<7\n+@cluster_113:UMI_ACAATA\n+GCTTCAGCTGCCCAGATCGGAAGAACACACG\n++\n+B?DBA?B?C:><A?=<?==>@?3@/><?=?5\n+@cluster_117:UMI_TCAGTA\n+GCACTACTATATTAGATTGTGTTATCCGTTA\n++\n+1)+-0.-0-4/82-+*45//.31--0/074.\n+@cluster_126:UMI_CATGAA\n+CCCCCCCAGATCGGAAAAGCACACGCCTGAA\n++\n+?.:8<;??=6?==>?:6><0;165B35;66:\n+@cluster_131:UMI_AGTGTA\n+GTGAGCACAGGGTACTTTATTGATGGTACAT\n++\n+;AB=B::>4:<@57=654187B;B:=4;9?9\n+@cluster_137:UMI_ACGGAC\n+GCAAATATAAACAGGTTTATCTATTCTGTCT\n++\n+9)75?C?:@6=36:6D<B78.0.5B1<=7.5\n+@cluster_144:UMI_CAGGGC\n+CCACCCCCCCCAAATCGGAAAAACACACCCC\n++\n+.A=@<<<<<;AACA=49>@DDD?53==@;85\n+@cluster_149:UMI_CGGCGC\n+GCCACTATATCTCAAGCATTAAAATACATGT\n++\n+3=7,.0>6287<2@47/4=5/;<62,38:18\n+@cluster_153:UMI_TACAAA\n+TTTTTTTTACACTTTATAACACACTTTTTAT\n++\n+EEEEEEE3995.6E848@?>=;=3:EEE3/9\n+@cluster_162:UMI_AACGGG\n+CCACAACATTCCATTTATACACAGAACTAAA\n++\n+>A=?A@?@EB?A@EEC?C=?=??=@@?A@D4\n+@cluster_165:UMI_AGTCGC\n+TTGGCTCTTTTTCGTTTATTGCATGCCCCCC\n++\n+CC:?<D;D?;<2-<@A<>B>2::B082,9*/\n+@cluster_172:UMI_GTTTCC\n+GGCTTTGCAACCATACTCCCCCCGGAACCCA\n++\n+=@?DEC::A@@A@C=?D?<<<<==>@@@<A=\n+@cluster_181:UMI_CTTGCC\n+TAAACAGAGTCTTACTCTATTGTCCAGGCTG\n++\n+/855.7768<0;5.084</9=191/.47/3.\n+@cluster_186:UMI_GGGTAG\n+CCTTTCCTTTCCCCCAGATCGGAAGAGCACA\n++\n+>>DEB?>DEB?8<<A?=<?==>@?:=B:===\n+@cluster_190:UMI_GGCGGA\n+CAAATCAATAGGTCTTTTATTGCATCATTTA\n++\n+?AA??AAAC=?@B?DEDB>EC::@?A@EEC=\n+@cluster_207:UMI_TGAACA\n+GTTTCCCCCCCCAAATCGGAAAAACACACCC\n++\n+;=B:9/193993=>?:88=694;555767+,\n+@cluster_215:UMI_TCAAAC\n+TCCCCCCCAAATCGGAAAAACACACCCCTAA\n++\n+3?<<<<<AADA?==>@DDD@?=?=@<<>A<=\n+@cluster_217:UMI_CTCGGC\n+CTAAACTTTTATTGAAAAAAAAACCGAGGAG\n++\n+>A@D@?DEEC?ECB@DDDDDDD?@=@=A>=B\n+@cluster_219:UMI_ACGTGG\n+TGTAATTAGTAGACATGGTCTTCTACCCATA\n++\n+A@C@AEC=AC===?@BB@B?DB?A=@<A@C=\n+@cluster_223:UMI_ATTTCC\n+CCTTCTGTTTCTTTTTCCCTTCTTTCCTTCC\n++\n+;>DB?C@EEB?DEEEB?<<DB?DEB?=D@=:\n+@cluster_229:UMI_CAAGTA\n+GAGGTTTGCAGCTATTTTATTTACAAGTATA\n++\n+==A@EEC::?B?A?EEEC?EEC=?A?AB?C=\n+@cluster_238:UMI_AGGTTG\n+GCTTCCTACTTTTCAGGTTTAAATTTATCTT\n++\n+@?DB?>@=?DEEB@?A@CEC@DAEEC???DB\n+@cluster_248:UMI_TTTTTG\n+TAGGAAAAAATGGTTTTGGACATGGGATGAA\n++\n+8=A>2DDDBABA@9@<BA.5>:BB=>7BA7;\n+@cluster_253:UMI_GCGCTC\n+TCGTCACTACCTCCCCGGGTCGGGAGTGGGG\n++\n+D=@BA=?A<@>D?<<===@B===>=?>B1:2\n+@cluster_256:UMI_AGACAG\n+CCGTGATCCTTTTTCAGTGCTTCTACAATGC\n++\n+>=@AB<??>DEEEBA?AA:?DB?A=?AAB:>\n+@cluster_265:UMI_AATTTG\n+TACCCCACCCAAATCGGAATAACACACCCAC\n++\n+@5?0<;7;845773245>:1<38,1-6*8,/\n+@cluster_273:UMI_TCGAAA\n+GGTTTTCCTTTTTATTTAATCAAAGACTGGT\n++\n+A@EEEB?>DEEEC?EEC@A?AAD?=+?CB@8\n+@cluster_286:UMI_CGGTGC\n+AACAATGATCAATTTTAAGAAATGGGTACAT\n++\n+A@>AABB<?A@AEEEB@9=@DABB=@C=>@/\n+@cluster_289:UMI_CTTCTA\n+CCCCCTCCCAAATCGGAAAAACACACCCCTA\n++\n+@<3<>:?:AAB@?==>@DDC??66:?8;>@2\n+@cluster_293:UMI_CGCACC\n+ATCACTTCTATCAAAGATTGC'..b'TTTTTTTTTTTTTT\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEB\n+@cluster_559:UMI_TCAACG\n+CCGGCACTAAGTCAAGTTCTTTACTTCCCCA\n++\n+>==@:=?A@?ABAA?AEB?DEC=?DB?<<A=\n+@cluster_564:UMI_TTCGCA\n+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEB\n+@cluster_569:UMI_GGCTCC\n+GCAGAACACTTCTTTATTATAGCAACATATA\n++\n+B:?=@@?=?DB?DEC?EC?C=B:A@?@C?B=\n+@cluster_578:UMI_GGGCTA\n+GGTACAGACAGGATCTCACTATGTTGCCCAG\n++\n+A@C=??==??A><??DA=?A?B@EC:><A?B\n+@cluster_587:UMI_TTCCGC\n+CCCCCCCAGATCGGAAAAACACACGCCTGAA\n++\n+<<<<<<A>=<64=>/DCD2>=><?<<>@;@?\n+@cluster_591:UMI_CAGGGC\n+CCCGGTCTAATGTTGCTTTTATTATTTTGAA\n++\n+<<==@B?A@AB@EC:?DEEC?EC?EEECB@@\n+@cluster_597:UMI_TTTTGG\n+GCGTAGGGGTTTTAGGTAAATGTCCTTTGAA\n++\n+9?@C8A==@7AEC,:/C<DA=@B=>6EB1:>\n+@cluster_604:UMI_TTAAGG\n+GCTACTACCACCAAGATCTGCACCTGCGGCG\n++\n+;?@=?@=@A=:A<?=;??C99=>>C:>;@;8\n+@cluster_613:UMI_CCCGTC\n+TGTTATATTTCACATCATTTTTTCCAGACAT\n++\n+C3BC/C?EB22-<76><BDEE5B?A:4;:?4\n+@cluster_619:UMI_TGTGAC\n+CCAGATCGGAAGAGCACACGTCTGAACTCCA\n++\n+<A?=<?==>@?=<B:;:=?@B?CB@@?C?85\n+@cluster_622:UMI_TGGCTG\n+GAGACAGAGTATTGCTGTGTCGCCCCCCAGA\n++\n+====??==AC?EC:?=@A@B=B><<;<A?<:\n+@cluster_632:UMI_TGGCAA\n+GAGATGGAGTCCCCAGATCGGAAGAGCACAC\n++\n+===<BB>=AB?<<A?=<?==>@?9=B:=?=@\n+@cluster_638:UMI_CCTTAG\n+TACTTTAAAATGCTTTATTGGAATTATTTTG\n++\n+?=>DE>@DC5A:?DEC?E;B>@3EC>EEE:0\n+@cluster_649:UMI_GACGGA\n+TTTTTTTTTTTTTTTTTCACACCCCACACAG\n++\n+EEEEEEEEEEEEEEEB11,.,/<<6./-//3\n+@cluster_664:UMI_CGCCGG\n+TCCCCCCCCCAAATCGGAAAAACACACCCCC\n++\n+B?<<<<<<<=ADA?==>@DDD??=>=@:<5*\n+@cluster_674:UMI_CGTTTC\n+AGACAAGTTCTCGCTCTGTCACCCAGGCTGG\n++\n+?==?A?AEB?D=B?D?C@BA=@<A?A@?CB@\n+@cluster_676:UMI_AGGTAG\n+TGGCATTTTTAATTTAGGTTTGTTTTATTTA\n++\n+AB@:@EEEEC@AEEC=A@EEC@EEEC?EEC=\n+@cluster_680:UMI_CCGCTA\n+TCTGATCTGACATTATTTCTATATTTTTAGA\n++\n+??CB<??CB=?@EC?EEB?A?C?EEEEC===\n+@cluster_682:UMI_GTGCAC\n+GTTTTTTTTTTTTTTTTTACCCCCCCCACAC\n++\n+8EEEEEEEEEEEEEEEEB=@<<<<<;=4/40\n+@cluster_687:UMI_ACGAAC\n+GACACTACTCTCCCACATCGCGAGAGAGCAC\n++\n+67/-01:5<::?:@5120+6531.8--2-68\n+@cluster_690:UMI_ATTTAG\n+GTTTTTTTTTTTTTTTTTTTTTTTTTTTCTG\n++\n+1EEEEEEEEEEEEEEEEEEEEEEEEEEB?:)\n+@cluster_693:UMI_CGGCCA\n+CTTTTGAGGCTTTTTCGTTGCCAGCAAGGGC\n++\n+?DEECB=A@?DEEEB=@EC:>A?B:A?A=@<\n+@cluster_700:UMI_ATCGAA\n+GCAGTTTTTACATTTATTTAAACAGAAAACG\n++\n+B:?AEEEEC=>@EEB?EEC@4>>?=@DD??B\n+@cluster_711:UMI_CTCCGA\n+ATTAATGAAAACATTCTTGGCAAATGCTTTC\n++\n+=EC@ABB6DD@??=B?DCB@:@DAB5?<EB=\n+@cluster_715:UMI_CTGTCG\n+TTTTGGGGCCCCCCCCAGATCGGAAAAGCAC\n++\n+EEEA1<<@>;<<<<<A6=;=:67>C@=B869\n+@cluster_717:UMI_CAGCCC\n+TCAGCTTTGCAACCATACTCCCCCCGGAACC\n++\n+DA?B?DEC:8A?@A@C=?D?<<<<;=>@@@;\n+@cluster_721:UMI_TTGTTC\n+GAGACGGAGACTCACTCTGTCGCCCCCCAGA\n++\n+3===>:><=<8AA683<;5912.<<;;>3./\n+@cluster_727:UMI_TTTACC\n+TTCTGAGCCTAAATGCCCTCAAAGCCCGTCC\n++\n+DB?CB=B-=?@DA@7>;>B8AD8?>;7:<?*\n+@cluster_731:UMI_GTCACA\n+TTGCTTCACTGACTTAACTCAAATTTCTTAA\n++\n+EC:?DBA;?CB=?=B@@?DAADAEEB?AC@?\n+@cluster_742:UMI_GAGACC\n+TGAGTGGGAGTCTCGCTCTGTACCCCAGGTG\n++\n+21,005-;,252605262746,/2231;54/\n+@cluster_757:UMI_TTGCAA\n+TCTTTGCACACTTATATTTTTTTTTGTGTTT\n++\n+?4?<<6:+?:16@3707EEE<E;EC1303DB\n+@cluster_766:UMI_TATTGG\n+CTTCCCAGTAACTGAGAGAAAATTACCATTC\n++\n+?DB?<A?AC@@?CB====@DDAEC=@A@EB;\n+@cluster_775:UMI_CCTGCA\n+GTGCAAAAACTGAATGTAGTCAATGGTCTTT\n++\n+AA::ADDD?>CB>AB?C:ABAAABB@><@EA\n+@cluster_780:UMI_GTTGCA\n+GGAGTTCCTAACCCAACAGTAATATCATTAG\n++\n+7.-072.0/7//33377781/46-/1371-<\n+@cluster_792:UMI_CGGCAC\n+TGTCACCATCCTTCTTTTCTTCTTCCTCATC\n++\n+@6>6,430:45?=;CDD:7A:7DA<9<7:70\n+@cluster_796:UMI_ATTTGA\n+TAGTCAGCTATTTAATTAGGTTCTTAAGACA\n++\n+@=ABA?B?A?EEC@AEC=A@EB?DC@?==?8\n+@cluster_805:UMI_CGTGGG\n+GTACTGCTCAAGCGCTGTCTATATCTCTCTA\n++\n+04904,.12:08/2/>16/74@4213<8.0.\n+@cluster_809:UMI_CTTTTA\n+CACAAGGAATATCATTTTATTACTGTAATCA\n++\n+?=?A?A>@AC??A@EEEC?EC=?C@C@A?A=\n+@cluster_814:UMI_GGGCTG\n+TTCTAGGTCCAATGGTAGTTTTTATTCCCCA\n++\n+DB?A=A@B?AAABB@@=A>DDEC?EB?;;@;\n+@cluster_819:UMI_AGTATA\n+GCTGTAGGAACAGCAGTCTTGGTGGTTAGCA\n++\n+B?C@C=A>@?>?B:?AB?DCB@AB@EC=B,<\n+@cluster_824:UMI_GAGTCC\n+AGCTTTGCAACCATACTCCCCCCGGAACCCA\n++\n+?B?DEC::A@@A@C=?D?<<<<==>@@@<@=\n+@cluster_834:UMI_TTAAGG\n+AGGGTGGGGGATCACATTTATTGTATTGAGG\n++\n+=A=@AB===>4?A=??EEB?EB@C?ECB=A?\n' |
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| diff -r 000000000000 -r 9839a3fe72f7 trim_adapters.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trim_adapters.xml Wed Jun 20 15:48:09 2018 -0400 |
| [ |
| @@ -0,0 +1,83 @@ +<tool id="atactk_trim_adapters" name="Trim putative adapter sequence" version="0.1.6"> + <requirements> + <requirement type="package" version="0.1.6">atactk</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input1' ./forward.${input1.ext} && + ln -s '$input2' ./reverse.${input2.ext} && + trim_adapters + #if '$settings.advanced' == 'advanced' + -d '$settings.edit_distance' + -f '$settings.fudge' + -s '$settings.trim_start' + -r '$settings.rc_length' + #end if + ./forward.${input1.ext} ./reverse.${input2.ext} + ]]></command> + <inputs> + <param type="data" name="input1" format="fastq,fastq.gz" /> + <param type="data" name="input2" format="fastq,fastq.gz" /> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"></when> + <when value="advanced"> + <param name="edit_distance" label="The maximum edit distance permitted when aligning the paired reads" type="integer" min="1" value="1" help="(-d)" /> + <param name="fudge" label="An arbitrary number of extra bases to trim from the ends of reads" type="integer" min="1" value="1" help="(-f)" /> + <param name="trim_start" label="Trim this number of bases from the start of each sequence" type="integer" min="0" value="0" help="(-s)"/> + <param name="rc_length" label="Use the reverse complement of this number of from the beginning of the reverse read to align reads" type="integer" min="1" value="20" help="(-r)"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output1" format="fastq.gz" from_work_dir="forward.trimmed.fastq.gz" /> + <data name="output2" format="fastq.gz" from_work_dir="reverse.trimmed.fastq.gz" /> + </outputs> + <tests> + <test> + <param name="input1" value="SP1_f.fastq" ftype="fastq" /> + <param name="input2" value="SP1_r.fastq" ftype="fastq" /> + <output name="output1" file="SP1_f.trimmed.fastq.gz" decompress="True"/> + <output name="output2" file="SP1_r.trimmed.fastq.gz" decompress="True"/> + </test> + <test> + <param name="input1" value="SP1_f.fastq.gz" ftype="fastq.gz" /> + <param name="input2" value="SP1_r.fastq.gz" ftype="fastq.gz" /> + <output name="output1" file="SP1_f.trimmed.fastq.gz" decompress="True"/> + <output name="output2" file="SP1_r.trimmed.fastq.gz" decompress="True"/> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +The trim_adapters utility is based on a script by Jason Buenrostro. +Instead of looking for known adapter sequence, it aligns paired reads to each other +and trims off sequence outside the alignment. More precisely, it searches +the forward read for the reverse complement of a specified number of bases +(20 by default) at the beginning of the reverse read, then falls back to finding +the best alignment of the two reads, using the minimum Levenshtein distance between them. + +**Input** + +It requires 2 inputs: The (optionally gzipped) FASTQ file containing the +forward reads and the (optionally gzipped) FASTQ file containing the +reverse reads. + +**Output** + +Generates 2 gzipped fastq files with adapters trimmed. + + ]]></help> + <citations> + <citation type="bibtex">@unpublished{atactk: a toolkit for ATAC-seq data, + title = "atactk: a toolkit for ATAC-seq data", + author = "The Parker Lab at the University of Michigan", + url = "https://github.com/ParkerLab/atactk/", + year = "2018" +}</citation> + </citations> +</tool> |