# HG changeset patch
# User bgruening
# Date 1432148390 14400
# Node ID 581e52f03c5ddb7f1e4a2ae6eadd537dc0e4b84b
Imported from capsule None
diff -r 000000000000 -r 581e52f03c5d pear.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pear.xml Wed May 20 14:59:50 2015 -0400
@@ -0,0 +1,160 @@
+
+ Paired-End read merger
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+ pear
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+ 0:
+ --max-asm-length $max_assembly_length
+ #end if
+ --min-asm-length $min_assembly_length
+ --min-trim-length $min_trim_length
+ --quality-theshold $quality_threshold
+ --max-uncalled-base $max_uncalled_base
+ --test-method $test_method
+ --empirical-freqs $empirical_freqs
+ -j "\${GALAXY_SLOTS:-8}"
+ --score-method $score_method
+ --cap $cap
+ $nbase
+]]>
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+ 'assembled' in outputs
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+ 'forward' in outputs
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+ 'reverse' in outputs
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+ 'discarded' in outputs
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+ 10.1093/bioinformatics/btt593
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+
diff -r 000000000000 -r 581e52f03c5d test-data/forward.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/forward.fastq Wed May 20 14:59:50 2015 -0400
@@ -0,0 +1,56 @@
+@EU861894-140/1
+CAACCATTCCACTCGCCTCTGCCGCACTCGAGGCCCCCAGTATGAGAGGCAGTTACGAGGTTGAACCTCAGAATCTCACCCCACACTTAAGGGCGCGCCT
++
+@#CAAF4FHFG;DIJJI?JG#GIIIDECD#4H*1IBIIIH#?IDID*DFIIF?C#HGBJICJBC#JEGEA>ECH#=7#DDF@##D#D<@C#CC@#C?D@,
+@EU861894-138/1
+TCCGAGGTTGAGCCTCAGAATTTCACCCCCCACTTAACGGCCCGACTCCGCGCTCCTTACGCCCAGTAAGTTCGGACAACGCTGGCCCCCTACGTACTAC
++
+@CCFFFBFFDHFHJJJ+#C@B9DEFDD@ED#EDBD>
+@EU861894-134/1
+TTGTGCAAGAGTCCTAATTGCTGCCCCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATCCGGCTGTTCGTCCCCTCAGACCATGTACCCGTAGATGCC
++
+=CCFDFFFA?#BHIJJJCIJJJJD;EEJB#@2GFIE#>A;C@FCA@##BD>AD=D#D?##A,
+@EU861894-132/1
+CGGAACACCCATGGCGAAGGCAGCTCGCTGGCCTGCAACTGACCCTGAGGCGCAAAAGCCGGGGGATCAAACAGGTTTATATACCCTGGTAGTCCCGAGC
++
+CCC4FFDFFFHH#AIJDEDBC#H;#E8A(?>##D
+@EU861894-130/1
+TCGTCACTAACCGAAGAACCTTACCAGGGTTTGACATCCCCGGCCAGCACGAGAGATCGGGTGGTGCCCGCAAGGGGACCGGGTGACAGGTGTTGACTAG
++
+:B@FDFDFHCA@:CDFDEDAA#DDF:-D,
+@EU861894-126/1
+GGAATGGTCGGTGTAGCGGTGAAATGCGTAGATATCGATCGGAACACCCATGGCTAAGGTAGCTTGCTGGCGTGCAACAGACGCTCAGGCGCAAAAGCCG
++
+BC?#FF=FBFHHHFGIGEIJ@IJJIFI@HJI9IJ;GHBGIIJGHDC<>#9E7@CG#D(BHED#=;CD:;#>C#C?B,
+@EU861894-124/1
+CTGTGCCGCAGCTAACCCAAAAAGTATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAACGGAATTGACGGGGAACCGCACAAGCGGTGGACCAT
++
+CCCFFFFD,GBBD@8D>:BDD<###,
+@EU861894-120/1
+CTGTCACCCGGTCCGCTTGCGGGGAACACCCGATCTCTCGCGCTGTCCGGGGATGTCAAACCCTGGTAATGTTCTTCCGTTAGTGACGAATTAATGCAGA
++
+@C@FAFFFAHHHFA#JJ#J:IJ?H:HJJH9IJ#9I?IG:J#*IEBIC;I?AEJDIJJHHCICCHDJJ;C##C2EF?B#C>?DD6(B+#(D@E:DCDCC#,
+@EU861894-118/1
+CGAGCGCAACCCTGACCCAATGTTGGCAGCGTAAAGTCGGCAACTCTTTGGGAACTGCCCGTGGAAGCGGGAGGAAGGTGGGGATGACGTCAAATAGGCA
++
+@?;FF?EFFHHHH#HEAIGJ@J1JIJIJJGDGIF7GGH=J#JGIJJ#:GFJID#FJJ#JID4?#DBDJHEFID;EA5EDD;C?CCDCBDA>:CB>#DD#C
+@EU861894-116/1
+GAGGCAGTTCCGAGGTTGAGCCTCAGAATTTCACCCCCCACTTAAGGGCCCGCCTACGCCCTATTTACGCCCATTAAATTCGGACAACGCTGGCCGCCTA
++
+C@@FFFD2GHHFFICFAGJJI3JJIIII8II#<*JJH#JJIID(EGEGJ;GE@D7IJHF#B;#C?H@GH;FCI#DD@DE6CCDCDDC<#ACD4
+@EU861894-114/1
+TTACTAGGGATTCCGGCTTCATGCAGGCGAGTTGCAGCCTGCAATCCGAACTGAGACCATATTTGTGCGATTGGCTCCTCTACGCGGCATAGCGTCGCGC
++
+@C:FFDD#BHHAAIJ(GIFGIJGHBHDI9ICHGE7JHEJI4IJBBIDIAHJIBCBFIF#J=BDFFDD8HCHJ8E:@@C#D##BA@DD5=E#A5B#D#B#F
diff -r 000000000000 -r 581e52f03c5d test-data/pear_assembled_results1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pear_assembled_results1.fastq Wed May 20 14:59:50 2015 -0400
@@ -0,0 +1,56 @@
+@EU861894-140/1
+CAACCATTCCACTCGCCTCTGCCGCACTCGAGGCCCCCAGTATGAGAGGCAGTTACGAGGTTGAGCCTCAGAATTTCTCCCCCCACTTAAGGGCCCGCCTACTCGCTCTTTACGACCAGTAAAATCGGTCAAAGCTCACCCCCTACGTATTACCGC
++
+@#CAAF4FHFG;DIJJI?JG#GIIIDECD#4H*1IBIIIH#?IDID*DFIIF?C#HjZmKE^ed@LEiedWfekA=7#iFmcD=W%Qc\g7ekeDjf_bU)G#EE=?'>:EHDG#CIHHJIH!#J:BI#JJH#IEGGGGCGJJH@*GJ;J#JJJD;EEiaAd4dFIG%ad^fciCdc6=ej_d^dlClbDAAT#7J#C>#J#F!#JDIBI(GGIIJCJHEH:JJ#IHJF=HJJHG+HIJI)kD_hQICPaCfaC`ERFfg@mAfjmeddfFPIIGI#HIG#HCI??JDIHIJBAG?F3?JJAJ*JJ!FG:?DD1HFDADF@@=
+@EU861894-126/1
+GGAATGGTCGGTGTAGCGGTGAAATGCGTAGATATCGATCGGAACACCCATGGCGAAGGCAGCTCGCTGGCCTGCAACTGACGCTGAGGCGCAAAAGCCGGGGGACCAACCAGGATTAGATACTCTGGTAGTCCCGGCCGTAAACGATGAATA
++
+BC?#FF=FBFHHHFGIGEIJ@IJJIFI@HJI9IJ;GHBGIIJGE;g7adIEkLfk_gFbbC][aDfeDlYkQHFGG'(HG?#@F2JGIIEDCJG>!J3EFGEJ3EGJGJHAJHDHF?:CADF8C@
+@EU861894-124/1
+CTGTGCCGCAGCTAACCCAAAAAGTATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATCTGCATTAATTCGTTACTAACCTAAGAACCTTAGCAGGGTTTGACATCCCCG
++
+CCCFFFFD,GBdlclfkD`kAiiCD5hZS##HGBGJFFI6HFG#IJF:JHI#FIEJFG2#HI#HJ:GL#NJJG#E@#<:J2JJCAIJEFHHJA2CH!422FF@@+
+@EU861894-120/1
+CTGTCACCCGGTCCGCTTGCGGGGAACACCCGATCTCTCGCGCTGTCCGGGGATGTCAAACCCTGGTAATTTTCTTCGGTTAGTGACGAATTAATGCACATGCTCCTCCCCTTGTGCGGGCCGCCGTCAATTCCTTTGAGTTTCAACCTTGCG
++
+@C@FAFFFAHHHFA#JJ#J:IJ?H:HJJH9IJ#9I?IG:J#*IEBIC;I?AEJJIJljHCkbbf[L^[C##jUYide=i_dheYBcSI(id^BdCll`CE7H=JGA!9G*#>E#HGC@4IF:#DEJCI#GJBAJJEJJGB4J;AJH#EF)#??BHHHHH;F=F=CC8
diff -r 000000000000 -r 581e52f03c5d test-data/pear_unassembled_forward_results1.fastq
diff -r 000000000000 -r 581e52f03c5d test-data/reverse.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reverse.fastq Wed May 20 14:59:50 2015 -0400
@@ -0,0 +1,56 @@
+@EU861894-140/2
+GCGGTAATACGTAGGGGGTGAGCTTTGACCGATTTTACTGGTCGTAAAGAGCGAGTAGGCGGGCCCTTAAGTGGGGGGAATAATTCTGACGCTCAACCTC
++
+;BCFDF#FHHFH)GJJHI##E'?=EE#G)JCB;A#C#E@###9CD#C<##@C
+@EU861894-136/2
+TACCGCATGTGGATGTGCTCTGCCCTCAGAGCTTATCCAAAGCCTTCGGGCGCTTCGGGATGGGCACGCGGTCTACCAGCTATTTGGGTGGGTAACGTCC
++
+1B@FDFF:HHHA#AHGGGEG?@J<#J;JG*@HJJGCGGGGE>IFFDJJJCC#GCBHAFEJGIDEG#J;DBG#EDC)#C(GFD#C#@2?#D8CCD53D#AA
+@EU861894-134/2
+GCCTTCGGGCACTTCGGGATGGGCCCGCGGCCTTTCAGCTAGTTGGGAGGGTACTGTCACATCAAGACTTCGACGGGTAGCTGCTCTGAGGGTTCGATCA
++
+@@+?+;FDDAHCHCIJFC#J7#I#?DDICIH;DBGD=6DD#DDDDDD####>#EA@@
+@EU861894-132/2
+GCGGCACAGGGGGGGTCGCTACCCCCAGCACCTAGTATTCATCGTTTACGGCCGGGAATACCAGCGTACCTAGTCCTGTTTGCTCCCCCGTCTTTTGCGC
++
+@1@DF=F)HH2H;JGJF3!FF+EIHH+#JC#BEHJ?JGBGFE8HDIFJJF?@GH#@B#B;ECEJ#C:I#D@C#C#A=D#CCD>C#DDB!5FB+##AD'
+@EU861894-130/2
+CAACATTGGGTGAGGGTTGCGCTTGTTGCATGACTTAACCCAACATCTCACGATAGTAGCTGACGACAACTGTGCAACCCCTGTCGACCGGTCCCCTTGC
++
+1@:DFDFDAH#+DGGG:EGFHI;+JJ::H##IF9CAI?IJ#I#D?GJDJBHF)#H##J@GJBADEGH;JC(!=3ACE>#DDE)C#AC
+@EU861894-128/2
+CAAGGCCCCCAGTATGGGAGGCAGTTCCGAGGTTGAGCCTCAGAATCTCACCCCCCACTTCAGGGCCCGCCTTCGGTCTCATAACGCCCAGTAACTTCGG
++
+=@@FDADFH1DD?:GF!JJ*JAJJ?3F?GABJIHIDJ??ICH#GIH#IGIIE#I@BJIGD#J@IF#8E=C>D#A6##:ED#D')BBC@;&F?#80D;@@C
+@EU861894-126/2
+TATTCATCGTTTACGGCCGGGACTACCAGAGTATCTAATCCTGGTTGGTCCCCCGGCTTTTGCGGCTCAGCGTCAGTTTCAGACCACCGAGCCGCCTTCG
++
+@C8FDAC:?FHDHJAHJGJGE3JEGFE3J!>GJCDEIIGJ2F@#?GH('GGFHFJ;JBCIBGB:#HFFD;DEEHE#BB#C#E#D>#!>A>#D#C##?DD'
+@EU861894-124/2
+CGGGGATGTCAAACCCTGCTAAGGTTCTTAGGTTAGTAACGAATTAATGCAGATGCGTCACCGTTTGTGCGGGCCCCCGTTAATTCCTCAGCGTTTCTAC
++
+=C@F#DDDHGHAHB<:JH#IH#2GFJEIF#IHJ:FJI#GFH6IFFJGBGH##H9G5##JF#F;!HGJEGB#ADHH#ECA>(CAFD##D##@6CC5@?##'
+@EU861894-122/2
+GTCCGAAGATACTGGGCGTAAAGAGCGCGTACGCGGCCCCTTAAGTGGAGGGTGAAATTCTGAGGCTCAACCTCGGAACTGCCACACATACTGTGGGCTT
++
++@@FF224!HC2AJHHFEJIACJJ2J:<#@E#GJJC!JG#II)JIIF:#EIBII;JHC.HHFI@DGFDF/D@#D>EAF#C=HF#D##BC77:D#C?D:#A
+@EU861894-120/2
+CGCAAGGTTGAAACTCAAAGGAATTGACGGCGGCCCGCACAAGGGGAGGAGCATGTGCGTTAATCCGTCACTAACCGAAGAAAGGTACCAGGGGATGGGA
++
+B1BFFDDBHHHHHB#*G9!AGJ=H7:C>JI#A):EF#GIB;DBEFBG=DFD5DH#!#A5#8?@@C##CC##'
+@EU861894-118/2
+CCAGTGTAGCATGTGTGAAGCCCAGGGCGTAAGGGCCATGCCGATTTGACCTCCTCCCCATCTTCCTCCCGTTTACATGGGCACTTCCCAAAGAGTCGCC
++
+@CC++DD?ABHFHA+G#I#J3D2IJGJJCJHJHEJIJGJ4IJII#I?(EA!GH#CGG8E##5JHEHCD@BE#=@H@##CDBC:&DCD>D>?#C:C###C@
+@EU861894-116/2
+AATGACCGTACCACACGAAAAAGCCCTGGATAACTACGTGCCAGCAGCCGCGATAATACGTAGGGGGCCAACGTTGTCCTAAGTGTCTGGGCGTATAAAG
++
+BBCFFD#BFHHH:G#JE@F#J+JJJ@#CJ#HIIGGF#GIGEF=HJ?ECFJBE!BDIGE#EEI=>BHHC@D#G#=A#CFA#DECD##CDBD>#CC?#@#@D
+@EU861894-114/2
+CCCTTACGCCCTGGGCCTGATACATGCTACAATGGCCGTTAATCAGAGCTACGCGATGCTACGAGGCGGAGCCAATCGCACAAGTAGGGTCACAGTTCGG
++
+8CC=F=F;HHHHHB??#)FE#HJA;J4BG>BI;@#JFI):GJ#D?
+
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