Galaxy |

Changeset 0:86fa46d3ce2e (2021-11-14)

Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"

added:
macros.xml
test-data/ngs_reads.fastq
test-data/ngs_reads.fastq.gz
test-data/ont_reads.fasta
test-data/scaffold.fasta
test-data/test_01.log
test-data/test_01_final_assembly.fasta
test-data/test_01_gapfill.log
test-data/test_02_final_assembly.fasta
test-data/test_03_final_assembly.fasta
test-data/test_04_final_assembly.fasta
test-data/test_05_final_assembly.fasta
tgsgapcloser.xml

diff -r 000000000000 -r 86fa46d3ce2e macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Nov 14 21:28:36 2021 +0000

@@ -0,0 +1,33 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">tgsgapcloser</requirement>
+            <requirement type="package" version="1.4.20">racon</requirement>
+            <requirement type="package" version="2.21">which</requirement>
+            <requirement type="package" version="1.24">pilon</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="11.0.9.1">openjdk</requirement>
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">TGS-GapCloser</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/gigascience/giaa094</citation>
+            <citation type="bibtex">
+ @misc{githubTGS-GapCloser,
+ author = {Mengyang Xu, Lidong Guo, Shengqiang Gu, Ou Wang, Rui Zhang, Brock A Peters, Guangyi Fan, Xin Liu, Xun Xu, Li Deng, Yongwei Zhang},
+ year = {2020},
+ title = {TGS-GapCloser},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/BGI-Qingdao/TGS-GapCloser}}
+ </citation>
+        </citations>
+    </xml>
+</macros>

diff -r 000000000000 -r 86fa46d3ce2e test-data/ngs_reads.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ngs_reads.fastq Sun Nov 14 21:28:36 2021 +0000

b"@@ -0,0 +1,8084 @@\n+@CL100050451L1C010R049_238898#554_496_307/2\n+GACCCTGACTTCAGAGCCCTTGCCTGAGGGCCTGGCCTGGCAGCTCTGCTGTTAGAAGCAGGAGGTGTGCAGAGGGTGGGGAGCAGCCCAGCCTCTGTGA\n++\n+B;EFC<=9DDCFBEDBF8E.F>;FD>;BFDEF.EEEFEDED=EF9F3DCEE9;@F>BDB@FF>FDAEDBFDF06FEBFBEF585?CF9EEEFE?E<F>ED\n+@CL100050450L1C014R006_28838#137_315_1367/2\n+GGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGGAGTCAGGGTCACCTACT\n++\n+B@BBA1;:EDB>;<D:6?C@DBCDCD?DCECEBBBD>9C9*2C+9D=C/>A7@DC?@@D41E1DDC79'8(E0&B=:<1D;4&/5,B0@113E5>D;<B:\n+@CL100050450L2C017R073_111136#137_315_1367/2\n+GGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACT\n++\n+FFFEFEEFEFFFFFFFFF;FFFFFFDFFFFEFFDFFGFFFD?FFF9EFEFFFFFFEFFDFEFFFDFF:BFFFBAFCFFFEFFCAFDFFFEFAEFEFEFFF\n+@CL100050451L2C012R081_202152#137_315_1367/2\n+GGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACT\n++\n+DEFEFBEEFD1DBFDEFFFF8BFFE5FDDFFEBFFFFFEFDBFDDFDF@FFFEEB>BEECC3FEDD?EFFEF9:DADEF4@F?9FB=FBEE7E:E1;FCE\n+@CL100050407L1C012R020_302181#36_815_466/2\n+GGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCC\n++\n+CFFEFFEFEFFFFFFFEFFFFEEFEDECFFEFEFF9FDFEFEFD8FFFFEFACDEFDFDF?FFFDEDEDFEEEFFEFFAB>DDDEF3?FF5FFFDFFEED\n+@CL100050451L1C001R075_152581#36_815_466/2\n+GGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCC\n++\n+:;=DEEE@BEFD@DEF1EFFD?EDCEEDFFEBAED?=ED;FFAE(ED8EEB9EBCEFFDEAEEFBDF:?A.=96DFCFAEFEEFFCCC<FEBC;E9CED4\n+@CL100050450L1C009R057_195293#172_1462_39/2\n+GGCCCTGGCAAGTAGGTGACCCGGACTTCAGAGCCCTTGCCTGAGGGCCTGGCCTGGCAGCTCTGCTGTTAGAAGCAGGAGGTGTGCAGAGGGTGGGGAG\n++\n+FDFFE;=FFEDFFFEGDFFFFG&F/F<1FFFEBCFFFEGCD:FG@FFFF8FFFF*FFFFFF?FDFFFFE@AFFEGFEFFBFFFFEFGEFAFFFEFFFFFF\n+@CL100050450L2C001R089_108384#582_419_63/2\n+ATCGGCCCTGGCAAGTAGGTGACCCTGACTTCAGAGCCCTTGCCTGAGGGCCTGGCCTGGCAGCTGTGCTGTTAGAAGCAGGAGGTGTGCAGAGGGTGGG\n++\n+FFFGFFFFFFFFEFFFDECEFFFFFFFFF9CFGGCFFFFF;>FF=FFFFFFF(FF<FEFFFEFF8%FFFDFB*FFFEEFFFFCFFFFFFFFFDFFFFFAF\n+@CL100050450L2C001R052_158600#441_387_721/2\n+AGATCGGCCCTGGCAAGTAGGTGACCCTGACTTCAGAGCCCCTGCCTGAGGGCCTGGCCTGGCAGCTCTGCTGTTAGAAGCAGGAGGTGTGCAGAGGGTG\n++\n+2D:-FFED6:5DFE9@:F<E@DB<CFFBD;E'+FC7AF:@C&=DBF6F3DFEEF*FEDF+FEF8@E*D*FF18,:-D=6BF6FB.FF=D2FF0F<F@DAE\n+@CL100050407L1C006R012_231273#432_927_1053/2\n+CCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGG\n++\n+FFEFEFFEEFFEEFFFFFFEEFEFFBFFEF?FEFFFEEFFFFDFEFFFFFEEFEEEEDFFFFEF>DFAFDFFFF@FFBAFFE@FDFD?BE;EFBCFF@FE\n+@CL100050450L2C014R041_378049#179_606_882/2\n+CCAAGATCGGAACNGGCAANTANGNGACCCTGACTTCAGAGCCCTTGCCTGAGGGCCTGGNCTGGCAGCTCTGCTGTTAGAAGCAGGAGGTGTGCAGAGG\n++\n+>F-?CB7FG3%%B!?@FFB!?=!F!EDFFGEF=FA-FFEFGG?FF1FFFCEFFFFFE>@7!G@GFFFFC<GEFG@GEF5FF@EFEEEDFFF@;FGE5FFB\n+@CL100050451L1C009R021_447765#179_606_882/2\n+CCAAGATCGGCCCTGGCAAGTAGGTGACCCTGACTTCAGAGCCCTTGCCTGAGGGCCTGGCCTGGCAGCTCTGCTGTTAGAAGCAGGAGGTGTGCAGAGG\n++\n+E9EAF-*FEFDFAFFFFDEFFDFFFFC7EFFFAF>BFFFAFDCF?AEFFB?EFFFFFBFFFFFFEFEFF9FEEFFFDEFFEFFEFFFFFEFFDFFEFEEE\n+@CL100050407L1C003R053_462172#24_803_901/2\n+CTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGC\n++\n+FFFAEFFFBEFEFFEGEFFEFFAB=FF4FFF@?F@@FFF4EBEE9FF=FE;DEE7EEFFFECDFF@FF*;F=FF>>E8>=>5BC.B:F?EB@8CG63GC9\n+@CL100050407L2C001R061_488869#24_803_901/2\n+CTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGNCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGC\n++\n+FFFFFFFFFFFFFFFFFFFEF<FF=FFEFFFBFFFFF!FEFFFFFFFFFFFFFFEFFFGFFFFFFFFFFFFGFFFFFFFFFFFFFFFEFFFFFFFFAFFA\n+@CL100050451L1C002R096_238410#24_803_901/2\n+CTNCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGC\n++\n+FE!FFCFFDFFFEFEFDFFFDC=FEFFBFFFFDFFFFEFFGF9FFFFFEFDFDF:CB;EEC7@FCFFEFE?DFEFFFF@FFEC>FE9EDFE@EFG6FBE5\n+@CL100050451L2C002R057_49097#414_338_347/2\n+GCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGCCA\n++\n+FFFGFBFEFEFEFFFGEFFFFEFFEFEFFEFFFGGFFFEFFFEFEFEGFFFBF"..b"GGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAGCTTATG\n++\n+FFDDFFFEFGFFFFFFFF?FEFGFFFF:EF;FFFF=FEFCFBFFEFFDFCFEF@FFFE9FFFFFFFFFFFFFFFFEFGFFF>EFGFFFFFFFFF@FFFFF\n+@CL100050450L1C006R091_70414#649_1162_107/1\n+TAAGCTCTGCATTCGAGGTCCACAGGGGCAGTGGGAGGGAACTGAGACTGGGGAGGGACAAAGGCTGCTCTGTCCTGGTGCTCCCACAAAGGAGAAGGGC\n++\n+F??1A0BA,A=?@=6C<6*>D9C>B646AA89:@:9)=0>>B7?@.=9<:<;?5@53:D9;8&;B7*D2=><8:>;17C9?,88<?DCB=;>931)866=\n+@CL100050451L2C012R024_108205#649_1162_107/1\n+TAAGCTCTGCATTCGAGGTCCACAGGGGCAGTGGGAGGGAACTGAGACTGGGGAGGGACAAAGGCTGCGCTGCCCTGGTGCTCCCACAAAGGAGAAGGGC\n++\n+@?@9=&@92&=E3<=D6-'5C:<>C8;8C<D<>@>;A18;/A66>C6<.CDCC2=@='E0468.E13@'F0>'>C;C>/7?8;@:6@>+BD,72-=97C;\n+@CL100050407L2C007R083_217356#344_873_127/1\n+TAAGCTCTGCATTCGAGGTCCACAGGGGCAGTGGGAGGGAACTGAGACTGGGGAGGGACAAAGGCTGCCCTGTCCTGGTGCTCCCACAAAGGAGAAGGGC\n++\n+G=1@C;GDAA)=+FD@6=FBG;DDDDF>DFFFFEEDBEFGF;FCCA8;.>GGBFEGBEDA6FCFDFAE&FFF1>A7CFF?CFD6@@F>E6>A=E@<B<GG\n+@CL100050407L2C016R035_180405#344_873_127/1\n+TAAGCTCTGCATTCGAGGTCCACAGGGGCAGTGGGAGGGAACTGAGACTGGGGAGGGACAAAGGCTGCTCTGTCCTGGTGCTCCCACAAAGGAGAAGGGC\n++\n+F>F4;BE9@=F=>:@FF2;(=FA12?F3E?AFAC3<<F7G17;GFAGFFE=8FABBCFF2F/9CFEF<AFDFFBFFGFFFE7FAF4FAF8FBFB3FFFF6\n+@CL100050450L1C015R093_246989#626_901_1426/1\n+TAAGCTCTGCATCCGAGGTCCACAGGGGCAGTGGGAGGGAACTGAGACTGGGGAGGGACAAAGGCTGCTCTGTCCTGGTGCTCCCACAAAGGAGAAGGGC\n++\n+C7EDD<E9EDCE+>FAFF5@9AE99FEFEEFAFFFFBEFFEBBFCFEF@FFFF:FFFFA@AEFFFC6F>FDE@FFEFFCFF<FFF9FFFEFFFFEEFFFF\n+@CL100050451L1C014R077_354768#570_1406_189/1\n+GCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAGCTTA\n++\n+FCFFFDFAFFFADFFFAE?CFEFF?FF7FDE@EEEFFFGFDFFFAFFCDFFBEFEFCF=?FFEFFFFFAFEFACFFFE9EE:FFFFD7FFFD2@AFEEFF\n+@CL100050407L1C004R065_31621#720_492_238/2\n+AGCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAGCTT\n++\n+4EFED67FC@FB@FFBEC/D+E<EF?<@DFEBCBDCC@F67D<EFFFACEBEEB1C;B8DCDEBECBFFCEDEDBEFF>FFECEEDFDEECEFEE>EFAD\n+@CL100050407L1C015R006_356975#720_492_238/2\n+AGCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCATTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAGCTT\n++\n+D>FDDA5CED?EFFEFCDFBDF5FEAEFBFFA9F>9CF1)96E5FED9CA9AEA=EF>EFBCE;4?/)DDE=EDDBFCE7FC3=E5ADB70DEBF@EFEE\n+@CL100050451L1C002R069_222115#518_281_1532/1\n+AGCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAGCTT\n++\n+FEFFGFFEFGBFFGEFEFFFFGFGEFGFEGFDAGEFEFBFFFEFEGEFFFGEEE9EFFFGFAEEFEFFEFFGEGG@GFFFE<7GFBFGFFFEGFEFFAG?\n+@CL100050407L1C009R092_229960#343_1510_481/2\n+CAGGCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAGC\n++\n+6(2D:DFBCCE7A9FDCFFF?:FF6CEDED@FDEB7E=DFF9FFE4D?E;@D.FEF=FBCEFC1ADC?@FE>DDFDD5FCEEFFCFD?DEED?AFDEBFF\n+@CL100050450L1C011R026_407688#291_293_339/2\n+ATCAGCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAG\n++\n+F?FDEFBEF9DEE<;EFEEFDEECE@0;DEDEFFEFDDFD?FFC?BEEEFEBFEEFEBEFFFDFDE4CED?DDEFDE;EDFDFFBEF?3CEEFEFFFEFC\n+@CL100050407L1C011R074_18770#68_254_455/2\n+ATCAGCCCTCCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAG\n++\n+E70<DD>>;)C<C?E,DF>EFFCEF*F>8?<ED,FD@F@FEFEF@A?=DC8CCEEA@2F9FEEB6DDF>F@@;>BE68AFEEFDE3FFCEEAC-FFE6EE\n+@CL100050407L2C008R009_473252#68_254_455/2\n+ATCAGCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAG\n++\n+F<FEFFFG6EECAFFFFGFFGFFFGFGGFGF8FFGFFFEFFF>CFGEFFGFFGDGCDFG@EFGCCFFFFFFFFFFEFFFFFFFGFEGFFGGFFFFFFGGG\n+@CL100050407L1C010R064_399725#253_6_203/1\n+TCTGCATTCGAGGTCCACAGGGGCAGTGGGAGGGAACTGAGACTGGGGAGGGACAAAGGCTGCTCTGTCCTGGTGCTCCCACAAAGGAGAAGGGCTGATC\n++\n+<G?FFBE>FFDFFEFFCFBFFFFFEFFFDFFFFFAE>FFFFF5FFFFFEFFFFFFFCEFFDFF=FFFAFFEFFFFFCFFFFFFFFFFFFFFFFFFFFFDF\n+@CL100050407L2C011R042_403162#21_223_258/2\n+CTGCATTCGAGGTCCACAGGGGCAGTGGGAGGGAACTGAGACTGGGGAGGGACAAAGGCTGCTCTGTCCTGGTGCTCCCACAAAGGAGAAGGGCTGATCA\n++\n+?FGFFFFEFFDEFFFFFFFDFFFFC=F@AFFFEAFEFDEFEFFFEEEFGFFF<GFFFDFFFFFGF>FFFFFBFAFFFFFFFFFF<9EDFFF;EFEB@FDF\n\\ No newline at end of file\n"

diff -r 000000000000 -r 86fa46d3ce2e test-data/ngs_reads.fastq.gz

Binary file test-data/ngs_reads.fastq.gz has changed

diff -r 000000000000 -r 86fa46d3ce2e test-data/ont_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ont_reads.fasta Sun Nov 14 21:28:36 2021 +0000

b'@@ -0,0 +1,92 @@\n+>a25b6205-6230-4808-969e-1c491dbcc416_Basecall_Alignment_template\n+CTTACTTCGTTCAGTTACGTATTGCTATTTATTAGGTAACAGTAGAATCTGTTTCTCAGGCAGGCATGGGAATTCTTGATATGTTACCTTTAGACGTGCTAAGCAACTGATAAATTTGCTGAAATTTGTCTTTATTCTTGAGGCACTAGAGGCTAAGTCTTAACCTTTAATAGTTCGGTCAACTTTTTGTCTAAAATTTTGTGGAGCTGCATCCACCTGTATGATGTAACTCAGTAACAGCTTCTTTCTACTAAGCCAGAACCATTACCTGCTGGTTTGTTTTAAATGTATGAGCTGTATTATATCACATTGATCAGTAAATGAAATAGATTCAGAGGTTATGGAAAGAAAGTACGGGCACACTAAAAATGAATTTGAATCTGGCGTGACACTGATTAACAGGTTGACAGATGGACTAGACCTGCATTCTAAACAATATTGAAAGGGAGGTGGTATCTTCAGCAACACGATAGGCCTATGAGATTTGAAAAGTAAATCGATTGTTTACCCATCTTCAGTCAATACTAGGTTAAGCGGAAAATTTGAACATTATTCCAAAAATGAAGTAGTAAATTATTCTCAGACTTAATATGATTAACAAGACTTCTGGGTATTTAAGCACAAATTAGTGATGAATATCCATTTGACAGATTCTTGATCTTATATATATATTACTACTAGTAAACCTAATACGATAGCTTTAATATATGAAATATTTGAATGTCTATCACTGTAGTGAAAATCAAGACATTATTTAAATCTAAATTTTGATTAAAATATTTGATATTTTAATTAGTGCCAATATTCATAGTATATTAGCTTACCCAGTTCTTCAGTATTCTGCAATTTTATAAAATATTAGAATTTGTGGAACATTTGTTAAAACAAAAACAAACAATCTTTTCTAAAAATCTAGACATCAGAAAATAGAGATATACTAATGTTACGCTATATAAACAATTTGCTGAACCCTACAGTAATCTGTGAAGTTTTGTCGTACAACAATCTTAGATTACCTAAAACAAAACGAGTTCTTTCTTCTGTAACACAAAGTCAAAATATCCGGACAGACTTAGGAACTGTGGCTGCCACTTTAAAAACAAACATTTCACCACGATACACTGTTTGTGTATGAACAGATGGAAAACCAACCTTTGAAGTTTTCAAATCATAAGCAGAAGCATTATTATAAACTTAAATATATGAAACAAATACACACAGTTTATTCTTCTTAATTTAAAGTATACTGTTCTTTGAACATCAGCATTAGACTATCAAAACCTCATAAGTCATACAAGTGTCAGCTGTAAAATTATAGAACTTGATAGTAAAAACTAAACAGCTACAGCTACAGTTTAGTTAAAAATAATAATAATAAGCTACTCTGTATTATTTGCCCTTGTGATGAGAATCACCTTTATTCATTTGGAACAAGCGAAATGCTGCAGTGGTAACTTGCTGAGTGGCGACTGCGATGGTGCATCTAGGGATGATAGGATCAGTGGACCAGAATCGTCAGCACCTTACCATGGTCACTGCTGTCTTCCTCTGTCATTCATTTATCAGACTTCTTCATGTTCCGTCTCTATCGTTGTGTGAACGGTTTGTACTGCTTTAGCATCTGCTTTGATTTCTGCTAATTTTCATGCGTTATCTTTCTGGTCCATCTTGGTAGCTGCTGTTCTCTTTGAGGAGTTCGCGCAACTTCACCCTCAAGTGTTTCTTGGTCATCCATCTGGCTCAAGCTGTCAGGCATTTTCCTGGTTCTTCTGTTCCTGGCGTCGAGATTTGTCAGAGACCTGGTTTTGGGGACCAGAGCTACCTTCTGCCCGCAGGCATCCTGCACACCTCCTGGCGGGCACCAGTTTCCCTTTAGTTTAGCCGAGAACGGAGAACCGCAACGTAGATAGACGCCACGTCGGGGTCGCCTCGGCTCTATTATGGTCATGGCTCAGCTTGGTGCGCAGAAACCGACGTCAAGCAGGTATTTTGCGCAGCTGGGCGAGCTTTCCTCGGCATGGGGCAGTTCCCCATCATCTTTATGCTGCCACCTCCGGCACAATCAGAGAGTTACACAGGATGGTGCAGGGGCCCAGAACACCGTGGAAGAGTCAGGGTGGAGGGCTGGAGCCAGTCTGGTAGCATGATAGCGCCTCACGCCTAGTGAAATCATACTACCACCTCAGGAGACAGAGACAGGCTTCCCCAACCAACCTCGCTCTGCAGCAGAGGAAAAATTATTTTCTAAAATAAATAAATAAATAAATAAACAAATGAATAAATAAGTATGGAAGAACTTTGCAGTTCTATTGTCAAGTACGTCTTTTTCTTTCATTTTTGTGTTTTCTCTTAATTGTGCTCTCCTGAAAGTCAGATTTCATGTTCTCCATCCTCACGTGGCAATTTAAATGTAATTATAATGGTCCCAAATTTAGAAACTAAAAATGTTAATGTATTTTACCCATGAGTAGGTTAACATTAAATTTTCAATAGTGCTCTCAATTCTACACTTCATTATTTTCTGTTGATCCTGTTAACTAAACTATAGAAATAAATAATAAAGTTTGTTGCATAGTTTCACAGTTTACAAATATTATTCATTCCTTTAACCAATAAATGTGTGACACACATGATATGCCATCATTTTGTAGCAAGTAAAATGAAAGGAAAGTTTTGATCTCTACTCCTCATGAAACTTCCAGTCTAACTTCATAAAATCTCATGCATTCCTGAGAAATTGGATACCTCTGAGTTCTATAAACCTCTACCCCAATCTGACTTCAGAGCACAGCTAAGAGGAAAAAGCAAAACAAAAAGATGAAAATGTGATTGAGTAAGATATGCAAGTTCTATTCCATAATTTTGTTTAGGAAATAGTTTTCATCTCTACTAGAGCAGAGGCTGGCTGGGAAACTGGGCTATCTATCCTCCTGCAGTGGTAGTGGTTGATCAGTCTCTGCTCAGGTGTGAGACCATGCACTGGAGCCTGGGCTACCTATTAACTCATCCCTCCTCCCAGGACTCTTCCGTGGTCACTCCAGGTATGTCATCCTGTACCATCCTTCTGATGGTAGAGGAGGTGGTAGCAGGAAGCTGATTGGGAGACCTGGCTCCATAAACGAGGAGGTTCACCCAGCTATGAAATGTCTGGATATTGTAGTTCTATGCAGTTAGCTGGACCTCATCCAGGGTTACAGCCAGGGCATCCCTGAGCTGGGTGACACCAGATGTGGATGCTCTGGCTGCTGCTATTGTTTCAGCACCCACCAAGTGCAAGAGCCACCCTGCAGGTGGAACGAGGTGGTAACCATGGTTCTGAAAACCACGCCTGCTGACAAATCAGATGCCACAAACAAGTAGGAGAAACTGCCCAGAGCAGGCAAATGAACGGACTGCAGACATCAGGGTGAGCCACCTGCACTTCTCAATCTGGTGCAACAAAGCAACCATAGAGATGGACAGAATGTCCTCAAGAAGTGTAAGTTAAAGGCAGATGCTAAACGCAAATCATTCATTACCACAATAGAAATAAGTTCATGAGGTTAATACAGGAGTTCTTAAGAATTATTTTAGGCAGTTAAGGGTAAAGAGTTCTTACTGGAATTTTCAGCACATAAAAGCAGCCCCAAACCATTTATTCTAACAGAAAGCAGCCTAAAAACTCAATCCGCAAACATAAGCAAGCTGAGGGTTGCATATGTAAATAAATGCCTGTACTAAAAGCCAGGTATATTTCAACATAGCAACTTCCTCTTCTTTTTCACCATGAGTGCAGATGTCATGGTGACAGCAGATAGTAGCCACGTTTGCAATAAAAAGGCTACGGTCGAAACCAGTCTTTTCTAGTATGTAATGTATGCCTGTTCAACCCTGGGCTATGTAAATCAATCACTCATAAGCCTCTCTACAAATCA'..b'TATGGGCAAGTGACTCATGTTCAAACACCAAAAAGCAATGGCAACAAAGACAAAATTGAGAATGGGATCAATTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACGAGTGAATATAGGCAAATCCTACAAATGTGGAAAATTTTCACAACCTACTCATCTGACAATGGCTAATATCCAGAATCTACAAGAACCTAAATAAATTTATAAGTAAACAACAACCTTATCAAAATTGGGCAAAGGATATGAATAGACACTTCTCAAAGGAAGACATTTATGCAGCCAAAAGACACAGGAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATAACATCTTACACCAGTTAGAATGGCAATCATTAAAAGTCAGGAAACAATAGGTGTTGAGAGGATGGGAAATAGAAATGGCCTTTACACTGTTGGTGGACTGTAACTAGTTCAACCATTGTGAAGCTGGCACCTCAGGGATTCAGAACTAGAAATACCATTTGACCCAGCCATCCCATTATTGCATATACCTAAAGGACTGCAATCATGCTGCTATAAAGACACACGCATTACATATGTTTATTGTGGCACCATTGGCAAAGACTTGGAACCAACCCAAATGTCCAATGCAACAAATGATAGGTTACGAGAAATGGGGCATATATATACCCATGGAATACTATGCAGCCATAAAATGATGAGTCATGTCCCTTTGTATTACGGATGAAATTGAAATTGTCATCTCAGTAAACTATCGCAAGAATGAACCAAACACCGCATGTTCTCACCATAGATGGGACCAGCAACAATGAGAACACTTGACACAGGAAGGGAACATCACACTCCAGGTACACAGTTGTGGGGTTGGAGGGATAGCATTAGACATACCCACGCTAAATGATGAGTTAATGCGTCAACATGGCACATGTATACATATGTAACTAACCTGCACAGCACATGTACCCTAAAACTTAAGGTATAATAATAATAATAATAAAAAGAAAAAGACAATGTAAGCGTTTGGCTTGAGATCGGGTAATGGTTCCACCATTGCATGCAAATTCAGGATTGAATACGATTTGTATAACTGTGTACTCCTAAAGAGACTGACACATCTACATGGGAATGGTCAAAGGACACCTTCTGGGTAGGAAGGTAATTTATCATTGACATAACTGAATAAAAATGTTCTTTGAAGCCTCTGAATCACTTATCCATTATACCAGAGAGCTGGTGCAGATCATGTGGTAGAAACTATATCAACCCACGACTTGGATTAGGTCTATTGTAATCTAATCAGCGGCAAATTTTGAATGTTTCTGTTTATTTGTTTGTCTTGTGCCAGACCAGTCAAAGAATCCAGTGTCAAAATGGAGACAATGAGGTGTTCATCATGGCACATTATATAAAAAGAGAAGGAGAAATGTTGCAGGAAGTCAGGGACCCTGAATGGAGGATCATGAAGCCGGTAGAAGAACATAAATTTGTGATGATTTTGTGGACATGTTAGTTCCACGCTTTTTATAATTTGCGATCTATCTTTACTGCAATCTCTGAACATAAATTGTGAGATATTTCATACATTTATCACTTCCCAAACCATACTTGTGTGATTTCATGCCTCTGTTGCTAAATTTAACCTATCATCTTCATAAGTTGAGGTGATGAATGCTGTCTTGTGACCGTGATGATTGTGTTAACTGCACAAATTGTTAAAACATTGCGCTACAACTTGAAAGCACAAGATAAGAGAGATGTTCAGGAATCTAGGGAGATAACCATTATGTTCAGCCATCTGAAAGAGCTGGCAGAACAGAACCATATTTCTTCAAAAGTAAATAGAGAAATATGGTTAATTCTTTTCAGCAAGGAGCAGCCTAGAAAGAGAATGCATTCCTAGGTGTAGGCCTTGAAATGGCCACCTGGAACAAGTCTGTCTTTTATGGATGTAGATAAGGACAGTCATTCTGGTTTCCCTATTTCCGATTTATTAGATGAAGAAATACCCACCCATAATATTGGTCGACTAGTTGTCTGTTTCAAACCGTTCTGATAGATGTTAAGAACAATAATGTAAAATAAACCATTAGCACTTTAATATCACCCTGTCCTGATCTTGCCCTGCCTGCATTTGCCTTGTGATATTTTATTACCTTGTGAAGTACGTGATCTCAGACCATCTATTCGCATACCTCCCATTTTGAAAATCACACAAAAACTTGTTGTGTTGCAGCTCAGGGCATCAAGCAGAACGTACAACATTGTGATGTTCCCCAGACACTCAACTTTAAAACTTCCTCTTTACTCTTCCCTTTATTTTCGATGGGTTGACATTATAGGGGAAATAGAAAAGGACTCACGTTGAAATACTGAGCTGATTTTCCCTGATAGGAGAGTTTCAAACCTACTACATCAAAATCAAAATTTAATTCTGTAAAGATGCAGAATACACACATCAGCAGTTTCAAAGACAGCTTTTTCTAGTTTTTATCTGGGGATATTTGGTTTTCACTATAGGCCTCAAAAGTCTCAACATTTCATACATTCTAAAAGTATGTTTCAATGCTGAATAAAAGAATGTTCAACATTGTGGTTGTTCCATAATGCGCAGTTTAACAAAGATATTCAGTTGTTATCTGTATATTTGATTTCACCAAAGGACTCAAAAGGTTTTCAAATGTCCCTTCGCGAGATCACAAAAGTACTGTTTGCAACCTGTTGAATTAAATGAAGATTTCACCTCTTGATGAGTCCATATCACAAAGAAGTTTTGTAATTCTAAATGTCTCTTGCAGATTCTACCTAAAGAGTGTTTCAAATCTGTTTTAATGAAAGAACAATTTAATCAGAGATAAATCCAATAATACAAAGCTGTTTTACAGGATAGCTTTTTCTGTTTTTATCTGGGGATATTTGGTTTTTCACCATAGCCACCATGGGCCCCTAAATGTCCTTCATGGATTTAACAAAGAGTGTTACAACTGTTAAATGAAAAGAAATACTTCAAACTGTGAGATGAATCCACACATCACAAGGCAGTTTCATAGATAGCAGTTTCAGTGTTTATCTGGGAATATTCGGTTTTTCACCACAGGCTCTGCTGGATTCTCAAGTTCTTCACAGATTGTACAAAAAGAGGTATGCAACTTACGATTCAATAGACAGGTTTGTCTGTGAAATGAACTACAGATCACAGGGTTGTTTCACAGATCACTTTCTGTATGAATCTGTGAACATTCTGTTTTTCTGTAGGTCCCAAAGCTCCATTTTCTCTTTGCAGATCCTAGAAACAGTGTTTCCAAAACATGATGTATCAAAGAAACGTTGACTCTTGTGAGAAGAATCCACACATCACAAAGAAGTACACACAGATAGCTACTTCCTGTTTTGAGGATTTTTAACTATACACCAAAGGGTTTCAAATGCCCCATGTAGATTCTACACAATAGTGTTTCCATTCTGAATTAAAGGAAAGGTTTATCTCTGAGATGAATCCACACATCAAAAGCAAATACAAACAGCTTCTTCTGTTTGTGTCTGGGGTATTCGGTTTTTCACTGCTTCCTGAAAGGTTTCAAATGTACCTTGCAGACCTATAAAAGAGTGCTTTAATCTGCTGAATCAAAGAAAGATTTAACTTTAGGATTTCAATCCAGATATATTTCACAAAGCAGTTTCATAGATAGCTTTTCAGTTTTTATCTGGGGATATTTGGTTTTTACCATATTCTAAGGACTTGAAATGTCCCTTGAAAGATTCTAACATAAGAGTTTTCCAATTTACCGAGTCAAAGTCATGTTTAACTCTGTGAAACGAATCCACATCAAGGCAGTTTCACAGATAGTTTGCCCTTTGTCTGGAAATATCTGGTTTTTCAAAATATGGGCTTAAAGTCCTTTATATCTCACGGTGAGGATTTCATGACCTGCTGAATCAAATAAACGTTTAATTTACTTTGA\n\\ No newline at end of file\n'

diff -r 000000000000 -r 86fa46d3ce2e test-data/scaffold.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scaffold.fasta Sun Nov 14 21:28:36 2021 +0000

b'@@ -0,0 +1,651 @@\n+>scaffold_1\n+TTTACACATGCACACATGGCTACTGATGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAGAGGGGGAACGGAGA\n+CCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAAATTCAGACGGGGAACTGCCCCTGCACATAGTGAACGGCTCACTGAGCAAACCCC\n+GAGTCCCGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggtgggcccagtgatatcagctgcctgctgttcccca\n+gatgtgccaagtgcattcttgtgtgcttgcatctcatggaacgccatttccccagacatccctgtggctggctccTGATGCCCGAGGCCCAAGTGTCTGA\n+TGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACGA\n+CATCCTCCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCATACTCCACGTGCAGAGCAGCCTCAGCACTCACC\n+GGGCACGAGCGAGCCTGTGTGGTGCGCAGGGATGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAAGGGCAGGAGGAGGGTGTGGGATGGTGGAGGGG\n+TTTGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAAAGGGAGGGGGAGGATGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTAGGGAAAGCTGGGA\n+TGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAACGTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTC\n+ACAATCCAGAAGTCCCCGTGCCCTAAAGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAG\n+GCACTCAAGCGACTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCG\n+GGGCCACCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTCTTAATTGACCCTAGT\n+TCCCAGGGCAGCCTCGTTCTGCCTTGGGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCcacaggggcagtgggagggaactgag\n+actggggagggacaaaggctgctctgtcctggtgctcccacaaaggagaagggctgatcactcaaagttgcgaacaccaagctcaacaatgagccctgga\n+aaatttctggaatggattattaaacagagagtctgtaagcacttagaaaaggccacggtgagtcccaggggccagcactgctcgaaatgtacagcatttc\n+tctttgtaacaggattattagcctgctgtgcccggggaaaacatgcaccacagcgcatctcgagtcagcaggattttgacggcttctaacaaaatcttgt\n+agacaagatggagctatgggggttggaggagagaacatataggaaaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactga\n+ttccagccttgcacggagggatctggcagagtccaTCCAGTTCATTCAACACCTGGTTAGAAAACTGGGGCCAGCACACAGGGGAAGGGTAAGCTGGTTT\n+CATGATCGAATCAAGGCTCAGACAATTTTTAAAGGCCAGAGGGTAGACTGCAATCACcaagatgaaatttacaaggaacaaatgtgaagcccaacattta\n+ggttttaaaaatcaagcgtataaatacagaaggtggagggaacttgctttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagc\n+tcagtaGGGGCTAAAAGCATGTTAATCGGCATAAAAAGGCAATGAGATCTTAGGGCACACAGCTCCCCGCCCCTCTTCTGCCCTTCATCCTTCTTTCAAT\n+CAGCAGGGACCGTGCACTCTCTTGGAGCCACCACAGAAAACAGAGGTGCATCCAGCACCACAGAAAACAGAGCCACCACAGAAAACAGAGGGTGACTGTC\n+ATCCCCTCCAGTCTCTGCACACTCCCAGCTGCAGCAGAGCAGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCAGGAGCTCACCTGCCTGCGTCACT\n+GGGCACAGACGCCAGTGAGGCCAGAGGCCGGGCTGTGCTGGGGCCTGAGCCGGGTGGTGGGGAGAGAGTCTCTCCCCTGCCCCTGTCTCTTCCGTGCAGG\n+AGGAGCATGTTTAAGGGGACGGGTTCAAAGCTGGTCACATCCCCACCGAAAAAGCCCATGGACAACGAAAAGCCCACTAGCTTGTCCAGTGCCACAGGAG\n+GGGCAAGTGGAGGAGGAGAGGTGGCGGTGCTCCCCACTCCACTGCCAGTCGTCACTGGCTCTCCCTTCCCTTCATCCTCGTTCCCTATCTGTCACCATTT\n+CCTGTCGTCGTTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTCGTATCCTGACTACAATAACAGCT\n+TCTGGGTGTCCCTGGCATCCACTCTCTCTCCCTTCTTGTCCCTTCTGTGACGGATGCCTGAGGAACCTTCCCCAAACTCTTCTGTCCCATCCCTGCCCTG\n+CTCAAAATCCAATCACAGCTCCCTAACACGCCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCCGTGGGCCCTAACTCACTCATCCCAACTCTTCACTC\n+ACTGCCCTGCCCCACACCCTGCCAGGGAGCCTCCCGTGGCACCGTGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGG\n+CCCACAGGCTCACGGAAAGTTAGCCTCTCATGCCCCGAGAGCTGAGTGCAAGGGAGAGGCAGCGCTGTCTGTGCTTCCCATGCAGAAGCACCCCCCTCCC\n+ACCCCTGTGCAGGCCGGCCTTCGCGGCAGACCACCATACACCACGTTCCAAGCCACACTGAGGCCTCCCTCCAAGCCTGCAGCCCCCATTTCCAGACCCT\n+GCCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCACgtggttttcctcttcagcaactatt\n+tcctttttactcaagcaatggccccatttcccttggggaatccatctctctcgcaggcttagtcccagagcttcaggtggggctgcccacagagctcctc\n+agTCTAAGCCAAGTGGTGTGTCATAGTCCCCTGGCCCCATTAATGGATTCTGGGATAGACATGAGGACCAAGCCAGGTGGGATGAGTGAGTGTGGCTTCT\n+GGAGGAAGTGGGGACACAGGACAGCATTCTTTCCTGCTGGACCTGACCCTGTGTCATGTCACCTTGCTACCACGAGAGCATGGCCTGTCTGGGAATGCAG\n+CCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCCGAAGGCTGCTCTACTGATTGGTTA\n+ATTTTTGCTTAGCTTGGTCTGGGGAGTTCTGACAGGCGTGCCACCAATTCTTACCGATTTCTCTCCACTCTAGACCCTGAGAAGCCCACGCGGTTCATGC\n+TAGCAATTAACAATCAATCTCGCCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGGCAGCCACATAATTGGTATCTCTTAAGGTCCA'..b'tccacacctccaacaagctg\n+cagtcgaccacaaagaagaaacaagtctgtctcccatgggtcctacccacaccccctgctgttcaccatgaatgatagagtcaacagtgtgaaaacgacc\n+atactgccaaaagcaacctacaaattcaatgcaattcccatcaaaataccaccatcattcttcacagaactagaaaaaacaaggctaaaattcacatgga\n+accaaaaaagagcccacatagccaaagcaagactaagcaaaaagaataaatctagaggcatcacattactcgacttcaaactatactataaggccatagt\n+caccaaaacagcatggtactggtataaaaataggcatatagaccaatggaatagaatagagaacccagaaataaagccaaatactttcagccaactgatc\n+tttgacaaagcaagcaaaaacataaagtggggaaaggacaccctattcaacaaatggtgctggtataattggcaagccacatgtagaagaatgcaactgg\n+atcctcatctctcaccttataaacaaatcaactcaagatggttcacagacttaaatctaagacctgaaaccataaaaattctagaagataagattggaaa\n+aacccttctagacattggcttaggcaaagacttcacaatcaagaacccaaaagcaaacacaacaaagataaatagatgggacttaattaaactgaaagcc\n+ttctgcacatcaaaataaataatcagcagagtaaacagacaacccacagagtgggagaaaatcttcacaaactatgcatccaacagaggactaatatcca\n+gaatctacaaagaattggaacaaatcagcaagaaaaaaaaccaaacaCAAGGATGACAGTGGAAATACAAAAACAAGACATAAATATTCTGAATAGTGAT\n+AATAAAACAGTGCATACCAGAATAcaaactgtttccaagttacaatggttcaaccatttttcagctttatggtggtgtgaaagtgatatccattcattag\n+aaaccatgctccaggatgggcgcagtgggtcacgcctgtaatcctagcactttgggaggccgaggagggcggatcacaaggtcaagagatcaagaccatc\n+ctggccaacatggtgaaaccccgtctctcctaaaaatacaaaaattagctgggcattgtggtgcgtgcctgtaatcccagctattcgggaggctgaggca\n+ggagaatcacttgaaccagggagtcggaggtgttgcagtgagccgagatcgtgccactgcctccagcctggcaacagagtgagactccatctcaaaaaaa\n+agaaagaaacccgactccgaattttgaattttgatattttcctggactaccaatatgtggcacaatgctctctcacaatgttgtgcaacagcggtgagct\n+gcagcttccagtcagccaaatgataataaaggtagataatccatcttgatatcttcctgaagaacataatgcctgcctaccatcaacaggcatcaatact\n+ttctaccagctattctcaaccctcatgatcggaagagacagagactgactgtgtcaaagtattagtcccatcattcagcaattaaccttagctcaatgct\n+tcaaaaattcttcaggccctgtgtaatttcagctacgtacattaatgataagtacccatacaaccattctgtttcttattttcagtaccatatttaataa\n+atatcagttattcaatactttatttagacattttgttagattattttgaccaactgaagtctaatctaaatgttctgagcatgttcaaagtaagctaggc\n+caacctataattttcggtgtgctaaatgcatttttaacttatgatattttcagtttacgggggtttgttgagacataacttcatcatacatcaaggagca\n+tctgTAtatgggatacagttaaagcagtgatcagaggaaaatctatagccttaacacatttattaataaaagtgtaggaattaaattatcagctgaaaaa\n+tgtaaaaagtatctaaaagagtaagcagaaagtacaagaaagaacccaaagtagaaaaaagtgaaaattaataaaataagaagccaaaaaacagatcaaa\n+tcagtaaaccaaaaatcttgttctttaaacaaatcaacaaagttgacaaaaaaattagatcttttaatcatgaataaaaaaaaagagaaagcacaaaaat\n+gaataaggaatggtgagagaaataactattgataatcagcaaataaaaaatcattaaaaacaatgttgttcacatctatgaaaaacattgaaagctagag\n+ggaatgggtaattttctagaaaaatacaattcaccacaactgacttcaaaaaaaaaaaaaagaagtacagcacttatgtgagcaatttccatagagaaat\n+acagttgtcatggaattataacacacacacaaacactaggtttagatgttttcacggagaattccaccaaacctttaGAAATCAGATCGTCCaaaggcaa\n+attaacaaccctcagccatttgcggcaaaatattacaattgaggcaagatatactgtactgaaaacttgaggaaaaagcaggagagaaagttcctttggg\n+aaattcgaatactcaaaagtgcttacatacaatgaaaaatttggaaatccataagcatggccaaggtgggacacatgctcagaaaaggcctgagaagaca\n+ctaataactcacctttagtaattcctaggctcacagcaagaaaaaatgaaggctaaggcagaattatacatggctccgctaagtgttgagggagccccaa\n+tacagagtcagtaagcaaagtctgggagatgtttttcatatttttttcttttttggctacttgcagtcaaggaaatcatttttaaatcactaaatgctaa\n+atgaacacaagctaaaggaaccgagccgccttcaaacatcaaacataaaaaagaatgcagatattacaaaaccagtttacaaaagttactaaacaaataa\n+aaactacatcccacagtgggtaacaaaaataaccttgaagaagggaaaaatttggtttccagaataaacacattataatatccaaaatgtccagttttca\n+acaaaaattaagaagcatgcaaataaacacaaaactatggcccatttacagaagaaataaatgagactctccctgagtaagcagatattggaaatattag\n+acaaaaactttatataactgtcttaaataaacttaaagagctaaagaaacccaagagaatgacatataaataaataagaaatatgaattttttaaaaggt\n+acaaaaaaattctgaggctgaaaagtacaataactaattaaaaagttactttttacttagggttccaatagaagatttgagcagctggaaaaaagaatca\n+gtgaacttgatagatcaagtgaaatgattcagtctgaagagcaggaaaatgaaagaatgacaacaaaaaagaatagagcctaaagacctgtgtaacaaca\n+tcaagaatgcctacatacagaatcctggtggggagtgaggggcaggaagactatttgaagaaatgtgtttgaaagcttcccaaatttcactaaaaacaaa\n+tatatacattcaaaaagctcagtgaacttcatcaaggaaatatacaaagatattcacaccaagacacactatgtttcaaattgtcaaaaggcaaagcgaa\n+tgtttgaaagcagcaagagaaaggcaacgcgtcatttacaaaggatcctcaataagtttgacagcagatagtgcattataatccatggatgccagaagag\n+cttaggaaaaaggcaatgcatcatttacaaaggatcctcagtaagtttgacagcagagagctcatgataaaccatgggtgccagaagagcttagaatgac\n'

diff -r 000000000000 -r 86fa46d3ce2e test-data/test_01.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_01.log Sun Nov 14 21:28:36 2021 +0000

@@ -0,0 +1,50 @@
+/usr/local/bin/tgsgapcloserbin/tgsgapcloser --prefix output --contig2ont_paf output.fill.paf --ont_reads_a /tmp/tmp0waeaugc/files/f/4/4/dataset_f44c5ccd-786b-4085-ba86-9dea34a7c4b2.dat --min_match 300 --min_idy 0.300000
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : TGSGapCloser start now ...
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadONTReads start now ...
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadONTReads finish. used wall clock : 0 seconds, cpu time : 0.000380 seconds
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadPAF start now ...
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the read2contig freq is
+1 9
+2 1
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the contig2read_num_freq freq is
+1 2
+9 1
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the contig2a_read_freq freq is
+1 9
+2 2
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadPAF finish. used wall clock : 0 seconds, cpu time : 0.000138 seconds
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadScaffInfo start now ...
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadScaffInfo finish. used wall clock : 0 seconds, cpu time : 0.000028 seconds
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : ParseAllGap start now ...
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the overlap cheked caused failed is 0
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the gapsize cheked caused failed is 0
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the gap_total is 5
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the no_match is 4
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the no choose is 0
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the no common is 0
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the scaff_negotive_gap_size is 0
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the ont_negotive_gap_size is 0
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the common reads count freq for a gap
+1 1
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the used idy freq is
+41 1
+54 1
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the correct oo reads count freq for a gap
+1 1
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the filler choose count freq for a gap
+1 1
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the one read provide filler choose count freq for a gap
+1 1
+
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the cut error is 0
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : ParseAllGap finish. used wall clock : 0 seconds, cpu time : 0.000165 seconds
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : PrintScaffInfo start now ...
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : PrintScaffInfo finish. used wall clock : 0 seconds, cpu time : 0.000045 seconds
+TGSGapCloser INFO UTC 2021/11/14 19:39:45 : TGSGapCloser finish. used wall clock : 0 seconds, cpu time : 0.000965 seconds

diff -r 000000000000 -r 86fa46d3ce2e test-data/test_01_final_assembly.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_01_final_assembly.fasta Sun Nov 14 21:28:36 2021 +0000

b'@@ -0,0 +1,650 @@\n+>scaffold_1\n+TTTACACATGCACACATGGCTACTGATGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAGAGGGGGAACGGAGA\n+CCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAAATTCAGACGGGGAACTGCCCCTGCACATAGTGAACGGCTCACTGAGCAAACCCC\n+GAGTCCCGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggtgggcccagtgatatcagctgcctgctgttcccca\n+gatgtgccaagtgcattcttgtgtgcttgcatctcatggaacgccatttccccagacatccctgtggctggctccTGATGCCCGAGGCCCAAGTGTCTGA\n+TGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACGA\n+CATCCTCCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCATACTCCACGTGCAGAGCAGCCTCAGCACTCACC\n+GGGCACGAGCGAGCCTGTGTGGTGCGCAGGGATGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAAGGGCAGGAGGAGGGTGTGGGATGGTGGAGGGG\n+TTTGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAAAGGGAGGGGGAGGATGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTAGGGAAAGCTGGGA\n+TGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAACGTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTC\n+ACAATCCAGAAGTCCCCGTGCCCTAAAGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAG\n+GCACTCAAGCGACTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCG\n+GGGCCACCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTCTTAATTGACCCTAGT\n+TCCCAGGGCAGCCTCGTTCTGCCTTGGGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCcacaggggcagtgggagggaactgag\n+actggggagggacaaaggctgctctgtcctggtgctcccacaaaggagaagggctgatcactcaaagttgcgaacaccaagctcaacaatgagccctgga\n+aaatttctggaatggattattaaacagagagtctgtaagcacttagaaaaggccacggtgagtcccaggggccagcactgctcgaaatgtacagcatttc\n+tctttgtaacaggattattagcctgctgtgcccggggaaaacatgcaccacagcgcatctcgagtcagcaggattttgacggcttctaacaaaatcttgt\n+agacaagatggagctatgggggttggaggagagaacatataggaaaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactga\n+ttccagccttgcacggagggatctggcagagtccaTCCAGTTCATTCAACACCTGGTTAGAAAACTGGGGCCAGCACACAGGGGAAGGGTAAGCTGGTTT\n+CATGATCGAATCAAGGCTCAGACAATTTTTAAAGGCCAGAGGGTAGACTGCAATCACcaagatgaaatttacaaggaacaaatgtgaagcccaacattta\n+ggttttaaaaatcaagcgtataaatacagaaggtggagggaacttgctttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagc\n+tcagtaGGGGCTAAAAGCATGTTAATCGGCATAAAAAGGCAATGAGATCTTAGGGCACACAGCTCCCCGCCCCTCTTCTGCCCTTCATCCTTCTTTCAAT\n+CAGCAGGGACCGTGCACTCTCTTGGAGCCACCACAGAAAACAGAGGTGCATCCAGCACCACAGAAAACAGAGCCACCACAGAAAACAGAGGGTGACTGTC\n+ATCCCCTCCAGTCTCTGCACACTCCCAGCTGCAGCAGAGCAGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCAGGAGCTCACCTGCCTGCGTCACT\n+GGGCACAGACGCCAGTGAGGCCAGAGGCCGGGCTGTGCTGGGGCCTGAGCCGGGTGGTGGGGAGAGAGTCTCTCCCCTGCCCCTGTCTCTTCCGTGCAGG\n+AGGAGCATGTTTAAGGGGACGGGTTCAAAGCTGGTCACATCCCCACCGAAAAAGCCCATGGACAACGAAAAGCCCACTAGCTTGTCCAGTGCCACAGGAG\n+GGGCAAGTGGAGGAGGAGAGGTGGCGGTGCTCCCCACTCCACTGCCAGTCGTCACTGGCTCTCCCTTCCCTTCATCCTCGTTCCCTATCTGTCACCATTT\n+CCTGTCGTCGTTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTCGTATCCTGACTACAATAACAGCT\n+TCTGGGTGTCCCTGGCATCCACTCTCTCTCCCTTCTTGTCCCTTCTGTGACGGATGCCTGAGGAACCTTCCCCAAACTCTTCTGTCCCATCCCTGCCCTG\n+CTCAAAATCCAATCACAGCTCCCTAACACGCCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCCGTGGGCCCTAACTCACTCATCCCAACTCTTCACTC\n+ACTGCCCTGCCCCACACCCTGCCAGGGAGCCTCCCGTGGCACCGTGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGG\n+CCCACAGGCTCACGGAAAGTTAGCCTCTCATGCCCCGAGAGCTGAGTGCAAGGGAGAGGCAGCGCTGTCTGTGCTTCCCATGCAGAAGCACCCCCCTCCC\n+ACCCCTGTGCAGGCCGGCCTTCGCGGCAGACCACCATACACCACGTTCCAAGCCACACTGAGGCCTCCCTCCAAGCCTGCAGCCCCCATTTCCAGACCCT\n+GCCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCACgtggttttcctcttcagcaactatt\n+tcctttttactcaagcaatggccccatttcccttggggaatccatctctctcgcaggcttagtcccagagcttcaggtggggctgcccacagagctcctc\n+agTCTAAGCCAAGTGGTGTGTCATAGTCCCCTGGCCCCATTAATGGATTCTGGGATAGACATGAGGACCAAGCCAGGTGGGATGAGTGAGTGTGGCTTCT\n+GGAGGAAGTGGGGACACAGGACAGCATTCTTTCCTGCTGGACCTGACCCTGTGTCATGTCACCTTGCTACCACGAGAGCATGGCCTGTCTGGGAATGCAG\n+CCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCCGAAGGCTGCTCTACTGATTGGTTA\n+ATTTTTGCTTAGCTTGGTCTGGGGAGTTCTGACAGGCGTGCCACCAATTCTTACCGATTTCTCTCCACTCTAGACCCTGAGAAGCCCACGCGGTTCATGC\n+TAGCAATTAACAATCAATCTCGCCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGGCAGCCACATAATTGGTATCTCTTAAGGTCCA'..b'tccacacctccaacaagctgcagtcgaccacaa\n+agaagaaacaagtctgtctcccatgggtcctacccacaccccctgctgttcaccatgaatgatagagtcaacagtgtgaaaacgaccatactgccaaaag\n+caacctacaaattcaatgcaattcccatcaaaataccaccatcattcttcacagaactagaaaaaacaaggctaaaattcacatggaaccaaaaaagagc\n+ccacatagccaaagcaagactaagcaaaaagaataaatctagaggcatcacattactcgacttcaaactatactataaggccatagtcaccaaaacagca\n+tggtactggtataaaaataggcatatagaccaatggaatagaatagagaacccagaaataaagccaaatactttcagccaactgatctttgacaaagcaa\n+gcaaaaacataaagtggggaaaggacaccctattcaacaaatggtgctggtataattggcaagccacatgtagaagaatgcaactggatcctcatctctc\n+accttataaacaaatcaactcaagatggttcacagacttaaatctaagacctgaaaccataaaaattctagaagataagattggaaaaacccttctagac\n+attggcttaggcaaagacttcacaatcaagaacccaaaagcaaacacaacaaagataaatagatgggacttaattaaactgaaagccttctgcacatcaa\n+aataaataatcagcagagtaaacagacaacccacagagtgggagaaaatcttcacaaactatgcatccaacagaggactaatatccagaatctacaaaga\n+attggaacaaatcagcaagaaaaaaaaccaaacaCAAGGATGACAGTGGAAATACAAAAACAAGACATAAATATTCTGAATAGTGATAATAAAACAGTGC\n+ATACCAGAATAcaaactgtttccaagttacaatggttcaaccatttttcagctttatggtggtgtgaaagtgatatccattcattagaaaccatgctcca\n+ggatgggcgcagtgggtcacgcctgtaatcctagcactttgggaggccgaggagggcggatcacaaggtcaagagatcaagaccatcctggccaacatgg\n+tgaaaccccgtctctcctaaaaatacaaaaattagctgggcattgtggtgcgtgcctgtaatcccagctattcgggaggctgaggcaggagaatcacttg\n+aaccagggagtcggaggtgttgcagtgagccgagatcgtgccactgcctccagcctggcaacagagtgagactccatctcaaaaaaaagaaagaaacccg\n+actccgaattttgaattttgatattttcctggactaccaatatgtggcacaatgctctctcacaatgttgtgcaacagcggtgagctgcagcttccagtc\n+agccaaatgataataaaggtagataatccatcttgatatcttcctgaagaacataatgcctgcctaccatcaacaggcatcaatactttctaccagctat\n+tctcaaccctcatgatcggaagagacagagactgactgtgtcaaagtattagtcccatcattcagcaattaaccttagctcaatgcttcaaaaattcttc\n+aggccctgtgtaatttcagctacgtacattaatgataagtacccatacaaccattctgtttcttattttcagtaccatatttaataaatatcagttattc\n+aatactttatttagacattttgttagattattttgaccaactgaagtctaatctaaatgttctgagcatgttcaaagtaagctaggccaacctataattt\n+tcggtgtgctaaatgcatttttaacttatgatattttcagtttacgggggtttgttgagacataacttcatcatacatcaaggagcatctgTAtatggga\n+tacagttaaagcagtgatcagaggaaaatctatagccttaacacatttattaataaaagtgtaggaattaaattatcagctgaaaaatgtaaaaagtatc\n+taaaagagtaagcagaaagtacaagaaagaacccaaagtagaaaaaagtgaaaattaataaaataagaagccaaaaaacagatcaaatcagtaaaccaaa\n+aatcttgttctttaaacaaatcaacaaagttgacaaaaaaattagatcttttaatcatgaataaaaaaaaagagaaagcacaaaaatgaataaggaatgg\n+tgagagaaataactattgataatcagcaaataaaaaatcattaaaaacaatgttgttcacatctatgaaaaacattgaaagctagagggaatgggtaatt\n+ttctagaaaaatacaattcaccacaactgacttcaaaaaaaaaaaaaagaagtacagcacttatgtgagcaatttccatagagaaatacagttgtcatgg\n+aattataacacacacacaaacactaggtttagatgttttcacggagaattccaccaaacctttaGAAATCAGATCGTCCaaaggcaaattaacaaccctc\n+agccatttgcggcaaaatattacaattgaggcaagatatactgtactgaaaacttgaggaaaaagcaggagagaaagttcctttgggaaattcgaatact\n+caaaagtgcttacatacaatgaaaaatttggaaatccataagcatggccaaggtgggacacatgctcagaaaaggcctgagaagacactaataactcacc\n+tttagtaattcctaggctcacagcaagaaaaaatgaaggctaaggcagaattatacatggctccgctaagtgttgagggagccccaatacagagtcagta\n+agcaaagtctgggagatgtttttcatatttttttcttttttggctacttgcagtcaaggaaatcatttttaaatcactaaatgctaaatgaacacaagct\n+aaaggaaccgagccgccttcaaacatcaaacataaaaaagaatgcagatattacaaaaccagtttacaaaagttactaaacaaataaaaactacatccca\n+cagtgggtaacaaaaataaccttgaagaagggaaaaatttggtttccagaataaacacattataatatccaaaatgtccagttttcaacaaaaattaaga\n+agcatgcaaataaacacaaaactatggcccatttacagaagaaataaatgagactctccctgagtaagcagatattggaaatattagacaaaaactttat\n+ataactgtcttaaataaacttaaagagctaaagaaacccaagagaatgacatataaataaataagaaatatgaattttttaaaaggtacaaaaaaattct\n+gaggctgaaaagtacaataactaattaaaaagttactttttacttagggttccaatagaagatttgagcagctggaaaaaagaatcagtgaacttgatag\n+atcaagtgaaatgattcagtctgaagagcaggaaaatgaaagaatgacaacaaaaaagaatagagcctaaagacctgtgtaacaacatcaagaatgccta\n+catacagaatcctggtggggagtgaggggcaggaagactatttgaagaaatgtgtttgaaagcttcccaaatttcactaaaaacaaatatatacattcaa\n+aaagctcagtgaacttcatcaaggaaatatacaaagatattcacaccaagacacactatgtttcaaattgtcaaaaggcaaagcgaatgtttgaaagcag\n+caagagaaaggcaacgcgtcatttacaaaggatcctcaataagtttgacagcagatagtgcattataatccatggatgccagaagagcttaggaaaaagg\n+caatgcatcatttacaaaggatcctcagtaagtttgacagcagagagctcatgataaaccatgggtgccagaagagcttagaatgac\n'

diff -r 000000000000 -r 86fa46d3ce2e test-data/test_01_gapfill.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_01_gapfill.log Sun Nov 14 21:28:36 2021 +0000

@@ -0,0 +1,12 @@
+>scaffold_1
+1 10000 S 1 10000
+10001 10887 F
+10888 20887 S 11001 21000
+20888 21887 N
+21888 31887 S 22001 32000
+31888 32887 N
+32888 42887 S 33001 43000
+42888 43887 N
+43888 53887 S 44001 54000
+53888 54887 N
+54888 64887 S 55001 65000

diff -r 000000000000 -r 86fa46d3ce2e test-data/test_02_final_assembly.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_02_final_assembly.fasta Sun Nov 14 21:28:36 2021 +0000

diff -r 000000000000 -r 86fa46d3ce2e test-data/test_03_final_assembly.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_03_final_assembly.fasta Sun Nov 14 21:28:36 2021 +0000

diff -r 000000000000 -r 86fa46d3ce2e test-data/test_04_final_assembly.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_04_final_assembly.fasta Sun Nov 14 21:28:36 2021 +0000

diff -r 000000000000 -r 86fa46d3ce2e test-data/test_05_final_assembly.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_05_final_assembly.fasta Sun Nov 14 21:28:36 2021 +0000

diff -r 000000000000 -r 86fa46d3ce2e tgsgapcloser.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tgsgapcloser.xml Sun Nov 14 21:28:36 2021 +0000

[

b'@@ -0,0 +1,246 @@\n+<tool id="tgsgapcloser" name="TGS-GapCloser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+ <description>fills the N-gap of error-prone long reads</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="xrefs"/>\n+ <version_command>tgsgapcloser --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ PILON=\\$(which pilon)\n+ PILON_JAR=\\$(readlink -f \\$PILON).jar\n+ && tgsgapcloser \n+ --scaff $scaff \n+ --reads $reads\n+ --output output\n+ #if $error_conditional.error_options == \'pilon\'\n+ --pilon \\$PILON_JAR\n+ --ngs $error_conditional.ngs\n+ --samtools `which samtools`\n+ --java `which java`\n+ --pilon_mem \\${GALAXY_MEMORY_MB:-4096}M\n+ #elif $error_conditional.error_options == \'racon\'\n+ --racon `which racon`\n+ #else\n+ --ne\n+ #end if\n+ --tgstype $tgstype_conditional.tgstype\n+ --min_idy $tgstype_conditional.min_idy\n+ --min_match $tgstype_conditional.min_match\n+ --chunk $chunk\n+ $g_check\n+ --thread \\${GALAXY_SLOTS:-16}\n+ ]]></command>\n+ <inputs>\n+ <param argument="--scaff" type="data" format="fasta" multiple="true" label="Scaffold file" />\n+ <param argument="--reads" type="data" format="fasta" multiple="true" label="Input reads" />\n+ <conditional name="error_conditional">\n+ <param name="error_options" type="select" label="Error correction">\n+ <option value="ne">Do not error correct</option>\n+ <option value="racon">Racon</option>\n+ <option value="pilon">Pilon</option>\n+ </param>\n+ <when value="ne"/>\n+ <when value="racon">\n+ <param argument="--r_round" type="integer" min="0" max="10" value="1" label="Number of Racon error-correction rounds" \n+ help="Although multiple rounds of racon can increase the quality of an assembly there are indications that it also \n+ fragments the assembly and may decrease quality by removing structural variants and SNPs. Published assembly workflows \n+ differ in the number of rounds but rarely apply more than 4 rounds of racon" />\n+ </when>\n+ <when value="pilon">\n+ <param argument="--ngs" type="data" format="fastq,fastq.gz" label="Illumina reads" \n+ help="Pilon can utilize Illumina short reads mapped to the draft assembly to \n+ improve the local accuracy of the sequence by correcting sequence errors, \n+ fixing misassemblies, and filling gaps"/>\n+ <param argument="--p_round" type="integer" min="0" max="10" value="3" label="Number of Pilon error-correction rounds" />\n+ </when>\n+ </conditional>\n+ <conditional name="tgstype_conditional">\n+ <param argument="--tgstype" type="select" label="Type of third generation reads">\n+ <option value="ont" selected="true">Oxford Nanopore Technologies (ONT)</option>\n+ <option value="pb">PacBio (pb)</option>\n+ </param>\n+ <when value="ont">\n+ <param argument="--min_idy" type="float" min="0" max="1" value="0.3" label="Minimum identity for filtering candidate sequences"/>\n+ <param argument="--min_match" type="integer" min="0" max="1000" value="300" label="Minimum matched length for filtering candidate sequences"/>\n+ </when>\n+ <when value="pb">\n+ <param argument="--min_idy" type="float" min="0" max="1" value="0.2" label="Minimum identity for filtering candidate sequences"/>\n+ <param argument="--min_match" type="integer" min="0" max="1000" value="200" label="Minimum matched length'..b'sta" ftype="fasta"/>\n+ </test>\n+ \n+ <test expect_num_outputs="1">\n+ <param name="scaff" value="scaffold.fasta" ftype="fasta"/>\n+ <param name="reads" value="ont_reads.fasta" ftype="fasta"/>\n+ <conditional name="error_conditional">\n+ <param name="error_options" value="pilon"/>\n+ <param name="ngs" value="ngs_reads.fastq.gz" ftype="fastq.gz"/>\n+ <param name="r_round" value="1"/>\n+ </conditional>\n+ <conditional name="tgstype_conditional">\n+ <param name="tgstype" value="ont"/>\n+ <param name="min_idy" value="0"/>\n+ <param name="min_match" value="0"/>\n+ </conditional>\n+ <param name="chunk" value="1"/>\n+ <param name="g_check" value="false"/>\n+ <output name="final_assembly" file="test_05_final_assembly.fasta" ftype="fasta"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**Purpose**\n+\n+TGS-GapCloser is a gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio,\n+Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly. This tool can close gaps in large genome assemblies\n+using raw long reads quickly and cost-effectively. The final assemblies generated by TGS-GapCloser have improved contiguity and \n+completeness while maintaining high accuracy.\n+\n+----\n+\n+.. class:: infomark\n+\n+**Quick usage**\n+\n+Input reads can only be in FASTA format. Both raw reads and pre-error-corrected reads are acceptable as input. If only raw long reads are \n+provided, it polishes raw TGS reads by calling Racon.If additional NGS short reads are available, it polishes raw TGS reads by calling Pilon.\n+\n+----\n+\n+.. class:: infomark\n+\n+**Gap fill details**\n+\n+\n+Format of a detailed information of gap fill report:\n+\n+- Each scaffold name is followed by its data lines.\n+- A data line consists of 3 or 5 columns and describes the source of each segment in the final sequence:\n+- Column 1 is the segment\'s first bp position in the final sequence.\n+- Column 2 is the segment\'s last bp position in the final sequence.\n+- Column 3 is the segment\'s type , \'S\' , \'N\' or \'F\'.\n+- \'S\' means this segment is a segment of the input sequence and this line includes other two more columns:\n+- Column 4 is the segment\'s first bp position in the input sequence.\n+- Column 5 is the segment\'s last bp position in the input sequence.\n+- \'N\' means this segment is a N area.\n+- \'F\' means this segment is a filled sequence from TGS reads.\n+\n+----\n+\n+.. class:: infomark\n+\n+**Algorithm and implementation of TGS-GapCloser**\n+\n+This is a brief description of the TGS-GapCloser algorithm. Please refer to the manuscript for more detailed information.\n+\n+TGS-GapCloser is coded in the C++ programing language (requires GCC 4.4+). It uses minimap2 to obtain alignments, and Pilon (requires Java runtime 1.7+)\n+or Racon (requires GCC 4.8+) to correct candidate fragments. The algorithm automatically identifies gaps and tries to find the best matched long-read \n+fragments to close gaps or merge adjacent scaftigs. To accelerate the gap closure without losing efficiency and accuracy, TGS-GapCloser only selects a \n+limited number of fragmented long reads as candidates for subsequent error correction and competition.\n+\n+TGS-GapCloser can accept as input any type of TGS long reads or other pre-assembled contigs to fill gaps in a draft assembly in the 4 steps :\n+\t(i) Identification of gap regions in the draft assembly; \n+\t(ii) Acquisition of candidates from the alignments of long reads against gaps; \n+\t(iii) Base-level error correction of alternative sub-long reads; and \n+\t(iv) Gap closure using the error-corrected candidates with the highest score for each gap or linkage of the neighboring scaftigs with overlaps.\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n'