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Changeset 0:8bc80c2a15b3 (2019-11-28)

Next changeset 1:36093854bfc7 (2020-01-18)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit ee0a9acc788f8c313bb9fd91a42c6f9c66ac5bef"

added:
test-data/ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq
test-data/ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq
test-data/Tn4401b-1.fasta
test-data/Tn4401b_snp_profiles.txt
test-data/Tn4401b_struct_profiles.txt
test-data/output_summary_1.txt
test-data/output_summary_2.txt
tetyper.xml

diff -r 000000000000 -r 8bc80c2a15b3 test-data/ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq Thu Nov 28 14:41:08 2019 -0500

b'@@ -0,0 +1,4000 @@\n+@ERR1911133.214867/1\n+CGGCCACCTCGCCTGACCTCGGCATCCACGTTACGGACGGCCTCCGGAAGTCCTGGCCAAGCCCCGACTATTGGGGCGCGAAGATAGCACCGAGGG\n++\n+:3B>4BCB@EHEBE5DECFD=<EACED;F@AG=F./EF+3BD;F3C;@D90DD:<@EE?BCF9EEE1DB7GF509B?AF@>DBB;=CDD>D?5>=<\n+@ERR1911133.213998/1\n+CGGTTGGCAGCAGCACAATCGAGCAGCAGCCCCGTGCCCTTCATCCGGGTCAGCAACGGGTTGTAGAAGCTCTCGCGGAAGTAGCGATTGAAGCGC\n++\n+<CBCCCCEFHDGFFFFHFGEEGEFGDEHEFFEFDFDEFEFGEGGFEEDEFGFEEGHEEEDFFDFFEEHFFGFGECEECFDDGEFHEEFFCAA?A?@\n+@ERR1911133.215602/1\n+GGGCCAATAGATGATTTTCAGAGCCTTACTGCCCGTTGACGCCCAATCCCTCGAGCGCGAGTCTAGCCGCAGCGGCGATGACGGCCTCGCTGTGCT\n++\n+:+BB,BC<6?F>B7DFC?D9=58EDD<>=6E@/5;F=@:D:.C1FDF95D7A@FA;C;D=5F?1E:3EB:A0<EB>B9<==>?C;<AEB?@44?6@\n+@ERR1911133.216076/1\n+CCGATCCGGACAGCCGGATCATGAAACACGCAGGTGGTGGCTCCGAGCAGAGCTACAACGGGTACACAGCGGTCGATGCCGAGCACCAGATCATCG\n++\n+=@DBBC8ADBBFBDDFF;F4GFDEEFCH6E@.DDDG47GFD?EDEED8H=EDDEG6GGDF\'F-GDFDCFD:FCDF>0@BCB9DCF;D2E6EC@7A2\n+@ERR1911133.214611/1\n+TCGGCCCACTGGCTGAACGGCAGGTTCGAGGTCAGGATCATCGCCCCTTTCTCATAGCGCTTCGCCACCACCTGAAAGAACAGGTTCGCTTCCTCG\n++\n+$/85//8+:?2\'6</2+C7,8-86*-**035%:,:.+(&3/+2..3;),1%12))611/71,5=610=61/2221.30//6.+%%+2&02$03\'2.\n+@ERR1911133.766827/1\n+TTAAATTTCAGGCTTGCCAGAGATACAGCGTTTGTCGCGTCCTGCGTGGCTTTCGTGTCCTGGGCGTTCTTCACCTGGTCGATAAGGTCGGCCATT\n++\n+<?BBCDDCDE8DEEACEBFDDDCFFDFDEEFGGBFECFBFEDEEFEFE@DEEFEDFDFFFGEBCEEFGEEG@EAEFCBEEBEEFF@??EB@BC?C@\n+@ERR1911133.212322/1\n+CCACGTCGCAGAACGGAAGCTTCTCGTAGAATGCCTTTTCGCGCGCTTTCTCATTCTCGCTCTTGGGCTTGCGCCAGGTCAGTTTCTGCGTGTCCT\n++\n+5?AAA:C66F9/CE2B<F><D?A;<5A?6?:;D<?@?ED=82A/D=BB:DE<BBFEDD2<;A7:<DC:@EE:>5EFB44A7DE<>BFBBB99693;\n+@ERR1911133.216045/1\n+GGTGGTGGCTCCGAGCAGAGCTACAACGGGTACACAGCGGTCGATGCCGAGCACCAGATCATCGTGGCGGCGGAGTTGACCAACTGCGCCGCGGAC\n++\n+?BABCDBAEDDEEFEFFEEEEFGFFD9DDEFFEDEDBFDCEEEEFEAFEECDFEEGCBFGEFEDGE>DFDBCD3B;FB0BEB>?BD=CED@C?:1>\n+@ERR1911133.211148/1\n+ATCTGCAAGAGGCAATAGACCTTGGCATGAAGACTGGGCCGGCTGTTGGCAAGCGCCAACTCGGTTTCTGTCACAGCCAGATATTCCAGCTGCTGC\n++\n+C?@BDCEECEEFDGGFGFFDDFFDFDEFFFFGEEFFDEDEEDEEFFFFFDFEFDEDEFFDEDFFFGFDGEFDFDFEEDFFEEFFFDDEEDEBBC@@\n+@ERR1911133.213818/1\n+NAACAACACCTCGCGGGGCACACCGCCCAGATAGTCAAAAGCCAGCAACAGGGAGTCCCGCACGGACTCGAAGGATTCGTCCGGTACGAAGGTGAC\n++\n+!CBADCCECDFEGDFEEEDFDGDDGDCDHGFGGEEEGFHFFEEFFDFHDEGDDCFFEEDHDGDFFFDGDEFEEDFFFDGGEDFGFFDFEDCBD@?A\n+@ERR1911133.209816/1\n+GTCGATGTATTTGCATGGCGATGAGCTCGAGCGCGCCAGGCAGATGCGGCAGGCTTTTGGCGCTCGTCACGTCAAGCGAGGAGTCGACTGAATTTT\n++\n+C?@DCDEEGDFEHDGFGFEIGFCFGDEDFFFDEDEEEGGFDEGGFFDGFEGEFDFGFFGHDGDFDFFDFDFFDDFFDFAFCEFDDEECGDBBDCCC\n+@ERR1911133.2187233/1\n+CATCTGGAGGTCACGTTGTTTACGTTCGGTAGCGCTGAAGCGAACAGCGACAACCTTGACTGCGTGCCCGACCAGCAGCATGAAAAGGTGCTCAGC\n++\n+(3$164+C.6&)/1:&)/.E,.,2<>3D$:,/"8+F54(=C)3F:*6$-(<)3.E.C,AEG$4)C7-2*D0-6F;2/6,+9"-3)\'0<=,%1>*.;\n+@ERR1911133.211477/1\n+TCCTGCTTGAGCGCCGCCAGTTGCGACAGGGTGTCATCACGGACCAGAAGCTGGCTCAGCGCGGCCTTGGCAGATTCGTCCAACGCTTGCTCCAGC\n++\n+;?A?CBDB>?C;=8E:4EFE<C?C<5DDDD34DADEG<BDB/5E6??>>CC@D?<FB:EDCF83=9FGEDD2<89FBDFEDE;@<E?FBC:BB?=@\n+@ERR1911133.211333/1\n+CCCCGGCGTTACGTCACGCCGCACGGTCCGTGCGGCCTGCTGCTCGAGCTGCGGCAGGAAGGCGGCCGACCACGGCCAGTAGCCGAATAGTTTGGC\n++\n+<?>A>>CA:CEA=E?FBC23>DG>=BFCE?F:86D;?DC?6E>4BF.<<EB79D:8<DD;D75C->E@.;CC;89A44=?6<08DE480B0CB65@\n+@ERR1911133.213376/1\n+CCAAACTAGCCCAGGTGGATCAGTTTTACTTCGCTGGGGTGGGTCAGTTTTACACTGCTGCTAACACGGAACCGCTGAAAATTCCGTCACTCCAGT\n++\n+<@CBCBDCDECEEC@>EDEFFGEFGGGGHHFEEEGDBCC:DEBGFGEFFFECEFEFDEFDEFDEDFEEDFFEDEEGFDFDCHFFFDFFEEECD?>C\n+@ERR1911133.213063/1\n+GCCGACCTGGGAAATGGACGAGCGTAGCTGTTGGTAGGACTCGAGGCGATTTTGCGAGCGGTGCACGTTGCGTTCCAGTTGCGGATCGCGCAGGTA\n++\n+93A.?:42:71./DD.5*E5F/8C07/+96/8E=+B2?.:39>44EE25E>B5>9:EA9D3;C(3=C13,.1D/8))413A8E<.<;6<B0)*.96\n+@ERR1911133.213183/1\n+GGCCGCCTCGTACTTGGTCACCAGCCGCGACAAGATTGCCGAGTTGTAGAAAATGATCGTGTTGGCGATCAGCCGTGCGCACTGGTTGCTGATCTC\n++\n+@C@2B17EBEFCDEFEC?DEC?@BDCCDECEEBC>FFH.?E:DEEFE@CEDCAEEDF:EFCFFCED<AFC<9<:FF=9D8-AFFFGF;AFBADBA8\n+@ERR1911133.215965/1\n+CCCAGACGCTGGCGGATGCGGGATTCCGTAGTGAGGCTGTTCTGGCAAAGGTCGCCGATCACCACGGCGATGTCATCGTTGCCCTCGGCCGCGAGG\n++\n+=@<CDCBCDDEBDEFAEF>D@FBFFDCFEBFF;@DAAFFGEDFAEDFGGEE2;E9D/?GDEDDF=9DD@4FA::?AD>;GCDDCFDAC>BBC:6>?\n+'..b'DFCCDFCFDDFCDEACC@@\n+@ERR1911133.214507/1\n+GTGGACCGAGGATGGCGCGGTTGAAGTATTCCTTCAGCCGCCCTTGTCGCTGCGCCGTGCTCAGTTGCAGCATCAGGTCGGCTGCCGTGATGAAGC\n++\n+C?CCDBBDCFEFFEEEFCFFEF=EEBBGFFDDEFDFEDDFBDEEECFCCDFEDDAD@>FDEDFFEFDDEDDEFDFE<EDECD8FDDDDD@EA@???\n+@ERR1911133.269686/1\n+AGCGATAAATGGTACTAACTAGCGACCCGAAACGTCTACACCACCTGGAGCTCGCACGAGCACAGCCAGAAGAATGGGCTGCCCAGCGCGGGCTGC\n++\n+\'"\'%#"%#\'\'.&*("$\',"""\'*")"*")#\'$-)##")$*4"#$.)-$,)$"""#&%(*"1+/%\',"%%(\'1&"%,"&*"-#5-\',*%$.(,0&#)\n+@ERR1911133.211161/1\n+TTGGCCTTGAATTAGCCGATCTGCAAGAGGCACTAGACCTTGGCATGAAGACTGGGCCGGCTGGTGGCTAGTGCCACCTCGGTTTCTGTCACAGCC\n++\n+:8/3?BDFB:-0E;8:FE4=9F69F2=*67G<,7647;=ABDF81FE;9>0D?6/>@7BD7:?2DE8E/9>&12E7..ADCEE52F?E>85C.3:8\n+@ERR1911133.211880/1\n+AGTGGACGAAGATGGCGGCGCATGCGGTCGGCCAGCCCGTCCACCGCCTGCCACTGCAAGGCCAGCTTGCTCGCCGGCTTCACGCTCATACGCTGC\n++\n+BCBBBECCFGGEEC?F>DEEEGFDDAEEFDEEFDCEEFAEDEDFFEEFGDEDFFFEECGDDFEEDDGGEFGEFEECBEFFEEFEFGEFFCD@BB>@\n+@ERR1911133.215052/1\n+TTAGCGAATGGTTCCGCGACGAGGTTGGTCAGCGCGGTGGCAGAAAAGCCAGCCAGCGGCCATGAGAGACAAGACAGCAGAACTAGACGGCGATAC\n++\n+;?BCBEEDDFECEDCEDEFADECGDED?FEFFDEAFEFFEDEHGEFFF?CEECDCEAEFDDFFFCGCFCDFEEDDFFCFFDFDFFFECED;B?C?@\n+@ERR1911133.2021922/1\n+GCCATCCTGCATTGGTTTGGCCGGCGGATCCGCAGGCGGCTCACCGTCACCAATTCGAGATTGGAAAGACTCTGCAGCGGTGACGACTGCTCCAAA\n++\n+/?A9?B->D68DF4CCG@D=8E2EDD;3:DDD4+319@:,E=D@F2*?0=.?9"$F6))14F>-@;8*7;.E)+25.D3>0*B+8>-,8@%+\'9?7\n+@ERR1911133.211019/1\n+GAGGTTTCGTAGAAACATGGGGCATTTTCGATTCTACTGAAATAATCGTTATTATCGCGTTACTCGCTTTTCGAATCGCAACCTGTCCATATGAAA\n++\n+CCDDCDECDDGFHGGEHFGFFFDFFFFFDFFHGFFIEFGFGFFGHFEGFFHGGEFDHDFFHGDFDFDGGFFDFDGGDFEFEDDFFGDEFFCEA???\n+@ERR1911133.211479/1\n+CTTGGCGTCCTGCTTGAGCGCCGCCAGTTGCGACAGGGTGTCATCACGGACCAGAAGCTGGCTCAGCGCGGCCTTGGCAGATTCGTCCAACGCTTG\n++\n+=?ADDDDEDDG>DEAAFECDCD>CEDDFEFDE?HD;6FF@FDGECFEE6=DDG?GE:@C;C;6EFFD8?A@D@GEEDDFEC>FDFGDD<D-ADCA:\n+@ERR1911133.210867/1\n+CTCTCGCGCGGCCGTTGAACACTACCTGGCGGCACGCAAGGCCGCCGGTCAATCAGCGCGAGGGATGCTGGGGCATATCCGCCGCCAGCTCATCGT\n++\n+=?ACCCCBECDFEEFFFFHEGEFIDFGECFEDFDEDFHFACDFEFEEDGFGEFFGDEGEDFECDFGDFGDECDFFGCFFDDFFGHGEEEFEADB?C\n+@ERR1911133.214924/1\n+GGATGTAATCAGGCCGCTACAGCTGGGATTATCACCGAGCTTGAAAAACGAATCAGGTCGGCGTTCATGGGTCGGCCACCTCGCCTGACCTCGGCA\n++\n+?CABD;EFDC?F/D<EAAGCGFD=E?CHEFFHDEAFD4EDGG@EGFFGA79DCDGEBFDE:DF8FED76E0DB9GEDECC;CF@EGDDDBEC@?A@\n+@ERR1911133.210855/1\n+TGAACACTACCTGGCGGCACGCAAGGCCGCCGGTCAATCAGCGCGAGGGATGCTGGGGCATATCCGCCGCCAGCTCATCGTTTTCGCCAACAGCCG\n++\n+<BCBCDCCEECEBCEC?FEDEEGDC=CFCEEDDDEDEGEDADDEEGD5DFABEFDCCCEEFFFEEEEEDFDDEEFEBEFD?FEFECDDDBD@?A@=\n+@ERR1911133.215680/1\n+TGCCAATTGCAGAGAGCGCCGCCGCCATCGTCAGTGCTCTACAGAAAACCGGTCACACGGCTCTGCCGCGCAGACTCCTAGCCTAAATGTGACAGT\n++\n+;C@ADDDEDDFFHEGDDEDDBDDEDDEFDEEDGDDGDFDGDDGHFFFHDDFDFDGEHDFDEFDFEDDGDEDEE@DFECFEDDDFFEEFEECBB?@@\n+@ERR1911133.214187/1\n+TAATGCGTTGCCACCCGTTCGAGTTTGAGTTGCTGGCACAGGGCGTCGATCCGCTCATGCTGGAGGTTCATCGGCAGGCCTCCCCAATTGCGTCAT\n++\n+<CCBDBEEDFCDGDDEFFFCEEDEFFEFFFEG@FEGDEDGECFCGFDGGFDDFDEEGFGDGGFEEEEFDDFDE@DFGE>C=CCCD6E;G<D=9:6;\n+@ERR1911133.766902/1\n+AATTGTTTCTCCTGGAAAGCAGCCTGTAACATTTTCTCCTTGTATTCTGCAAGATCGCGCTGCTTATCGCGATACATTTCATACTGAAATTTGAGC\n++\n+ACABDCCCCD:DFFF8FGECGFDBFBDGCDEFFF@EFADGECFFEFDDECFDE>EEFDFDEEDFFFED>@FEDDDFF=FCCEFDFE@>;EEEA?@=\n+@ERR1911133.212638/1\n+CCGAAGTACTTGCGCGAATAGCGCGCCTTCACGGTCGGCCGTTCGACGCTGAATTTCTGCCCGTCGACGGCACCGTACAGCGTTTCGAGGTCGAAC\n++\n+=@DBCEBIDDFFDFDFFGFFFDECFDDFFEFDGCEFEFDEFEFCGFDGDEGEBFFFEFFDDDFFDFBDFDDEEDGFFCFGEFEFFCFAEDECA??@\n+@ERR1911133.211905/1\n+GGAGAGGTCGAGCGCAACGTACAGTGGACGAAGATGGCGGCGCATGCGGTCGGCCAGCCCGTCCACCGCCTGCCACTGCAAGGCCAGCTTGCTCGC\n++\n+CDDCDEEEDFGEEFDGHEGFHDIGFFEHDFGHGEFGEDGFDDDGFFEFFEDEEDDHGEDDEFDEGEDFEEFEEEGEFGGGEFFDEFFDGFBCDB@B\n+@ERR1911133.215994/1\n+GCTGCTGGGCATGCTGGCAGCAGTTCAGGCCAACACCGGAGAAATGCCGGCCCAGACGCTGGCGGATGCGGGATTCCGTAGTGAGGCTGTTCTGGC\n++\n+2?><@DB+BA;EEEFC7G;@DGD8=EFF2C7FEEEE@<>DCED>FC5A=AD=DF;AE;D68EDAD?4=D:DC6=BDD2C?6<3F4=/-9<E41>>-\n+@ERR1911133.212833/1\n+CCTGATACTGTGCTGGATCGTCAGCGCAGTAGAGTTCTTTCAATTGCGCGTTGAGGTCGGTGAAGCGCGGCTCGAACCGCCGGCCAAACCAATGCA\n++\n+:8ABCDAC?=F<E>D=@FD6B;7;?4ED94E;??;FAEAFE8>8>0979:;D2AE22?=/E/@@C@@ECDD;89C;<8(?@C-45E=G@B7?71?/\n'

diff -r 000000000000 -r 8bc80c2a15b3 test-data/ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq Thu Nov 28 14:41:08 2019 -0500

b'@@ -0,0 +1,4000 @@\n+@ERR1911133.214867/2\n+GTTGGTGTTGACACCGGCGTACCCTCGGTGCTATCTTCGCGCCCCAATAGTCGGGGCTTGGCCAGGACTTCCTGAGGCCGTCCGTAACGTGGATGC\n++\n+C=BC2BFDDFG:F5=DGD*>GD9F;D?0FFDE>DEDC>?DFBCD><GEEEDDE94EEF?3D7;F0;1B*E9DB6;2EDF@9CDB/8EDA9B?748<\n+@ERR1911133.213998/2\n+TGTTGCTGGCTTTTGACTATCTGGGCGGTGTGCCCCGCGAGGTGTTGTTCGACAACATGAAGACCGTGGTGCTGGAACGCGATGCCTACGGTGACG\n++\n+<DBCDCDDDEGFGFFGEGGFEFDDFDEFFFEGFFEFEEHFFDDGFFFFGEGDDEGDHFFGEGGEDEEGFEHDFFFGHCGDCFGGEDFHDEBEA?A@\n+@ERR1911133.215602/2\n+ATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGC\n++\n+B?A@BC;EDD7::5<48ADCFFD44D2F<FEAEFCEGFF3DDFBA2FDE>8DCFDF@>B<C>FEFD4?7;DDFD69;5FA65FDFG.-DD5E;,63\n+@ERR1911133.216076/2\n+CTGCCAGCATGCCCAGCAGCGCCTGACTGTCCGCGGTGCAGTTGGTCAACTCCGCCGCCACGATGATCTGGTGCTCGGCATCGACCGCTGTGTACC\n++\n+;6B=@CC8DDD>EEC<DFD6@4>FCDAEAFEE7ED83C;D@BDE5FADIDE7EE5ECEE8EE>DCFGG?9EE7E:ECCE:CFDF<FEDFBD?B>B@\n+@ERR1911133.214611/2\n+CCTCTGGCATCGGCCGGCCGCACCTCGCCATCGCCTTGGGTTACCACGCCGCGCAAGCCGGGGGCAAGACACGCTCCATCCCGGCAGCCGACCTGT\n++\n+6@@B75DC+4C+@,2:F,D55E(/8D9.D1+3ED3-@740>E-C.A,4C<6DGD)1-ED3-.F,DF:AADGD6-25E-763?F8E%469@/;6.4$\n+@ERR1911133.766827/2\n+GCCACGACGTCGATGTATTTGCATGGCGATGAGCTCGAGCGCGCCAGGCAGATGCGGCAGGCTTTTGGCGCTCGTCACGTCAAGCGAGGAGTCGAC\n++\n+C@@BBEECCDCEFEFEGFFFEDDEFACFGFAGEDEEDFFDEDECCEEECBF?EDDEEDFEDCFFFFDC2DD@DAFC9CEDEEFFBEEF<@B?B5=0\n+@ERR1911133.212322/2\n+GGTGAACTCTACCTCGACGACAGCCTGCAACACCGGCACTTCTCAGATGAACTGGTTGAGATGGACAGGAAGATCGATGTGCTCGCAAAAATGGAG\n++\n+CC8C>63E=DDCBEAC8C>FCDB>BA<DFCDG<D38D?D?ADF@AE>9D=DAFB74FDF<>9EFA?<FF:BED=D6B923C@FCB9=B:D73@?:5\n+@ERR1911133.216045/2\n+CCCAGCAGCGCCTGACTGTCCGCGGCGCAGTTGGTCAACTCCGCCGCCACGATGATCTGGTGCTCGGCATCGACCGCTGTGTACCCGTTGTAGCTC\n++\n+=@@CDCEDCFCEGFGEFEFCCFDEFDEDHFEGGEDEFFDFDDHDDFEDBDFCFEGFEFGGFGAFDEDDFEDEFDDFEFEFCEFCE?EFFDEBAAA?\n+@ERR1911133.211148/2\n+GCCCCATGTTTCTACGAAACCTCAAGATAGCAAGAACGGGCCATGAGCAAGAAGAACAAGCTACTCAGCGTCCTATCCGACGCCGAACAGGAGGCC\n++\n+??ABCCDADDFEEEFEFFFEEFEGFDFEEEFGEEFEDDCCEDFGFGDFGFACFEFHFDFEGFDFGEEFEDGFEGFFEECDEEFEDEEFEC????A@\n+@ERR1911133.213818/2\n+CTGATTTCGTGGTCTTGCGCCGGGCCAGATCCCCCATGTCGGCCTTCGTCGCCACGCTGGGATACAGCCGCATGACGTTTGTCACCTTCGTACCGG\n++\n+;?DACEDDEDHEEFFFEEEEED@>DEFFCGFEEFFDGDFEDEEFFFEDGFEDDDEEEGEDDFGFEFFFEDECGECECEFEDIEFFGHFECFABB@=\n+@ERR1911133.209816/2\n+GTAATCATCAATGAAGGAGTTCCCCTGGTCGTAAATGGGGTTCTAAGCGGGAATCCCAGAAAATTCCGTCATTCCGTATGATGAAAATTCAGTCGA\n++\n+??CCC?>G>CDEDFCCB?EEGDE9@FECE:EGBCAFDCDBDF?GG8D4FCAA=F>EECDEFE:FG1EFFFFHGEEFEEFDAFEFFEBFE8@<C;??\n+@ERR1911133.2187233/2\n+CTCCAGGGTCTTGATGACCGGGAAGCAAGCCATCCGCGTCAGAAGTTCGCGGCTGCGCTGCTGACGACACCCCGCTTCATGCCGCAACAGGTGTTC\n++\n+=)@2C-BCD2/92GFF).35/C093@<;.06C96D339F.D+\'<,FF392::/49:3D@88FC+=+0).23611<-10F-2<D>D*EB6A2;.74@\n+@ERR1911133.211477/2\n+GCTATCCGCCGAGCGCCGGCGCCTGGGCAATCTGCTGGAGCAAGCGTTGGACGAATCTGCCAAGGCCGCGCTGAGCCAGCTTCTGGTCCGTGATGA\n++\n+B?ADCBCCCDE68DE>DE5D?AD?F5CDB2EDF:DF;;F5DD>ICF;>F=6:E1G;E:FDC<EFAB:==3DC4AFCA;E;E?D>DE<CDD9B98?6\n+@ERR1911133.211333/2\n+ACAGCCGGCCCAGTCTTCATGCCAAGGTCTATTGCCTCTTGCAGATCGGCTACTTCAAGGCCAAGCATGCCTTCTTCAGTTTCGACTGGGACGAAG\n++\n+:?DEBCE0CD;:><D>EDADDDC<5CD0DF>FFAEEFEF3E8G@?F9>GE8DADE2A:@EEDCDF0:@9C9?89<ED8D=D?DF;CCF?D:8@77>\n+@ERR1911133.213376/2\n+ATCACAAAAATTTCGCCTGCGGCATGGCGGCACATCCTGCTCAACGGGCACTACACCTTTCAAAGCAGCGGCAAGACGATCGATCTCGATGCGATC\n++\n+B?@CBEEFEFFDFDFEDFGDDFDEFDDDEEDGDDEDEFGDEDGFBEDECDDEGDGEEFGFDGGFFEDFDDEDFDFFEDFFEEEFEGDFEEBCA?A@\n+@ERR1911133.213063/2\n+GACTGCGATCTCATCCATCGCGAGAAGCCGGACATCGACCGGATCGTCGCCACACTCGGGCTGAAGGAAATGACGCAGGGCACGCTGATCCGCAAG\n++\n+B0?B3<D259ECC/DCF78:;>C:=DCA311.35DD=514?=987/F*F1?66?DE,3"F9FB0?D*?;@:4=D@.20E9EADF*G@93C519:68\n+@ERR1911133.213183/2\n+TCAGCTACGCTCGGCCATTGCCCAGGTCGGCGGGAAGGAGGAACTGACCGGTCGCACCGACATTGAAATCGAGATCAGCAACCAGTGCGCACGGCT\n++\n+:8ABCD3C;8BABCD:=@@1A9><B8=F>D9D>0\';@,>C?C:+FB>.84<10E3?B<6.C;FECD6A=10614E353C96B=04698A:9<:7:3\n+@ERR1911133.215965/2\n+TTCGGAGCCTCCACGATCGACTTGCGCCGGCGGTAAGCTGCATCGCCTTGCTCCGTTTTCAATTTCGCCGCAATCGCCGCCGTATGCGGATGGGTC\n++\n+<?6BABBBDCDEDEEFFDEBCFFCDBE;;E?DD.5>0.9=:5=F25DFE8:<DE>8FFF?9BFFG87EEDE>BF>AE@B7?8=FDADB@88?>:A9\n+'..b'<C@BDEFFEDEFFE@CAAA\n+@ERR1911133.214507/2\n+AGCGGGGTGTCGCCAGCAGCGCAGCCGCGAACTGCTGACGCGGATGGCTTGCTTCCCGGGCATCAAGACCCTGGAGGACTATGACTTCAGCTTCAA\n++\n+AB:=:C<7BCC?EEDDFFBDCBFDDB4@@BDEGBEF=DDBDCC=FD?CFEBDFFEEE=@:EFAEFECEEEEEBE?@A=BBCECAEFFDD<DCCA>>\n+@ERR1911133.269686/2\n+CTTGAGCGTGGCGAGGAAGGCGCGCAATAACGAGAGACCGCCGCCATACCCTTGAGCGCGGATTTCCCGATTCAGGACGGTGGCAGGCAGCCAGAT\n++\n+>?AB5E3<DED@CDFDAG@8CFCDC?@FBCDF??AFEDD@CADCCEF>CCDFFD4:EDBF?G<FFDBDF0FDDDFB8DFE9E9CCEECED0;>?06\n+@ERR1911133.211161/2\n+TCGAAAATGCCCCATGTTTCTACGAAACCTCAAGATAGCAAGAACGGGCCATGAGCAAGAAGAACAAGCTACTCAGCGTCCTATCCGACGCCGAAC\n++\n+:6EB??<E3DBDDGFD9=FCEAECE?AD7GEAED7AFE=FEE>DCE;BECEEEC?@=FD<@GIACF7BDBGE:@BE@GFBEEEFD@?DCB>CA:79\n+@ERR1911133.211880/2\n+CGTGGCCGATCCCACGCCCTTCGGCGAGGTGCGGCAGCGCGCCTACAAGATCATGCCTCGCGATACGCTGCAAACCACGGCGCAGCGTATGAGCGT\n++\n+>CBCDDCDGDCEEGDFDEEGGDEFDGEFFFGDGEEGGEFEFDEEIDGHGFFDGFFEEFDIFGFFGEEEHEEEIDEEHDGGEFDGFDFFFECBAC@B\n+@ERR1911133.215052/2\n+TCGTTTTTCAAGCTCGGTGATAATCCCAGCTGTAGCGGCCTGATTACATCCGGCCGCTACACCTAGCTCCACCTTCAAACAAGGAATATCGTTGAT\n++\n+<?CCBDDCDFDEEFDDDBDFFGGFDEEEADFDBCDEB>D@FDAGF9DDFCFBDAECEFEGCFDFBAEGEFFEEFEE=DFDBADC>EFEDEA@D@=@\n+@ERR1911133.2021922/2\n+CCGACTGGCCGAATCAGGCACGCCTGATACTGTGCTGGATCGTCAGCGCAAAAAAGTTATTTCAATTGCGCGTTGAGGTCGTTGACGCCCGGCTCG\n++\n+?3E01:30:=.F<DBGF(CE/4D6A2E78?5/1DD?7+0F;8E42G#C@/D7.7+9F2&FF228?@8F+;46;2FED*76C,G>86;1(CB-AC+$\n+@ERR1911133.211019/2\n+ACGGCCGCGCGAGAGCTGAGTCCCGCGTACCAGCCGCGCAAGGCAGCCAGCGAATCCGCATCGGGAAAGCCGACTGGGGTAGAACTCGAAGCCGTA\n++\n+B@B?CBCCAECECECFGEFEFDEFCEDEEDFGDFFDEDEDEEBFGFEFGDFCFGFEECEFGFCDDFEGHFEDEEGFBCCEDFCFEGECDCACB?A@\n+@ERR1911133.211479/2\n+CGCCGGGGTTCGTCGCCGCCGAGCTGATCGTCTGGCTCAATGAGCACAAGATTATCCGGCCCGGCTATACGACCTTGCAAGAGTTGGTCAGCGAAA\n++\n+4A:BBD6/5?CBEE<FECD?CG:FF9?EA<=85B=8CF;DE::AFCEAGCBDCEFADC@EDFC:8FEGE:E5<=EFADBD=A11A4D@CBAC?;>2\n+@ERR1911133.210867/2\n+CGTGGGCAAGAGCCGGATCGCGCGTTCGACGGCACCCGCGCGCCCCTGTCGCTCTTCGGGGGCGTGCTGGAACACGTCGGCCAGATCCGGCCGGTG\n++\n+>EBDDECGFGGFEDGGHGEHDFDGFFDGHFGFFEEFEIDHDEFEDDFHGEIDGEGHEFGGEGDFFIEGFEGEEDDFFDGGEEGGFGDEEEDCA@B?\n+@ERR1911133.214924/2\n+GATTCAGGGGTAAAGTGGGTCAGTTTTCAGTTGGTGTTGACACCGGCGTACCCTCGGTGCTATCTTCGCGCCCCAATAGTCGGGGCTTGGCCAGGA\n++\n+??ABC@C61B5@<E6<6A-3DGEFBEFFBE?GE5FCCF;=EEDEE2D=?FFD7:EE87EDFDFD5BEE5D4C7ED<ECA9F77:BD9<8B@85+:3\n+@ERR1911133.210855/2\n+TCAGCGCCGAGAGGGTGTGGATACCGTACGCCTGCAGTGCCCTGACGGTCCTCGGAGACAGCCACTGGTCGATGCTGTCGCTGATCTGGGGCTTCG\n++\n+<@CDBEBCDGFFGFFDGFFHGFFFEDDHDEDDFEEGEFHDDEFIGDEGFDDEDDEGGGDGEDDFDGDFFEFEFDDFHFDFEEFGGDFFEDCCDCA?\n+@ERR1911133.215680/2\n+GGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGC\n++\n+?AABCBA6DFEEEF;@AEFDFEEC>BEFCE=DEECCEBDDEECEE@E7E@BDDDEFDAEEE@DEDBEGFFEAEE@EADCACEECFADBAB>??<>@\n+@ERR1911133.214187/2\n+CCCGTGTGCGGCGCGACGAGGCCCCCCTGCTGGATAACAGTCTCCGCCCGGTACCACTGGAATCTCTCCAGCACCCACTGTCTGTCTATGACGCAA\n++\n+;?ACCDDAD<<EFEBFFEFDDEEFDEEEDEFDDDFEEFDCFEFFFGEFEEBEFEEGEGFDCFFEGEFFEDEEEEEEBEFDEFFGFGHFEB@BAA?:\n+@ERR1911133.766902/2\n+AATGACGGAATTTTCTGGGATTCCCGCTTAGAACCCCATTTACGACCAGGGGAACTCCTTCATTGATGATTACATTAAGAACCCGGAAGCCACCCT\n++\n+AC;8C8B60<EEEF@EED8FBFE;D?;EFF>F@E9@C=D7DEDAC?EAFE?;<>@FD@?FD<FFC9DE@FG?DCE=C=C@<B;C>A9FCD:?BA@9\n+@ERR1911133.212638/2\n+AACTGACCTGGCGCAAGCCCAAGAGCGAGAATGAGAAAGCGCGCGAAAAGGCATTCTACGAGAAGCTTCCGTTCTGCGACGTGGCCGACGTGTTTC\n++\n+>CAC??CCD>=BCFEB@DDEFGDGCDEED@<GE@DCE@=DADCBEG@DCCBDFFFEF@EDBEA>CBFCEFEDGEFCEBBDBE7CF?DFEB?A>BA@\n+@ERR1911133.211905/2\n+GGCAGCGCGCCTACAAGATCATGCCTCGCGATACGCTGCAAACCACGGCGCAGCGTATGAGCGTGAAGCCGGCGAGCAAGCTGGCCTTGCAGTGGC\n++\n+?BABCBDCEEDEEFEFEFGEGFEFDFEEGEGGFGIEFDEDEGDFGEDDEDFDDEEGHGFFEFDFEFEFEFEAEEDCEDFDEGCBFFHFCDA@C??A\n+@ERR1911133.215994/2\n+CCGCCGTATGCGGATGGGTCTTGGCATTGACCTTGGCATCTTCACGTCCCTCGCGGCCGAGGGCAACGATGACATCGCCGTGGTGATCGGCGACCT\n++\n+=@CABECEDFCED?FDEECCEFBBDDDF=FEDG>CADEFEFEDFCFBDCDFDE@CEEDFG?9EEE=DEF?EEEDFDDBDE7EF6FACDE@D??AAC\n+@ERR1911133.212833/2\n+ATAGCGGCTACCAGCAGTACCTGCGCCAGGCAACGCTGCACGCGGCCAACGACTGCATCAGCAACGCCATCGCCACGCTACCGATCTTCCCATACT\n++\n+B?CCBE<CDHADG?DGFCFDEF9CFDDEB=EHEDCEFFDFBDCFEDDGGAEECFEDGFBGCCGFDFCEG>DEEBFCFCFEEEF>DCEFCCDAD@A?\n'

diff -r 000000000000 -r 8bc80c2a15b3 test-data/Tn4401b-1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Tn4401b-1.fasta Thu Nov 28 14:41:08 2019 -0500

b'@@ -0,0 +1,168 @@\n+>Tn4401b-1\n+GGGGTTCTAAGCGGGAATCCCAGAAAATTCCGTCATTCCGTATGATGAAAATTCAGTCGA\n+CTCCTCGCTTGACGTGACGAGCGCCAAAAGCCTGCCGCATCTGCCTGGCGCGCTCGAGCT\n+CATCGCCATGCAAATACATCGACGTCGTGGCGATCGACGCATGGCGTAGGTTGTCGCGCA\n+CCGCGGTGAGCTGAGCTCCCCGGGCCAACGCATGGCTGGCATGACTGTGACGCATCCAAT\n+GAGGCGTGGCACGGCGCAGCTTTTCGGCGGCGACCGGATGATCGGCCTCAATGGCCTCAG\n+CGGCTTGCGTAAAGAATCTTCGCAACACGCACCAAAGGTGAGGGCCGGTGATGCCGGCAT\n+TACCGTCTTCCCCAAGACTGCCCACCAGGGGCGTTTTCGGATTCCACCGTTCCCGGCTGA\n+CTGGCAGTTGACGCTGTGCCAAGTATTGGTCCAGCGCCGTATACGCGAGCGGCGGCAAGG\n+CCACCTTACCTGGTTTGCCACCTTTGCCAACCAAATGCAGCCAGTGGTCACCGTGCTCGT\n+CGAGGCGGACATTACCCAGGACGGCGCCGACCAGTTCGCTAGCGCGCAGGCCCGTGGCAT\n+AGCCGAAGTCGAGCATGAAGCGCAGGCGTTGTGCTGCCGGCTCGGACCAGCCGTAGGACC\n+ATTCCAGGCCGTCTGCAATGGCGCGCAGCAGTAGCCATTCTCCCTCGGTAAAGCCTCGCG\n+CCGTATCCAGTGCGGGCCGCAAGGCGTGACCGCGTACCTTGACGCCGGCGAAAGGGTTGG\n+CCAGCACATAGCGCTGCTCGATGAGCCACCGGAACAGCGCCGAGAGCACCGTCAGCGCAT\n+ACGCTGCCGAGCGTGCGGACAAGCCGCCCGAGAAGGGGCGCCATTCCACCGAATCGCGTG\n+GTCGAGGTGGCCCCACCCAACGCTCGCGCGGGGTCGGGTGCCGGACAAAGGCCCGGTACG\n+CGATTGCATCGTCCGTGGTCAGGGATGATAGCGCCCGTCCGCGTTCGACGATGGCCCACA\n+GGATTAGCCGCGCAGCCTCCTTGCGATAGGCGCGCTGTGTGGCGACAGTCTCGTGCAGCG\n+CCAGCCAGGCCTGCACGGCCTCGTAGTCGTTGGTCGCATTCAGCGTGCAAGCGTTGCGCG\n+GGGCCCGGAAATTGCCCTGCGAGCCGTCGACTTCGTTCGGCAGACGCAACTGCTCCCACG\n+GCACGATGCCGCTGGGCTGAATAATCGGGATCAGGGCCCGGGCGCGCTCGGTGAGCTGCG\n+GATGTGCGGCAAAGAAAGCCTCGACCTGCCGGGCGCCTGTCATGCCGAGTCCCTCGATGG\n+CTTTCCACCAGCCACGCCGGCGGGGAATGCGCACGGTCAGCGCCGAGAGGGTGTGGATAC\n+CGTACGCCTGCAGTGCCCTGACGGTCCTCGGAGACAGCCACTGGTCGATGCTGTCGCTGA\n+TCTGGGGCTTCGGCGCCGGCAGCGTGGGCAAGAGCCGGATCGCGCGTTCGACGGCACCCG\n+CGCGCCCCTGTCGCTCTTCGGGGGCGTGCTGGAACACGTCGGCCAGATCCGGCCGGTGGC\n+GGCTGTTGGCGAAAACGATGAGCTGGCGGCGGATATGCCCCAGCATCCCTCGCGCTGATT\n+GACCGGCGGCCTTGCGTGCCGCCAGGTAGTGTTCAACGGCCGCGCGAGAGCTGAGTCCCG\n+CGTACCAGCCGCGCAAGGCAGCCAGCGAATCCGCATCGGGAAAGCCGACTGGGGTAGAAC\n+TCGAAGCCGTAGTCTGGCCCGTTTTCATATGGACAGGTTGCGATTCGAAAAGCGAGTAAC\n+GCGATAATAACGATTATTTCAGTAGAATCGAAAATGCCCCATGTTTCTACGAAACCTCAA\n+GATAGCAAGAACGGGCCATGAGCAAGAAGAACAAGCTACTCAGCGTCCTATCCGACGCCG\n+AACAGGAGGCCTTGTATGGCCTGCCGGAGTTCGATGATGCGCAGCAGCTGGAATATCTGG\n+CTGTGACAGAAACCGAGTTGGCGCTTGCCAACAGCCGGCCCAGTCTTCATGCCAAGGTCT\n+ATTGCCTCTTGCAGATCGGCTACTTCAAGGCCAAGCATGCCTTCTTCAGTTTCGACTGGG\n+ACGAAGTCGAGGACGATTGCGCTTTCGTGCTGAGCCGCTATTTCCACGGCGAGGTGTTCG\n+AACCCAAGGCGATCACCAAGCATGAACGCTACACCCAGCGCGAGCAGATCGCCAAACTAT\n+TCGGCTACTGGCCGTGGTCGGCCGCCTTCCTGCCGCAGCTCGAGCAGCAGGCCGCACGGA\n+CCGTGCGGCGTGACGTAACGCCGGGGTTCGTCGCCGCCGAGCTGATCGTCTGGCTCAATG\n+AGCACAAGATTATCCGGCCCGGCTATACGACCTTGCAAGAGTTGGTCAGCGAAACGCTAT\n+CCGCCGAGCGCCGGCGCCTGGGCAATCTGCTGGAGCAAGCGTTGGACGAATCTGCCAAGG\n+CCGCGCTGAGCCAGCTTCTGGTCCGTGATGACACCCTGTCGCAACTGGCGGCGCTCAAGC\n+AGGACGCCAAGAATTTCGGCTGGCGCCAGATGGTCCGCGAGCGCGAAAAGCGCGCCACGC\n+TGGAGCCGCTGCACGCAATCGCCAAGACACTGCTGCCTAAACTCGACGTCTCGCAGCAGA\n+ACCTGCTGTACTACGCGAGCCTGGCAAACTTCTACACCGTCCACGACCTGCGCAATCTGA\n+AGGCCGATCAGACCCAACTCTACCTGCTGTGCTATGCCTGGGTACGCTACCGGCAGCTCT\n+CCGACAACCTGGTCGATGCGATGGCGTACCACATGAAGCAGTTGGAGGACGAAAGCAGCG\n+CTGGTGCCAAACAATCCTTTGCCGACGAGCAGGTGCGCCGTCAGCAGGAAACGCCGCGGG\n+TAGGCCGCCTGCTGTCACTCTACGTTGATGATAGCGTGGCCGATCCCACGCCCTTCGGCG\n+AGGTGCGGCAGCGCGCCTACAAGATCATGCCTCGCGATACGCTGCAAACCACGGCGCAGC\n+GTATGAGCGTGAAGCCGGCGAGCAAGCTGGCCTTGCAGTGGCAGGCGGTGGACGGGCTGG\n+CCGACCGCATGCGCCGCCATCTTCGTCCACTGTACGTTGCGCTCGACCTCTCCGGCTCCA\n+ATCCAGACAGTCCATGGCTTGCCGCGCTGGCCTGGGCCAAAGGTGTTTTTGCCAAGCAGC\n+AGCGGCTGTCGCAACGGCCACTCGACGAGTGGCCCGCGGCGACACTTCCGAAACGCTTGC\n+GGCCGTACCTGCTGACCTTCGACGCCGACGGTAAACCAACCGGCCTGCACGCTGACCGCT\n+ACGAGTTCTGGCTGTACCGCCAGATCAGGAAGCGTCTCCAATCGGGTGAACTCTACCTCG\n+ACGACAGCCTGCAACACCGGCACTTCTCAGATGAACTGGTTGAGATGGACAGGAAGATCG\n+ATGTGCTCGCAAAAATGGAGATCCCCTTCCTGCAGCAACCCGTCCATGCCCAACTCGATG\n+CGCTGACTGCCGAACTGCGCACGCAGTGGCTGGCGTTCAACCGCGAGCTGAAACAGGGCA\n+AGCTGACGCACCTCGAATACAACAAGGACACGCAGAAACTGACCTGGCGCAAGCCCAAGA\n+GCGAGAATGAGAAAGCGCGCGAAAAGGCATTCTACGAGAAGCTTCCGTTCTGCGACGTGG\n+CCGACGTGTTTCGCTTCGTCAACGACGAGTGCAAGTTTCTGTCGGCGTTCACGCCCATGC\n+AGCCGCGCTACGCGAAGAAGGTCGCCGACGCTGACAGCCTGATGGCGGTCATCATCGCGC\n+AAGCGATGAACCACGGCAACCACGTCATGGCGCGCACCAGCGACATCCCGTACCACGTGC\n+'..b'GGACTTCAGCTTCACCGACTTCCTGGAACACCTGTTGCGGCATG\n+AAGCGGGGTGTCGCCAGCAGCGCAGCCGCGAACTGCTGACGCGGATGGCTTGCTTCCCGG\n+GCATCAAGACCCTGGAGGACTATGACTTCAGCTTCAACCCCGGCGTGCCCAAGGCACTGG\n+TGCAGGAGCTGGGCAGTCTGGCGTTTGTCGAACGGGCCGAGAACGTGGTGCTGATCGGAC\n+CCTCTGGCATCGGCAAGACCCACCTCGCCATCGCCTTGGGTTACAAGGCCGCGCAAGCCG\n+GGGTCAAGACACGCTTCATCACGGCAGCCGACCTGATGCTGCAACTGAGCACGGCGCAGC\n+GACAAGGGCGGCTGAAGGAATACTTCAACCGCGCCATCCTCGGTCCACGGCTGCTGGTGA\n+TCGATGAGATCGGCTACCTGCCTTTCGGACGCGAGGAAGCGAACCTGTTCTTTCAGGTGG\n+TGGCGAAGCGCTATGAGAAAGGGGCGATGATCCTGACCTCGAACCTGCCGTTCAGCCAGT\n+GGGCCGACGCGTTTGCCGGCGATACCACCCTGACAGCCGCGATGCTGGATCGGCTGCTGC\n+ACCATGCCCATATCCTGACCCTGAGCGGCGAAAGCTACCGCTTGAAGGACAAGAGGAAGG\n+CGGGAGTGGTCAGGAAAAATTCCAAACCCGAATGATCCAGGTGGGTCAGTATTACTTTGG\n+TGATTCAGGGGTAAAGTGGGTCAGTTTTCAGTTGGTGTTGACACCGGCGTACCCTCGGTG\n+CTATCTTCGCGCCCCAATAGTCGGGGCTTGGCCAGGACTTCCTGAGGCCGTCCGTAACGT\n+GGATGCCGAGGTCAGGCGAGGTGGCCGACCCATGAACGCCGACCTGATTCGTTTTTCAAT\n+AGCGCTGGACGTTGTGGTGCCAGGGACTTACCAACCCGATGTGTGCCCATCCGGGGCAGT\n+TACAGCCGTTACAGCCTCTGGAGAGGGAGCGGCTTGCCGCTCGGTGATAATCCCAGCTGT\n+AGCGGCCTGATTACATCCGGCCGCTACACCTAGCTCCACCTTCAAACAAGGAATATCGTT\n+GATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTT\n+TTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTT\n+TGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCG\n+CGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCT\n+GGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGC\n+GCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGA\n+GCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGA\n+GTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCG\n+TCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTC\n+ATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGC\n+GCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCAT\n+CCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTA\n+TGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGC\n+CGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGC\n+GGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAAGGCTCTGAAAATCATCT\n+ATTGGCCCACCACCGCCGCCCTTGCGGGCGGCATGGATTACCAACCACTGTCACATTTAG\n+GCTAGGAGTCTGCGCGGCAGAGCCGTGTGACCGGTTTTCTGTAGAGCACTGACGATGGCG\n+GCGGCGCTCTCTGCAATTGGCAAGGCGTCGGCGCCAAGGATACCAATCTTGCGGCGCGCG\n+GCGTGTTATGACGACTGGGGTGCATTTGAGCCGCCCCATTTAACCTTCGCCCTCACAGAT\n+ACGCCATTCGCCTCAGATTTAGCGCCATGCAGACGAGCTTCCACTCGGCTTGCACCTTGT\n+CCAGGCCCCTCATGCTGAACTGACGCAATCCCATCACCGCCTTGATCCAACCATTCGGAG\n+CCTCCACGATCGACTTGCGCCGGCGGTAAGCTGCATCGCCTTGCTCCGTTTTCAATTTCG\n+CCGCAATCGCCGCCGTATGCGGATGGGTCTTGGCATTGACCTTGGCATCTTCACGTCCCT\n+CGCGGCCGAGGGCAACGATGACATCGCCGTGGTGATCGGCGACCTTTGCCAGAACAGCCT\n+CACTACGGAATCCCGCATCCGCCAGCGTCTGGGCCGGCATTTCTCCGGTGTTGGCCTGAA\n+CTGCTGCCAGCATGCCCAGCAGCGCCTGACTGTCCGCGGCGCAGTTGGTCAACTCCGCCG\n+CCACGATGATCTGGTGCTCGGCATCGACCGCTGTGTACCCGTTGTAGCTCTGCTCGGAGC\n+CACCACCGGCGTGTTTCATGATCCGGCTGTCCGGATCGGTGAAGCTTTCCTGATCACGGT\n+CATCCGGCACACCAAACTCGCGTTTGTACGAGCCACCGCCCTTGTCCGAGCCATCCGGAT\n+GGCGAGGCCGGCGGCCATCGTCTTCGCTGCGCCCCCGGGCCTGGTCCGCTTCACGCTGGC\n+GCGCTTCCAGGCGCGCCTTTGCCGCCTGGATCGCCTCCAGGCGCTTCTCGCGGCGAGAAA\n+TCTCGGCAGGAATGTCCAGCTCCGGCTCGTTACGCTCCTGGTCGTCGGTAGCCTTGGCGC\n+GATCAAGCAGCGCCTTGATCTCGCAATGCAATTCGTCCTCGGCCGGCTTCATGCGCTTAT\n+AGCTCATCGCCTTGTGGCGGCTGGCGTTGGCTTTTACCTTGGTGCCGTCGACCGCGATCG\n+TGCCAAGCTTCACCAGCCCACATTCGCGCGCCAGTTGCACCACCTGAACGAACAAATTCT\n+CAAGCTCGGTCAGGTGTAGGGCACGGAAGTCACTCAGCGTGCGGTGGGCCGGGAAGTTTC\n+CAGCGGCCAGCACACGCAACGCGACATCCTCGTACAGCTTCCTGGCTAGTTTGCGCGAAG\n+AGAAGACGCCGCTCGCGTAACCATAGATCAGCACTTTGACCATCATCGCCGGATGAAACG\n+GCTGATTGCCCGGACCACCGCCGGCATACCGGGCGTGGAATGCGCTCAAGTCCAGCGTAT\n+CGACAGTCTCGCTGATGAAGTAGGCAAGATGCCCTTCAGGTAGCCACTCTCCCAGAGAAG\n+GGGGCAGCAGATAGGATTGGTCGGGTCGGTAAGGAAGGTAACTGGCAGCCATCCCCGTAT\n+CGTCCTCGATCTTCCGCCGATTTGGCTTCTGCCGCGCAGGCTCCTAGGCCACCGTAGCTA\n+AACATACGAGAAAAACCGCTTCTTGAGCGCTCTCTGAGACCACCTTGCCGACAACGCAGA\n+AACGGTTGCGGAAAAATCGGCGTTTCCGGCGTACGCCACCCGACCTGGACGAACTATTGC\n+GGACCTGGAACTGGAGTAGCGGAATTCCCCGGGGTTTCAGCGTCGCGCCACAGCGCCTCA\n+GATAGATGCGGTAGCCTTTGGCGGGTCGTCATGCCGCGGACCACCCCCCCAAAAAATTCC\n+ACAATGCGGAATGGCGGAATTTTCTGGGGTTCCCGCTTACCCCCCC\n'

diff -r 000000000000 -r 8bc80c2a15b3 test-data/Tn4401b_snp_profiles.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Tn4401b_snp_profiles.txt Thu Nov 28 14:41:08 2019 -0500

diff -r 000000000000 -r 8bc80c2a15b3 test-data/Tn4401b_struct_profiles.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Tn4401b_struct_profiles.txt Thu Nov 28 14:41:08 2019 -0500

@@ -0,0 +1,11 @@
+Tn4401b none
+Tn4401a 7020-7118
+Tn4401h 6919-7106
+Tn4401d 7008-7075
+Tn4401e 6920-7174
+Tn4401_UA 7075-7153
+Tn4401_truncA 1-6654
+Tn4401_truncB 1-6727
+Tn4401_truncC 1-7127|9198-10006
+Tn4401_truncD 9985-10006
+Tn4401_truncE 9299-10006

diff -r 000000000000 -r 8bc80c2a15b3 test-data/output_summary_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_summary_1.txt Thu Nov 28 14:41:08 2019 -0500

@@ -0,0 +1,2 @@
+Deletions Structural_variant SNPs_homozygous SNPs_heterozygous Heterozygous_SNP_counts SNP_variant Combined_variant Left_flanks Right_flanks Left_flank_counts Right_flank_counts
+7020-7118 unknown none none none unknown unknown-unknown TAAAT TAAAT 17 13

diff -r 000000000000 -r 8bc80c2a15b3 test-data/output_summary_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_summary_2.txt Thu Nov 28 14:41:08 2019 -0500

@@ -0,0 +1,2 @@
+Deletions Structural_variant SNPs_homozygous SNPs_heterozygous Heterozygous_SNP_counts SNP_variant Combined_variant Left_flanks Right_flanks Left_flank_counts Right_flank_counts
+7020-7118 Tn4401a none none none 1 Tn4401a-1 TAAAT TAAAT 17 13

diff -r 000000000000 -r 8bc80c2a15b3 tetyper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tetyper.xml Thu Nov 28 14:41:08 2019 -0500

[

b'@@ -0,0 +1,170 @@\n+<tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy0">\n+ <description>Transposable Element Typer</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.1</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">tetyper</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ TETyper.py\n+ --threads \\${GALAXY_SLOTS:-1}\n+ #if $collection_paired.selector == "paired"\n+ --fq1 \'${collection_paired.forward_input}\' --fq2 \'${collection_paired.reverse_input}\'\n+ #elif $collection_paired.selector == "collection":\n+ --fq1 \'${collection_paired.input_pair.forward}\' --fq2 \'${collection_paired.input_pair.reverse}\'\n+ #end if\n+ --ref \'${reference}\'\n+ --flank_len \'${flank_length}\'\n+ --min_reads \'${min_reads}\'\n+ --min_each_strand \'${min_each_strand}\'\n+ --min_mapped_len \'${min_mapped_len}\'\n+ --min_qual \'${min_qual}\'\n+ #if $snp_profiles\n+ --snp_profiles \'${snp_profiles}\'\n+ #end if\n+ #if $struct_profiles\n+ --struct_profiles \'${struct_profiles}\'\n+ #end if\n+ --outprefix output\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="collection_paired">\n+ <param name="selector" type="select" label="Collection or paired reads" >\n+ <option value="collection">Collection</option>\n+ <option value="paired" selected="True">Paired</option>\n+ </param>\n+ <when value="collection">\n+ <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />\n+ </when>\n+ <when value="paired">\n+ <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>\n+ <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>\n+ </when>\n+ </conditional>\n+ <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>\n+ <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>\n+ <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>\n+ <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>\n+ <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>\n+ <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />\n+ <param name="snp_profiles" type="data" format="text" label="SNP Profiles" optional="true" />\n+ <param name="struct_profiles" type="data" format="text" label="Structural Variant Profiles" optional="true" />\n+ <param name="include_log" type="boolean" label="Include log in output"/>\n+ </inputs>\n+ <outputs>\n+ <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>\n+ <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>\n+ <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${'..b'------------------------------------------+\n+| SNP_variant | If --snp_profiles is specified and the pattern of homozygous and heterozygous SNPs corresponds to one of these profiles, then the profile name is given. Otherwise "unknown". |\n++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Combined_variant | Single name combining Structural_variant and SNP_variant, separated by "-". |\n++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Left_flanks | A list of distinct sequences passing quality filters that flank the start position of the reference. |\n++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Right_flanks | A list of distinct sequences passing quality filters that flank the end position of the reference. |\n++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Left_flank_counts | The number of high quality reads supporting each of the left flanking sequences. |\n++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Right_flank_counts | The number of high quality reads supporting each of the right flanking sequences. |\n++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n+| X_Y_presence | If --show_region is specified as --show_region X-Y, this column shows 1 if the entirety of that region is classified as present (i.e. no overlap with deleted regions), or 0 otherwise. If --show_region is unspecified, this column is omitted. |\n++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1099/mgen.0.000232</citation>\n+ </citations>\n+</tool>\n'