# HG changeset patch
# User rnateam
# Date 1529524089 14400
# Node ID 9839a3fe72f7aa00b6d820899fc86b08f607682b

planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d

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
@@ -0,0 +1,500 @@
+@cluster_2:UMI_ATTCCG
+TTTCCGGGGCACATAATCTTCAGCCGGGCGC
++
+9C;=;=<9@4868>9:67AA<9>65<=>591
+@cluster_12:UMI_GGTCAA
+GCAGTTTAAGATCATTTTATTGAAGAGCAAG
++
+?7?AEEC@>=1?A?EEEB9ECB?==:B.A?A
+@cluster_29:UMI_GCAGGA
+CCCCCTTAAATAGCTGTTTATTTGGCCCCAG
++
+8;;;>DC@DAC=B?C@9?B?CDCB@><<??A
+@cluster_36:UMI_AACAGA
+TCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+5?:5;<02:@977=:<0=9>@5>7>;>*3,-
+@cluster_39:UMI_GAACCG
+CCTTCCATCACCAGATCGGAAAAACACACGC
++
+00>7;8@5<192?/8;0;;>=3=/3239713
+@cluster_53:UMI_GTGGGG
+GGAAAATGAAAATGTTGGATGAGAACAATTA
++
+<>=CCA@A8>?=86AB@>0?76<993=@=7.
+@cluster_58:UMI_GTTTTG
+AAAGCAATCCACAGAAGGGCATTTCTACCGA
++
+@D?B:AA??=;>?=@?A=@:@EEB?A=@<@<
+@cluster_63:UMI_TTTCCC
+GCAACCATACTCCCCCCGGAACCCAAAGACT
++
+@:A@@A@C<?D?;;98<=>=@;<AAD?==?D
+@cluster_70:UMI_CCGGGA
+CTTTTTCTTCTAAAATTTTTTCTTCTCTGGC
++
+?DEEEB?DB?A@DD?EEEEEB?DB?D9CB/.
+@cluster_82:UMI_TTTTTG
+GCTTATGTTTTATAAAAATAAGTTGCCCCAG
++
+75;6>>>>DEC7?6CC>A=9=>@C1<<9>12
+@cluster_87:UMI_TGACAC
+GGTTGAGCACAGGGTACTTTATTGATGGTAC
++
+=@E@B=B::;;A=?A=9DEB9ECB8?B@@97
+@cluster_90:UMI_ACGGGG
+TTTTTTTGTGAAGGAGTCTTTCCCCCCAGAC
++
+CEEEEDB96203:8+01.3353/897?.+,0
+@cluster_96:UMI_ACTAGG
+GGAATGCAACAACTTTATTGAAAGGAAAGTG
++
+=>@AB::A??A@?DEC?ECB@D?A>=C?A;9
+@cluster_99:UMI_CAACAA
+TTTGTTTTTTTTTTTTCCACCCCCACATGGA
++
+<DB1BD:5?9BB:=63<5+56721--/11;3
+@cluster_107:UMI_TCCATG
+ATCGGAAGAGCACACGTCTGAACTCCAGTCA
++
+<?;=>?<=9;59:6<@?>C<99=D79<?354
+@cluster_114:UMI_TTTATG
+TCTTTTTTTCTTTTCTTTTTTTTTTTTTTTA
++
+B?DEEEEEB?DEEB?DEEEEEEEEEEEEE<.
+@cluster_124:UMI_CGGCGC
+GAGACGGAGTTTCACTCTTATTGCCCCCCAG
++
+2///1:>7A7;B3.8C?@>.4C5><;;9A23
+@cluster_130:UMI_GTAGGG
+GGTAGAGATAGGGTCTTGCTATGTAGCCCAG
++
+4@:<=8=;B69;@9<9=:?87@:B:8.293;
+@cluster_134:UMI_TAGTGA
+TGTTAGACAAAATAAATGTATTTTTTCACTC
++
+1/32++,2668/1/5/<14/69A=@62*-40
+@cluster_140:UMI_TTACTC
+GGACCCCCCCCAAAGTCGGAAAACACACCCC
++
+9//865/-71336003/2-566620433.2+
+@cluster_148:UMI_GCCTGG
+CATACCCCCCCCAGATCGGAAAAACACACGC
++
+9@C=@47;;9<A?,<?==>?C;D3><:=?32
+@cluster_152:UMI_TCGAAA
+GCTGTCTAGTCATCCTCGTCGGTCTTCTGCT
++
+B?C@B?A=ABA@??>D=@B==@B?DB?C:?D
+@cluster_159:UMI_CGGGGG
+GTCTGCACAGATAAATCTTTCTTCTCATTAC
++
+4:7<+*-/0.,3@B300=;41=3=20=9;-2
+@cluster_164:UMI_GCTGAG
+TATTTTTTTTTTTTTTTTTTTTTTTTGTGTG
++
+??E7EEECEEDEEEECEEEEEEEED20101*
+@cluster_169:UMI_TGAGCC
+AAAAATGCCTGGAAATCACTTGCTAGTTACA
++
+ADCB<B:>>CB>@DA?A9?DB:?A=AEC=>3
+@cluster_176:UMI_TGGGCG
+GGGTTCAAACCCCCAGATCGGAAAAGACACA
++
+<=@BB;AD?96:;@?=:?<=>:>9</,-+-+
+@cluster_182:UMI_TATCAG
+AATGTTCTTTCCTCTGTTGGCTTTGGCCATT
++
+@@41EB05E1>.6140DC5@68EC70=65E3
+@cluster_189:UMI_GCCTTG
+TTGGTATATAAACTATTTATTAACAGACAAG
++
+ECB@C?C?C@D??@?EEC9EC@@>?==>A=B
+@cluster_197:UMI_AGGATG
+GGCATATGAAAATTTATTACTACAGTGTTTT
++
+=@:@C?BB@DDAEEC?@C=?A=??AA@DEE=
+@cluster_211:UMI_ACTGGC
+CCCCCCCCAAATCGGAAAAACACACCCCTAA
++
+<<<<<<<AADA?==>@DDC??=?=@<;>@@?
+@cluster_216:UMI_TATTCC
+GCTTTGCAACCATACTCCCCCCAAGATCGGA
++
+<>D87:-A9@::>;;9?;;<<@14;2;/=.9
+@cluster_218:UMI_TGCTCC
+CCCCCCCAAAATCGGAAAAACACACCCCTAA
++
+;;;<<;1/7>=?2=;@D<C=<797@7235@<
+@cluster_222:UMI_TTTGTG
+TGAGACAGGGTTCGCCAGCGTGGACCCTTTA
++
+4:/4+5275/34,4-060./54.+0*0472,
+@cluster_228:UMI_GCCTTC
+CAGGTGTTTTTTCTCCCAGATCGGAAGAGCA
++
+@?A@A@EEEEEB?D?<A?=<?==>@?==B58
+@cluster_232:UMI_TGTTCC
+TCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+D?<<<<<<<AADA?==>@DDD@?=?=@:<5+
+@cluster_241:UMI_CTCTCA
+CAACTTTCCCTTACCCCAGATCGGAAGAGCA
++
+?A@?DEB?<>DC=@<<A?=<?==>@?==B:<
+@cluster_252:UMI_CAAAAG
+TACCTTTGAGACAGAGTCTCGCTCTGTCACC
++
+B=@>DECB==:=;==AB?D=B?D?C@BA=@;
+@cluster_254:UMI_TGTGCC
+TAATGTGCTACTTTTAATTTATTAAAATCCC
++
+A@AB@A:?A=?DEEC@AEEC?E;@DDA??<<
+@cluster_258:UMI_TGCGGC
+GTTTGTTTTTTTTTTTTTCCCAGATCGGAAG
++
+>BEC;EEEEEEEEDEEC48-543197=>?.2
+@cluster_272:UMI_ACTCGA
+AACTTGACACCTTTAAAATAGCATTAAACAG
++
+D72D>?<==1=4EC3DD24/4.@8C1D0/48
+@cluster_281:UMI_CCGATA
+TAGTCTTAGCATTTACTTTCCCCCCAGATCG
++
+B=A>?DC=B:@EE@=>DEB?<;<<@?=<=8B
+@cluster_287:UMI_GGATGC
+GGACATAATAATAACAATTGAATGTCTGCAC
++
+=>=?@C@AC@AC@@?AAECB@AB@B?C::<?
+@cluster_290:UMI_TTCCCC
+ACTTTTGAGACAGGGTCTTGCTCTTGCTATG
++
+=?DEECB===?>A=@B?DC:?D?DC:?A?B:
+@cluster_295:UMI_TCGGGG
+CTTGGTACATGATTTTATAGCAAGCACATTT
++
+?DCB@C=?@BB<EEEC?C=B:A?B:=?@EEB
+@cluster_298:UMI_TTGACA
+GTCAAATATTTATTGAATGGTGGAAAACCAT
++
+/AAADAC>EEC?ECB@ABB@=B>@DD@@=?:
+@cluster_301:UMI_GCGGGC
+GGCTTTGGGAAGCCCCGCGGGGGACCGGCAC
++
+6@>;E4B=-:.1<<;,4429==>,/6-?)24
+@cluster_303:UMI_AGTCAA
+GTCAAAAGAAAAGCGTTTATTTAAAAAAATC
++
+0100CD0745B.2/04DC3C462;DDD6A=1
+@cluster_310:UMI_TAAACC
+CTTATCATTTTAATCGATTTTAATGATTATT
++
+=DC??A@EEEC@A?=@<EEEC@ABB<EC?E5
+@cluster_321:UMI_AGAGGA
+TTGACGACCGCGCCATGCTGTAATATACAAC
++
+8?9:10+/2:240/.1)59/1/3599-/000
+@cluster_330:UMI_TACCGC
+GAGATGGAGTCTTCTCTCAGATCGGAAGAGC
++
+>0=-AA<::1-5?75:3473454.576-:90
+@cluster_338:UMI_TTACCC
+GTTGTCAAATTATCCTTTATTGAAATGTTTT
++
+/3B46=9D<9408895E?17B<:D?1059D6
+@cluster_340:UMI_GGTTAC
+CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+>DEEEEEEEEEEEEEEEEEEEEEEEEEEEEB
+@cluster_347:UMI_ATCAAC
+GACTGAACTAAGTGGTTTTTTTATTAGAGAA
++
+>=?CB@@>A@>AAB85EEDEEC?EB<==9?5
+@cluster_351:UMI_TGTTAG
+CTGACTAATATGCCCCAGATCGGAAAAGCAC
++
+?CB=?A@AC?B:><<A?=<?==>@DA?B:=7
+@cluster_359:UMI_CTACAC
+CCTAGAAACAGAATAGTCTTTACTTTTACTG
++
+<>A==@D@??=@AC=AB?DEC=?DEEC=?C:
+@cluster_367:UMI_GAGGTG
+CCCCCCCCCAAATCGGAAAAACACACCCCTA
++
+><<<<<<<AADA?==>@DDD@?=?=@<;>A=
+@cluster_373:UMI_ACTGCA
+CAACTATTTAAAAACGTAAAAACTATTCTTA
++
+=A??A?EEC@DDD??@C@DDD??A9EB?6:5
+@cluster_376:UMI_AAGCAC
+TCTTTGTACAAAATTTTATTAAAGGTCTTTA
++
+9:CDC@<<<ADD>EEE8:E2@D7A@2>DD:5
+@cluster_382:UMI_CGCGCG
+CGGTCATAAGTTTAATGAAGTCCCCAGATCG
++
+?=@;A@C@?A@EC@ABB@?;B?<<A?=<=<B
+@cluster_388:UMI_GCGGGC
+TCTTCCTCTTCTTTCTCCCCAGATCGGAAGA
++
+C?DB?>D?DB?DEB?D?<<A?=<?==>@?==
+@cluster_390:UMI_CGGTGG
+AGACAGAATTTCGCTCCTGTAGCCCCCCAGA
++
+=<<:?=@<EE:=B>C?=C?77;<7;926?2:
+@cluster_399:UMI_CAAACA
+CTTTCTCCAGTTGTTCCCAGATCGGAAGAGC
++
+9DE@?C?A?AEC@E<?<@;7<?===@?<=@9
+@cluster_404:UMI_CTTAAA
+TTTCACACTGAAATATCCTTTTATTGCAACT
++
+EEBA=?=?CB@DAC???>DEEC?EC:9A@?9
+@cluster_408:UMI_AAACAC
+CTTTTACACTGGCCACAGAGCGTTTATTGAC
++
+9DEE<=>=?CB@>A=??==B?@EE<?E:A=7
+@cluster_428:UMI_GGACCG
+CCTTTTCCTTTCTCTTTTTTTTCTTTAGTGT
++
+>>DEEB?>DEB?D?DEEEEEEB?DEC=AA@?
+@cluster_435:UMI_TCGTCA
+GGCTTTGCAACCATACTCCCCCCGGAACCCA
++
+A@?AEC::@>=A@C=?D9:;;<==>7?<;@9
+@cluster_441:UMI_GCATAG
+GCTCTAGAGGGGGTAGAGGGGGTGCTATAGG
++
+@?D?A===A===@C===A===@A:?A?C=A@
+@cluster_448:UMI_GAGAAC
+GGAAATAAAAGCACAACTATATTTGGGCACC
++
+=>@DAC@AD?>9<?A@?A>C?EECB=@:=@;
+@cluster_455:UMI_GTGAGC
+CCTTTCTTCTCTCCCCAGATCGGAAAAGCAC
++
+<>DEB?DB?D?D?<<A?=<?==>@C=?B9=@
+@cluster_460:UMI_TCTCAC
+GCTTTTCTTTCTTTCTCTATTCTTTCTTCCC
++
+1-34461:992967.3./-410983.51-*)
+@cluster_467:UMI_AATCTG
+GTTGGTTAAATCTTTACTCACAGTAATTTAC
++
+@ECB@EC?CA??DEC=?DA=??AC@AEEC=@
+@cluster_472:UMI_GAGGCA
+CCCTTGGACCATAAATTTTTATTGGCAGGTC
++
+@<>DCB>=@A@C@DAEEEEC?ECB@:?A@9=
+@cluster_478:UMI_TGAGTA
+CTTTGTACAAAATTTTATTAAAGGTCTTTAG
++
+?DEC@C=?ADDAEEEC?EC@D>A@B?DEC=B
+@cluster_489:UMI_GGCGTG
+TGTGTTCCAATTCTTTTATTATTCGGGCCTC
++
+87323771148305=D6-48.:5.,.:.438
+@cluster_491:UMI_TTCCCG
+GAGACAGAGTTTCGCTCTTGTCACCCAGGCT
++
+>===??==AEEB=B?D?DC@BA=@<A?@@5?
+@cluster_493:UMI_TTATTG
+GGCCAACTGAATGTAATCTAGTTTATTCAAC
++
+=@>AA@?CB@AB@C@A??A=AEEC?EBAA@@
+@cluster_503:UMI_CGGTGA
+CAGACTGAGTTTCACTCTTTGTTGCCCAGGC
++
+??==?CB=AEEBA=?D?DEC@EC:><>?A@8
+@cluster_513:UMI_TCGCTC
+CACTGTTAAAAACATTTATTCTGATACATTC
++
+A=?C@EB@DDD@?@EEC?EB?CB<C=?@EB4
+@cluster_521:UMI_TCCATA
+TGTCCAGCTGCTCCTGATCGGAATACAGCAC
++
+1/22@36;C-03--2674,1-/424122),/
+@cluster_524:UMI_AGGGAC
+TTTTTTTTTTTTTTTTTTTTTTTTCTCCAGC
++
+CEEEEEEEEEEEEEEEEEEEEEE415=97;-
+@cluster_530:UMI_GACACA
+GGTGCATATGCATAAGTGGAGCCCAGAGGGC
++
+>@A::@C?B::@C@?A?B>=B>;A?==:1:>
+@cluster_535:UMI_CCGCTA
+CTCAGCACCCATTGTAAATTATTTGTGGATG
++
+9DA?B8=?<A7DC@B9D0EC?EEC@A>.<A+
+@cluster_537:UMI_GACTCC
+GACGCTCACACTTAGTTTTTATTAGCCACAG
++
+7;651C=9<8:D78?D>DE4855<396;1;1
+@cluster_545:UMI_ACGATC
+CTTGCTTCAGTTTTATTTGTACAAATATCAC
++
+79A6?66@;A;EE52EE41?=:A56B<.547
+@cluster_563:UMI_GCCTCG
+CCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+0;;71;;;<@3:??=8>:@;?=>8>9453;/
+@cluster_566:UMI_CGCATA
+GACGGATGAGTCTTTTAATAGAAAAACACAC
++
+==?=><BB=AB?DEEC<AC==@DBC@>=?;7
+@cluster_572:UMI_AAGACC
+GCAACCATACTCCCCCAGATCGGAAAAGCAC
++
+B:A@@A@C=?D?<<<A?=<?==>@D6?B:=@
+@cluster_586:UMI_AATTCA
+CTGCTCAGCTCTTTATTGATTGGTGTGCCCA
++
+??:?>A?@2><<59=E?@<B?5?9@7:8:?6
+@cluster_588:UMI_ACATGG
+AGTTAGAGTCTCAGTCACCCAGGCTGGAATA
++
+=AE?===A@=D@4AA@=?855A@>;B<@;=5
+@cluster_592:UMI_GCCGTC
+TGTGTCTCTCTGTCCCCAGATCGGAAGAGCA
++
+C?@7B?@?C1@;<;598?883846@?0792@
+@cluster_602:UMI_CTCTCA
+GGTTTCCGCCCCCCAGATCGGAAGAGCACAC
++
+A@DEB<;:>695:@?=<?=//:6+790<<=:
+@cluster_607:UMI_TCCGAC
+GATTAATGAAAACATTCTTGGCAAATGCTTT
++
+@<EC@ABB?CB?>@DB?DCB;:ADAB::>?6
+@cluster_615:UMI_TGGGAC
+TCTAAACCTGGAAATTTATCTGGAGTCTTCC
++
+611@D@0>651@DA6E2.?377>-0?:>B/;
+@cluster_621:UMI_TTCGTC
+GTTTTTTACCCCCTCCCCAGATCGGAAGAGC
++
+@EEEEEC=@:<<>C><<A7<:?=7>@?7=@8
+@cluster_626:UMI_CGCGCA
+CTTTTTTTTTTTAAAAACCCCCAGATCGGAA
++
+?DEEEEEEEEEC@DDD?@<<<A==<?4=>@<
+@cluster_634:UMI_AGATCA
+GTTTTTTTTTTTTCTCTCCTAACACCCCAGA
++
+?EEEEEEEEEEEB?D?D?>@@@?=@<<A;69
+@cluster_648:UMI_CCTATG
+TTTTTTCCCCCCAAGATCGGAAAAACACACC
++
+EEEEEB?<<<<A1?=<?9=:@DDD32121@9
+@cluster_663:UMI_CAAAGG
+TAAGACCCTCATCAATAGATGGAGATATACA
++
+B@?==@<>DA@?AA@C==<BB>==<C?C=?5
+@cluster_672:UMI_GGACGA
+ATTTTGTCTTTTGTTTTCATTTTTTCTTGCT
++
+AEEDB@A?DEEC@BEEBA;EEEEEB?DC:?D
+@cluster_675:UMI_GTATTG
+CAGTTGTCAAATGATCCTTTATTGAAATGTT
++
+:?AEC@BAADABB<??>DEC?ECB@DAB@DB
+@cluster_677:UMI_CCTGGA
+GCACCCCCTCCCAGATCGGAAAAACACACCC
++
+B:=@<<<>D?<A?,<?==>@DDD>?=?=@:>
+@cluster_681:UMI_GGACCC
+AGCTTTGCAACCATACTCCCCCCCCAGATCG
++
+?B?DEC::A@@A@C=?D?<<<<<<A?=<?=B
+@cluster_684:UMI_GTTCAC
+TGCAACCATACTCCCCCCCCCAGATCGGAAT
++
+C::A@=A@C=?D?<3<<<<<A?=;?4.>@A/
+@cluster_689:UMI_CCTTCA
+AAAGAAGTAAGCCTTTATTTCCTTGTTTTGC
++
+DD?=@?AC@?B>>DEC?EEB?>DC@EEEC:;
+@cluster_692:UMI_GCGTCC
+GAGGTGAAGTTTCACTTTGTCCCCAGATCGA
++
+@=@@:?<3@D=A@27DDC7>?<;A?14;2<,
+@cluster_699:UMI_TGTTTC
+CTTTCTTTCTTTCTTTTGTTTCTTTCTTGCT
++
+>DEB?DEB?DEB?DEEC@EEB?DEB?DC:?D
+@cluster_706:UMI_CCACGG
+GCCCTTCTGCTCCCCCAGATCGGAAGAGCAC
++
+@><>DB?C:?D?<<<A?=<?==>@?1=B:=@
+@cluster_714:UMI_ACGCGA
+TTTTTCCCCCCCCCAGATCGAAAAAGCACAC
++
+EEEEA?<<<<<<;8?=<?=@8DD4?:8<><@
+@cluster_716:UMI_GGGGTC
+CCCCCCCCAAAATCGAAAAAACACACCCCTA
++
+<<<<<<;<1C?0.4@/DDA:;>3>8=;626<
+@cluster_719:UMI_GAGAAA
+GGGAGTAGTGTCTTTATTCATTAAAGCCTGA
++
+A=>=AC=AA@B?DEC?EBA@EC@D?B>>CB=
+@cluster_722:UMI_TCCATA
+GTTTTTTTTTTTTTTTTCAGTAAGCACAGGT
++
+AEEEEEEEEEEEEEEEBA?@:@?B:=??A@4
+@cluster_730:UMI_ACCTTG
+TCCCCCCCCCCAAATCGGAAAAACACACCCC
++
+B?<<<<<;<76AB@?=<5@DCD??=>2@;;6
+@cluster_732:UMI_AGGAAG
+CCCCCCCCCAAATCGGAAAAACACACCCCTA
++
+6<<<<<<<AADA?==>@DAD?><?=@:;>@0
+@cluster_756:UMI_TCGATA
+CTTTGTTTCAAGTTTTAATCAAAGCTTGTAT
++
+?DEC@EEBAA?AEEEC@A?AAD?B?DC@C??
+@cluster_764:UMI_ACGACC
+CACGCTTAATTCACTTTATTTTTCCCCAGAT
++
+>=?B?DC@AEBA=?DEC?EEEEB?<<A<=<9
+@cluster_772:UMI_AGGAAA
+AAGACCACAAAGATTTAATTTAAAATCACAG
++
+D?==@A=?AD?=<EEC@AEEC@DDA?A=??B
+@cluster_778:UMI_TTGGGC
+ATTTAACATGAGGAAACCCCAGATCGGAAGA
++
+@EEA@?>@BB;A>@D<@;:64=8?==>@?<6
+@cluster_787:UMI_GCAGTC
+TGATAGCATTGCGAGACGCTGGAGCCGGAGC
++
+CB<C=B:;EC:?@===?B?CB><@>==>6A9
+@cluster_794:UMI_GCATCC
+CCCCCCCAGATCGGAAAAGCACACGCCTGAA
++
+;;9<<<A?=8>===@D;?B:=<=?B:>C><8
+@cluster_799:UMI_CGTGCA
+GCTCGTCTTTCTCCCCCAGATCGGAACAGTA
++
+=.B10486=:2989;58/-4=255::.=684
+@cluster_807:UMI_GATATG
+TTTTTCCACACGTAAAATTTATAAACATTTA
++
+83EEA3:620725;DD5CAB:53C3=/472-
+@cluster_810:UMI_TCTCGC
+GAAGAGCACACGTCTGAACTCCAGTCACCGT
++
+9?<9;@23538<88>@348<396;;365/=4
+@cluster_816:UMI_ATGTAG
+TGAGACAACATCTCACTCTGTTACCCCCCAA
++
+AA===>A?:@>?C@=?C?C@BC3/;<;<A1.
+@cluster_823:UMI_TTTTTA
+CCATTATAATAGCCATCTTTATTTGTAAAAA
++
+?A@EC?C@AC=B>A@??DEC?EEC@C@DDD:
+@cluster_828:UMI_CTCGTA
+GCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+B><<<<<<<AADA?==>@DDD?>=>=@;<<3
diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_f.fastq.gz
Binary file test-data/SP1_f.fastq.gz has changed
diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_f.trimmed.fastq.gz
Binary file test-data/SP1_f.trimmed.fastq.gz has changed
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
@@ -0,0 +1,500 @@
+@cluster_8:UMI_CTTTGA
+TATCCTTGCAATACTCTCCGAACGGGAGAGC
++
+1/04.72,(003,-2-22+00-12./.-.4-
+@cluster_21:UMI_AGAACA
+GGCATTGCAAAATTTATTACACCCCCAGATC
++
+>=2.660/?:36AD;0<14703640334-//
+@cluster_34:UMI_AGCTCA
+TCTTGCAAAAACTCCTAGATCGGAAGAGCAC
++
+-/CA:+<599803./2065?6=<>90;?150
+@cluster_37:UMI_GAGGAG
+GTCTTTGTACAAAATTTTATTAAAGGTCTTT
++
+?B?DEC@A=?ADDAEEEC?EC@D6A@@>DE4
+@cluster_43:UMI_GGATTG
+GAGTTATAATCCAATCTTTATTTAAAAATCT
++
+>=AEC?C@;??0A>?0DEB9EEB@DDC1?=6
+@cluster_55:UMI_CTAATG
+AGACAAAAGGATTTATTTGGAAATTTCCAAA
++
+===>7DD?A>;EEC?EECB>?DAEEB?AAC3
+@cluster_62:UMI_CCTTGC
+GAGTTGCGACAATACTCTCCCCCGAGACCCA
++
+9/96C1954/12?=7=?5::94,40125442
+@cluster_66:UMI_TTGGGG
+CCAACTAACTTTTATTTTAAGTTCAGGGGGT
++
+<AA@?A@@?DEEC?EEEC@?AEBA?A===@9
+@cluster_71:UMI_CCAATA
+CAGCTTTGCAACCATACTCCCCCCGGAACCC
++
+<?B?DEB::9>@?@C=?:=<<<:===@?=83
+@cluster_83:UMI_CCAGTC
+CTCCCACAGTTCTGCGCCAGAGCGGAAGAGC
++
+=:?*>4>;>66;C:612661<2322141=:-
+@cluster_88:UMI_TGCCGA
+TCACTACCTCCCCGGGTCGGGAGTGGGGTAT
++
+/@=>@=@<D;;;<==@B9==>,75<:593=7
+@cluster_93:UMI_ATTGTA
+TCCTCACTATCTGATTCCTCCCCAGATCGGA
++
+;9=BA=?@<??CB;EB?=C?;8@:=:=88:7
+@cluster_98:UMI_CTTTGG
+AGTTCCCCCCCCTATATCGAAAAACACACCC
++
++670.98;.+460.1533=09;3481/14*3
+@cluster_105:UMI_TCGCGC
+GATTGAGACAGAGTCTGCTGTGTTGCCCCCC
++
+?<E=====>?==A@?C:?C@A=EC7>;;<<7
+@cluster_113:UMI_ACAATA
+GCTTCAGCTGCCCAGATCGGAAGAACACACG
++
+B?DBA?B?C:><A?=<?==>@?3@/><?=?5
+@cluster_117:UMI_TCAGTA
+GCACTACTATATTAGATTGTGTTATCCGTTA
++
+1)+-0.-0-4/82-+*45//.31--0/074.
+@cluster_126:UMI_CATGAA
+CCCCCCCAGATCGGAAAAGCACACGCCTGAA
++
+?.:8<;??=6?==>?:6><0;165B35;66:
+@cluster_131:UMI_AGTGTA
+GTGAGCACAGGGTACTTTATTGATGGTACAT
++
+;AB=B::>4:<@57=654187B;B:=4;9?9
+@cluster_137:UMI_ACGGAC
+GCAAATATAAACAGGTTTATCTATTCTGTCT
++
+9)75?C?:@6=36:6D<B78.0.5B1<=7.5
+@cluster_144:UMI_CAGGGC
+CCACCCCCCCCAAATCGGAAAAACACACCCC
++
+.A=@<<<<<;AACA=49>@DDD?53==@;85
+@cluster_149:UMI_CGGCGC
+GCCACTATATCTCAAGCATTAAAATACATGT
++
+3=7,.0>6287<2@47/4=5/;<62,38:18
+@cluster_153:UMI_TACAAA
+TTTTTTTTACACTTTATAACACACTTTTTAT
++
+EEEEEEE3995.6E848@?>=;=3:EEE3/9
+@cluster_162:UMI_AACGGG
+CCACAACATTCCATTTATACACAGAACTAAA
++
+>A=?A@?@EB?A@EEC?C=?=??=@@?A@D4
+@cluster_165:UMI_AGTCGC
+TTGGCTCTTTTTCGTTTATTGCATGCCCCCC
++
+CC:?<D;D?;<2-<@A<>B>2::B082,9*/
+@cluster_172:UMI_GTTTCC
+GGCTTTGCAACCATACTCCCCCCGGAACCCA
++
+=@?DEC::A@@A@C=?D?<<<<==>@@@<A=
+@cluster_181:UMI_CTTGCC
+TAAACAGAGTCTTACTCTATTGTCCAGGCTG
++
+/855.7768<0;5.084</9=191/.47/3.
+@cluster_186:UMI_GGGTAG
+CCTTTCCTTTCCCCCAGATCGGAAGAGCACA
++
+>>DEB?>DEB?8<<A?=<?==>@?:=B:===
+@cluster_190:UMI_GGCGGA
+CAAATCAATAGGTCTTTTATTGCATCATTTA
++
+?AA??AAAC=?@B?DEDB>EC::@?A@EEC=
+@cluster_207:UMI_TGAACA
+GTTTCCCCCCCCAAATCGGAAAAACACACCC
++
+;=B:9/193993=>?:88=694;555767+,
+@cluster_215:UMI_TCAAAC
+TCCCCCCCAAATCGGAAAAACACACCCCTAA
++
+3?<<<<<AADA?==>@DDD@?=?=@<<>A<=
+@cluster_217:UMI_CTCGGC
+CTAAACTTTTATTGAAAAAAAAACCGAGGAG
++
+>A@D@?DEEC?ECB@DDDDDDD?@=@=A>=B
+@cluster_219:UMI_ACGTGG
+TGTAATTAGTAGACATGGTCTTCTACCCATA
++
+A@C@AEC=AC===?@BB@B?DB?A=@<A@C=
+@cluster_223:UMI_ATTTCC
+CCTTCTGTTTCTTTTTCCCTTCTTTCCTTCC
++
+;>DB?C@EEB?DEEEB?<<DB?DEB?=D@=:
+@cluster_229:UMI_CAAGTA
+GAGGTTTGCAGCTATTTTATTTACAAGTATA
++
+==A@EEC::?B?A?EEEC?EEC=?A?AB?C=
+@cluster_238:UMI_AGGTTG
+GCTTCCTACTTTTCAGGTTTAAATTTATCTT
++
+@?DB?>@=?DEEB@?A@CEC@DAEEC???DB
+@cluster_248:UMI_TTTTTG
+TAGGAAAAAATGGTTTTGGACATGGGATGAA
++
+8=A>2DDDBABA@9@<BA.5>:BB=>7BA7;
+@cluster_253:UMI_GCGCTC
+TCGTCACTACCTCCCCGGGTCGGGAGTGGGG
++
+D=@BA=?A<@>D?<<===@B===>=?>B1:2
+@cluster_256:UMI_AGACAG
+CCGTGATCCTTTTTCAGTGCTTCTACAATGC
++
+>=@AB<??>DEEEBA?AA:?DB?A=?AAB:>
+@cluster_265:UMI_AATTTG
+TACCCCACCCAAATCGGAATAACACACCCAC
++
+@5?0<;7;845773245>:1<38,1-6*8,/
+@cluster_273:UMI_TCGAAA
+GGTTTTCCTTTTTATTTAATCAAAGACTGGT
++
+A@EEEB?>DEEEC?EEC@A?AAD?=+?CB@8
+@cluster_286:UMI_CGGTGC
+AACAATGATCAATTTTAAGAAATGGGTACAT
++
+A@>AABB<?A@AEEEB@9=@DABB=@C=>@/
+@cluster_289:UMI_CTTCTA
+CCCCCTCCCAAATCGGAAAAACACACCCCTA
++
+@<3<>:?:AAB@?==>@DDC??66:?8;>@2
+@cluster_293:UMI_CGCACC
+ATCACTTCTATCAAAGATTGCTCTATTATCT
++
+@?A=?DB?A??;AD?=<DA5?D?A?EA>9:D
+@cluster_296:UMI_TTTTTC
+GAGATTGAGCCTCGTTGACCAGGCTGGAGCA
++
+4==<>1=5B=<D9?DC66@?77@??=>37)2
+@cluster_299:UMI_ATCGCC
+GCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+?>;;;;<;;?@AA>==>@CCC=;<>7;095+
+@cluster_302:UMI_TCGGCC
+TTGCTACTACCACCAAGATCCCCAGACCGGA
++
+?>3=5,-25<74766=,34<;:20,/254.2
+@cluster_309:UMI_TTTCAA
+ATAGTTTAATGTATTTTAATAGCAAACTTAC
++
+AC=ADEC@AB@C>EEEC@=C;B:@C9>DB=?
+@cluster_316:UMI_TGCTAC
+TTGAGGGATGGAAGAATATATAATCTATCAA
++
+CCB=8=><BB=4>31=A:C?C@A??@?>A>5
+@cluster_323:UMI_CAGAGC
+CCCTTTTTCCCCCAGATCGGAAAAACACACC
++
+<<8DEEEA?<<<6?=<?===@ACC9:<==>.
+@cluster_337:UMI_TTCCCG
+CCTTCCTATTTATTGCCCAGATCGGAAGAGC
++
+1986:</-4<4-522702:.22674743740
+@cluster_339:UMI_GCCCAC
+AATTTTGTAAAAAATGGTTTATCAATTCCAT
++
+AAEDEC@A@DDDD7BB@EE9??A<6E<?@@?
+@cluster_344:UMI_GAGGTG
+CTTTTCCTCCGCTGCCCAGATCGGAAGAGCA
++
+?DEEB?>D?=B?C:><A?=<?==>@?==B::
+@cluster_349:UMI_CTATGA
+CAGCTTTGCAACCATACTCCCCCCGGAACCC
++
+??B?DEC::A@@A@C=?D?<<<<==>@@@;0
+@cluster_357:UMI_CGCTCA
+GAGATTTTAATTAATTTTTATAAAATCTGAG
++
+===<EEEC@AEC@AEEEEC?C@DDA??CB=B
+@cluster_362:UMI_TTATAA
+CTTCTTTCCTGTTTTTTTTAAAATCCTTCTT
++
+?DB?DEB?>C@>BDD>CEC@DDA??>DB?=6
+@cluster_368:UMI_GGGCGA
+TAGGTTTTTCAGTGTATTGCTTTGAGGACCC
++
+;=A@CBEE@A?A@>@?E=9>6:B>661=@,1
+@cluster_375:UMI_ATCCGG
+CCCCCTCCCCAAATCGGAAAAACACACCCCT
++
+=;<;=D?;;:A?@<==>@C?C9>;?:@0862
+@cluster_381:UMI_GGAACA
+GAGACGGAGTCTCGCTCTGTTGCCCCCAGAT
++
+;===?=>=AB?D=B?B?>@DC:><<<A?=<8
+@cluster_387:UMI_TGTACG
+TGCCTTTTGAAACCAAATATTTAATATTTTC
++
+A:>>DEECB@D@@AADAC?EEC@AC?EEEB?
+@cluster_389:UMI_AATTCC
+TTGCAACCATACTCCCCCCGGAACCCCCCAG
++
+CC:7A?5=3B:?>?<<<;;0.0995;;;721
+@cluster_391:UMI_TCTATA
+GTTCATTTTGCCATGACTAAGCCACTATAAA
++
+AEBA@EEEC6>A@BB=?A@?B>A=?A?C@D?
+@cluster_400:UMI_TCCGTG
+GTGCGCAAAAGTTTTATTGTAAAAAAAGACC
++
+00).1(/9;//=D?40=424@DB83::7359
+@cluster_406:UMI_AACGGC
+AGATGGAGTCTCGCTCTGTCGCCCAGGCTGG
++
+?=<BB>=AB?D=B?D?C@B=B><A?A@4CB@
+@cluster_410:UMI_GTGTTA
+TGGTGTGTGGGATGGAGTCTTGCTCTGTTGC
++
+BB@A@A@AB=><BB>;AB?DC:?D?C@EC:>
+@cluster_434:UMI_CGTCAC
+GACAGTCTCACTTGGTCACCCCCCAGATCGG
++
+@=??AB?DA=?DCB@BA=@<<<<A>.47=</
+@cluster_438:UMI_CCGTAA
+AAAGTTCAGCTTTTTATTGAACATGTTATAA
++
+DD?AEBA?B?DEEEC?ECB@@?@B@EC?C@@
+@cluster_444:UMI_ATAGAA
+TGGTACCCCCCCAAATCGGAAAAACACACCC
++
+BB@?=@<<<<;AAAA?==>@DDD??=?=@<;
+@cluster_454:UMI_GAATGG
+ATTTCATAATTCTCCTTTATTAGGCACAGGT
++
+;EEBA>C6?E??D?>DEB:C<<A<:<>?A=1
+@cluster_456:UMI_ACTGTG
+GCTAGCTTTCTATTTGTAAACTTTGTGTCGG
++
+>?A=B?BEB?@?EEC@C@D@?DEC@A2A==@
+@cluster_464:UMI_CCCGTG
+CCCCCCCCCAAATCGGAAAAACACACCCCTA
++
+><;:<<<;AA>2>=71@DCA=7797@86;@6
+@cluster_470:UMI_GCTTTC
+CTGAGACGAAGTCTCACTCTGTCGCCCAGGC
++
+>CB===?@@?AB?DA=?D?C@B=B><A?A@4
+@cluster_475:UMI_TGTCGA
+GTACCCCCCCCAAATCGGAAAAACACACCCC
++
+1>:@<<<<<11AD?75=3@DDD?><<:@<64
+@cluster_485:UMI_CATTCC
+CAGCTTTGCAACCATACTCCCCCCCCAGATC
++
+A?B?DEC::A@@A@C=?D?<<<<<<A?=<??
+@cluster_490:UMI_TAGGCC
+AGAATCTTAAACTAAATCCTTTATTTCAAAA
++
+?=@A??DC@C??A@DA??2DEC?EEB9ADD=
+@cluster_492:UMI_TCGTAC
+CCCCCCCAGATCGGAAAAGCACACGTCTGAA
++
+<;;7<;@?=<?==>@D;?B:=?=?@2?CB@?
+@cluster_496:UMI_GTATCA
+ACGAATGAGGCAATTTATTAACCCAGCATGG
++
+@?@@ABB=A@:AAEEC?EC@@@<A?B:@BB@
+@cluster_510:UMI_TCGTGC
+GCAACACGTTTATTGAGAGGCAGTTGTGCTC
++
+=:A@?=?@ECC?ECB===:::>AEC@A:?D>
+@cluster_519:UMI_CTTAAA
+GGTTGAGCACAGGGTACTTTATTGATGGTAC
++
+A@ECB=B:=??A=@C=?DEC?ECB<BB@B=>
+@cluster_523:UMI_TGCCTG
+TTGCAGATTTCCTTCATCAAATTAAAACAGT
++
+4B::?=.DDB9<DBA@?A@DAEC@DD@>?A?
+@cluster_525:UMI_AGGGGC
+GTTCGTTCAAGTGCACTTTCCAGTACACTTA
++
+@EB=@EBAA?AA::=?DEB?A?AC=?=?DC<
+@cluster_533:UMI_GGGGTC
+GGTACCCCCCCCCAGATCGGAAAAACACACC
++
+:@C=@<<<<;;;A?:<>=<9;C@A?:=:=@1
+@cluster_536:UMI_GTTACA
+CCCCCCCCCACATCCGAAAACACACCCCCGC
++
+@<;;<<;3A=./46-77@A?/231517900-
+@cluster_542:UMI_CCGACA
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEB
+@cluster_559:UMI_TCAACG
+CCGGCACTAAGTCAAGTTCTTTACTTCCCCA
++
+>==@:=?A@?ABAA?AEB?DEC=?DB?<<A=
+@cluster_564:UMI_TTCGCA
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEB
+@cluster_569:UMI_GGCTCC
+GCAGAACACTTCTTTATTATAGCAACATATA
++
+B:?=@@?=?DB?DEC?EC?C=B:A@?@C?B=
+@cluster_578:UMI_GGGCTA
+GGTACAGACAGGATCTCACTATGTTGCCCAG
++
+A@C=??==??A><??DA=?A?B@EC:><A?B
+@cluster_587:UMI_TTCCGC
+CCCCCCCAGATCGGAAAAACACACGCCTGAA
++
+<<<<<<A>=<64=>/DCD2>=><?<<>@;@?
+@cluster_591:UMI_CAGGGC
+CCCGGTCTAATGTTGCTTTTATTATTTTGAA
++
+<<==@B?A@AB@EC:?DEEC?EC?EEECB@@
+@cluster_597:UMI_TTTTGG
+GCGTAGGGGTTTTAGGTAAATGTCCTTTGAA
++
+9?@C8A==@7AEC,:/C<DA=@B=>6EB1:>
+@cluster_604:UMI_TTAAGG
+GCTACTACCACCAAGATCTGCACCTGCGGCG
++
+;?@=?@=@A=:A<?=;??C99=>>C:>;@;8
+@cluster_613:UMI_CCCGTC
+TGTTATATTTCACATCATTTTTTCCAGACAT
++
+C3BC/C?EB22-<76><BDEE5B?A:4;:?4
+@cluster_619:UMI_TGTGAC
+CCAGATCGGAAGAGCACACGTCTGAACTCCA
++
+<A?=<?==>@?=<B:;:=?@B?CB@@?C?85
+@cluster_622:UMI_TGGCTG
+GAGACAGAGTATTGCTGTGTCGCCCCCCAGA
++
+====??==AC?EC:?=@A@B=B><<;<A?<:
+@cluster_632:UMI_TGGCAA
+GAGATGGAGTCCCCAGATCGGAAGAGCACAC
++
+===<BB>=AB?<<A?=<?==>@?9=B:=?=@
+@cluster_638:UMI_CCTTAG
+TACTTTAAAATGCTTTATTGGAATTATTTTG
++
+?=>DE>@DC5A:?DEC?E;B>@3EC>EEE:0
+@cluster_649:UMI_GACGGA
+TTTTTTTTTTTTTTTTTCACACCCCACACAG
++
+EEEEEEEEEEEEEEEB11,.,/<<6./-//3
+@cluster_664:UMI_CGCCGG
+TCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+B?<<<<<<<=ADA?==>@DDD??=>=@:<5*
+@cluster_674:UMI_CGTTTC
+AGACAAGTTCTCGCTCTGTCACCCAGGCTGG
++
+?==?A?AEB?D=B?D?C@BA=@<A?A@?CB@
+@cluster_676:UMI_AGGTAG
+TGGCATTTTTAATTTAGGTTTGTTTTATTTA
++
+AB@:@EEEEC@AEEC=A@EEC@EEEC?EEC=
+@cluster_680:UMI_CCGCTA
+TCTGATCTGACATTATTTCTATATTTTTAGA
++
+??CB<??CB=?@EC?EEB?A?C?EEEEC===
+@cluster_682:UMI_GTGCAC
+GTTTTTTTTTTTTTTTTTACCCCCCCCACAC
++
+8EEEEEEEEEEEEEEEEB=@<<<<<;=4/40
+@cluster_687:UMI_ACGAAC
+GACACTACTCTCCCACATCGCGAGAGAGCAC
++
+67/-01:5<::?:@5120+6531.8--2-68
+@cluster_690:UMI_ATTTAG
+GTTTTTTTTTTTTTTTTTTTTTTTTTTTCTG
++
+1EEEEEEEEEEEEEEEEEEEEEEEEEEB?:)
+@cluster_693:UMI_CGGCCA
+CTTTTGAGGCTTTTTCGTTGCCAGCAAGGGC
++
+?DEECB=A@?DEEEB=@EC:>A?B:A?A=@<
+@cluster_700:UMI_ATCGAA
+GCAGTTTTTACATTTATTTAAACAGAAAACG
++
+B:?AEEEEC=>@EEB?EEC@4>>?=@DD??B
+@cluster_711:UMI_CTCCGA
+ATTAATGAAAACATTCTTGGCAAATGCTTTC
++
+=EC@ABB6DD@??=B?DCB@:@DAB5?<EB=
+@cluster_715:UMI_CTGTCG
+TTTTGGGGCCCCCCCCAGATCGGAAAAGCAC
++
+EEEA1<<@>;<<<<<A6=;=:67>C@=B869
+@cluster_717:UMI_CAGCCC
+TCAGCTTTGCAACCATACTCCCCCCGGAACC
++
+DA?B?DEC:8A?@A@C=?D?<<<<;=>@@@;
+@cluster_721:UMI_TTGTTC
+GAGACGGAGACTCACTCTGTCGCCCCCCAGA
++
+3===>:><=<8AA683<;5912.<<;;>3./
+@cluster_727:UMI_TTTACC
+TTCTGAGCCTAAATGCCCTCAAAGCCCGTCC
++
+DB?CB=B-=?@DA@7>;>B8AD8?>;7:<?*
+@cluster_731:UMI_GTCACA
+TTGCTTCACTGACTTAACTCAAATTTCTTAA
++
+EC:?DBA;?CB=?=B@@?DAADAEEB?AC@?
+@cluster_742:UMI_GAGACC
+TGAGTGGGAGTCTCGCTCTGTACCCCAGGTG
++
+21,005-;,252605262746,/2231;54/
+@cluster_757:UMI_TTGCAA
+TCTTTGCACACTTATATTTTTTTTTGTGTTT
++
+?4?<<6:+?:16@3707EEE<E;EC1303DB
+@cluster_766:UMI_TATTGG
+CTTCCCAGTAACTGAGAGAAAATTACCATTC
++
+?DB?<A?AC@@?CB====@DDAEC=@A@EB;
+@cluster_775:UMI_CCTGCA
+GTGCAAAAACTGAATGTAGTCAATGGTCTTT
++
+AA::ADDD?>CB>AB?C:ABAAABB@><@EA
+@cluster_780:UMI_GTTGCA
+GGAGTTCCTAACCCAACAGTAATATCATTAG
++
+7.-072.0/7//33377781/46-/1371-<
+@cluster_792:UMI_CGGCAC
+TGTCACCATCCTTCTTTTCTTCTTCCTCATC
++
+@6>6,430:45?=;CDD:7A:7DA<9<7:70
+@cluster_796:UMI_ATTTGA
+TAGTCAGCTATTTAATTAGGTTCTTAAGACA
++
+@=ABA?B?A?EEC@AEC=A@EB?DC@?==?8
+@cluster_805:UMI_CGTGGG
+GTACTGCTCAAGCGCTGTCTATATCTCTCTA
++
+04904,.12:08/2/>16/74@4213<8.0.
+@cluster_809:UMI_CTTTTA
+CACAAGGAATATCATTTTATTACTGTAATCA
++
+?=?A?A>@AC??A@EEEC?EC=?C@C@A?A=
+@cluster_814:UMI_GGGCTG
+TTCTAGGTCCAATGGTAGTTTTTATTCCCCA
++
+DB?A=A@B?AAABB@@=A>DDEC?EB?;;@;
+@cluster_819:UMI_AGTATA
+GCTGTAGGAACAGCAGTCTTGGTGGTTAGCA
++
+B?C@C=A>@?>?B:?AB?DCB@AB@EC=B,<
+@cluster_824:UMI_GAGTCC
+AGCTTTGCAACCATACTCCCCCCGGAACCCA
++
+?B?DEC::A@@A@C=?D?<<<<==>@@@<@=
+@cluster_834:UMI_TTAAGG
+AGGGTGGGGGATCACATTTATTGTATTGAGG
++
+=A=@AB===>4?A=??EEB?EB@C?ECB=A?
diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_r.fastq.gz
Binary file test-data/SP1_r.fastq.gz has changed
diff -r 000000000000 -r 9839a3fe72f7 test-data/SP1_r.trimmed.fastq.gz
Binary file test-data/SP1_r.trimmed.fastq.gz has changed
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>