Galaxy |

Changeset 4:2c1f0fe810f7 (2015-04-15)

Previous changeset 3:eb546ac2aab2 (2013-07-19) Next changeset 5:f11ff7be8c78 (2015-04-15)

Commit message:
Uploaded

modified:
tool_dependencies.xml
trim_galore
trim_galore_wrapper.xml

added:
test-data/bwa-mem-fastq1.fq
test-data/bwa-mem-fastq2.fq
test-data/paired_collection_example_pair1_results3.fastqsanger
test-data/paired_collection_example_pair2_results3.fastqsanger
test-data/paired_collection_example_results3.txt
test-data/paired_collection_example_unpair1_results3.fastqsanger
test-data/paired_collection_example_unpair2_results3.fastqsanger
test-data/paired_example_pair1_results2.fastqsanger
test-data/paired_example_pair2_results2.fastqsanger
test-data/paired_example_results2.txt
test-data/sanger_full_range_original_sanger.fastqsanger
test-data/sanger_full_range_report_results1.txt
test-data/sanger_full_range_report_results2.txt
test-data/sanger_full_range_results1.fastqsanger
test-data/sanger_full_range_results2.fastqsanger

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/bwa-mem-fastq1.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa-mem-fastq1.fq Wed Apr 15 11:32:11 2015 -0400

b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACC'..b'FHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...//////\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;/////9/////.\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA\n++\n+AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF/\n'

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/bwa-mem-fastq2.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa-mem-fastq2.fq Wed Apr 15 11:32:11 2015 -0400

b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/2\n+TCGCCTTACCGCTACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG\n++\n+1>11111@11111A111A100000000////011110//>>/12@1@22B/////1@>21/>>/-----9/;////9////--;-;-;-----;--------9/-/-///9-;-------9//////9/////-//-/9-;-;9--/////99-;--9-:-;----/---/-----////---9-/////--;A-//////---------9/-----;-----/-/-----;--;//////////9;///-\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n++\n+BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/2\n+GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\n++\n+3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/2\n+ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT\n++\n+CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA/\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF0/.\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCCA\n++\n+AA?A34BF>AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<BAGHB?11F/FGFGGBFBGBD.11><.<<<C0<A</<<=0GFHC@-.;FF09BFFGB00B0;FE.C/:CCF0;0C0;BBBFF@.9AF.:9EFF.;.BFF/FF/;/./BFB/..;;ABF/9FF//.;AAF9BBBA;-A.B/9///9/BF////;///:9.\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTG'..b'HGGGGGGGGGFEACFFFFFFFFFFFFFFFDFFFAFFFFBFAB@EFAAEFFFFF.ACF.BBFFEBFFFEB;FFFFFFFA/BFBFBBBFFFBFFFFFED.>DFFF.\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/2\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+BBBBCFCCCCCFGGGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF.\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/2\n+ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGAGTTCTGTGGGGCCGGGGATCCTTATAAAAAAAATAGA\n++\n+BCCDDFFFFFFFGGGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGHHGHGAGAEEDG.CGCGHC0CGBFHGFBBF0ABDDEFF@?--:BB@.;:BF;0.0:0.0:000:BF.-.------.9/;000::0;0:--.000\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/2\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC\n++\n+CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A....\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG\n++\n+CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/2\n+ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACATT\n++\n+CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFFFF.9//;FFFFF/BFFB/\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/2\n+AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTTA\n++\n+CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B0\n'

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/paired_collection_example_pair1_results3.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_collection_example_pair1_results3.fastqsanger Wed Apr 15 11:32:11 2015 -0400

b'@@ -0,0 +1,396 @@\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTG\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTAC\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGG\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTT\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACAC\n++\n+ABBBBFFFFFFFGGGGGGGCGGGHHHHHGHHHHHHHHHGHHHHHHHHHHHGHHHHHGGGGGHGHHHHHHHHHHHHHBGFHHHHGHGHGGHGGGCGGGHHHGGGGGGGHHHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFEDBDFFFFFFFEFFFE0F0FBFFFF0FFFFFFFFFFFFFFFFF\n+@M01368:8:000000000-A3GHV:1:1102:13809:1733/1\n+ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGA'..b'HGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTAT\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCA\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTT\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATT\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACAT\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTT\n++\n+AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF\n'

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/paired_collection_example_pair2_results3.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_collection_example_pair2_results3.fastqsanger Wed Apr 15 11:32:11 2015 -0400

b'@@ -0,0 +1,396 @@\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAAT\n++\n+CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFB\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n++\n+BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/2\n+GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\n++\n+3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/2\n+ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGT\n++\n+CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCT\n++\n+BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCC\n++\n+AA?A34BF>AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<BAGHB?11F/FGFGGBFBGBD.11><.<<<C0<A</<<=0GFHC@-.;FF09BFFGB00B0;FE.C/:CCF0;0C0;BBBFF@.9AF.:9EFF.;.BFF/FF/;/./BFB/..;;ABF/9FF//.;AAF9BBBA;-A.B/9///9/BF////;///:9\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGCTGTCTCTTATAC\n++\n+CDDDDFFFFCCFGGGGGGGGGGHHHHHGGGGHHHHHHHHHHHHHHHHGGHHGGHGGHHHHHHGHGHGHHHGGGGGGGGHHHHHFHHHFHHHHGGGGGGHHGHHGGHHHGGGCGGHFFFGGGHHGGGFHHGHHHGGGCGGHFHHGGGGGGFHGC<@GGHGHHCHE00:CFHHHFGACGFFEG:D.E;FG;EFBBFGGGFEE0CBBBFFGBFFGFGFFFFFFFF0:B0:BFFFFFFF/0.;:0F0B:BFF\n+@M01368:8:000000000-A3GHV:1:1102:13809:1733/2\n+NATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGG'..b'TAC\n++\n+BAABCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHGHHHHHHHHHGGGGHHHHHHHHHFHHHHHHHHHHHHGGGGGHHHHHHHGHHHHHHHHHHGGHHHHGHHGGHHHEGGGGGHHHHHHHHHGHHHHHGHHHHHGGHGHGHHGGGGGGGGGFEACFFFFFFFFFFFFFFFDFFFAFFFFBFAB@EFAAEFFFFF.ACF.BBFFEBFFFEB;FFFFFFFA/BFBFBBBFFFBFFFFFED.>DFFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/2\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTAC\n++\n+BBBBCFCCCCCFGGGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/2\n+ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGT\n++\n+BCCDDFFFFFFFGGGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGHHGHGAGAEEDG.CGCGHC0CGBFHGFBBF0ABDDEFF@?--:BB@.;:BF;\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/2\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCC\n++\n+CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAAT\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/2\n+ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACAT\n++\n+CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFFFF.9//;FFFFF/BFFB\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/2\n+AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTT\n++\n+CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B\n'

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/paired_collection_example_results3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_collection_example_results3.txt Wed Apr 15 11:32:11 2015 -0400

@@ -0,0 +1,86 @@
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: ./input_mate1
+Trimming mode: paired-end
+Trim Galore version: 0.3.7
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC'
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+
+
+cutadapt version 1.1
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1
+Maximum error rate: 10.00%
+   Processed reads: 100
+     Trimmed reads: 20 ( 20.0%)
+   Total basepairs:        24894 (0.0 Mbp)
+ Trimmed basepairs:           26 (0.0 Mbp) (0.10% of total)
+   Too short reads: 0 (  0.0% of processed reads)
+    Too long reads: 0 (  0.0% of processed reads)
+        Total time:      0.00 s
+     Time per read:      0.03 ms
+
+=== Adapter 1 ===
+
+Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times.
+
+Lengths of removed sequences
+length count expected
+1 16 25.0
+2 2 6.2
+3 2 1.6
+
+
+RUN STATISTICS FOR INPUT FILE: ./input_mate1
+=============================================
+100 sequences processed in total
+
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: ./input_mate2
+Trimming mode: paired-end
+Trim Galore version: 0.3.7
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC'
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+
+
+cutadapt version 1.1
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate2
+Maximum error rate: 10.00%
+   Processed reads: 100
+     Trimmed reads: 24 ( 24.0%)
+   Total basepairs:        24354 (0.0 Mbp)
+ Trimmed basepairs:           36 (0.0 Mbp) (0.15% of total)
+   Too short reads: 0 (  0.0% of processed reads)
+    Too long reads: 0 (  0.0% of processed reads)
+        Total time:      0.01 s
+     Time per read:      0.10 ms
+
+=== Adapter 1 ===
+
+Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times.
+
+Lengths of removed sequences
+length count expected
+1 15 25.0
+2 7 6.2
+3 1 1.6
+4 1 0.4
+
+
+RUN STATISTICS FOR INPUT FILE: ./input_mate2
+=============================================
+100 sequences processed in total
+
+Total number of sequences analysed for the sequence pair length validation: 100
+
+Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.00%)

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/paired_example_pair1_results2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_example_pair1_results2.fastqsanger Wed Apr 15 11:32:11 2015 -0400

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/paired_example_pair2_results2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_example_pair2_results2.fastqsanger Wed Apr 15 11:32:11 2015 -0400

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/paired_example_results2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_example_results2.txt Wed Apr 15 11:32:11 2015 -0400

@@ -0,0 +1,86 @@
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: ./input_mate1
+Trimming mode: paired-end
+Trim Galore version: 0.3.7
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC'
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+
+
+cutadapt version 1.1
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1
+Maximum error rate: 10.00%
+   Processed reads: 100
+     Trimmed reads: 20 ( 20.0%)
+   Total basepairs:        24894 (0.0 Mbp)
+ Trimmed basepairs:           26 (0.0 Mbp) (0.10% of total)
+   Too short reads: 0 (  0.0% of processed reads)
+    Too long reads: 0 (  0.0% of processed reads)
+        Total time:      0.00 s
+     Time per read:      0.02 ms
+
+=== Adapter 1 ===
+
+Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times.
+
+Lengths of removed sequences
+length count expected
+1 16 25.0
+2 2 6.2
+3 2 1.6
+
+
+RUN STATISTICS FOR INPUT FILE: ./input_mate1
+=============================================
+100 sequences processed in total
+
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: ./input_mate2
+Trimming mode: paired-end
+Trim Galore version: 0.3.7
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC'
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+
+
+cutadapt version 1.1
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate2
+Maximum error rate: 10.00%
+   Processed reads: 100
+     Trimmed reads: 24 ( 24.0%)
+   Total basepairs:        24354 (0.0 Mbp)
+ Trimmed basepairs:           36 (0.0 Mbp) (0.15% of total)
+   Too short reads: 0 (  0.0% of processed reads)
+    Too long reads: 0 (  0.0% of processed reads)
+        Total time:      0.01 s
+     Time per read:      0.12 ms
+
+=== Adapter 1 ===
+
+Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times.
+
+Lengths of removed sequences
+length count expected
+1 15 25.0
+2 7 6.2
+3 1 1.6
+4 1 0.4
+
+
+RUN STATISTICS FOR INPUT FILE: ./input_mate2
+=============================================
+100 sequences processed in total
+
+Total number of sequences analysed for the sequence pair length validation: 100
+
+Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.00%)

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/sanger_full_range_original_sanger.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_original_sanger.fastqsanger Wed Apr 15 11:32:11 2015 -0400

[

@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/sanger_full_range_report_results1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_report_results1.txt Wed Apr 15 11:32:11 2015 -0400

@@ -0,0 +1,40 @@
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: ./input_singles
+Trimming mode: single-end
+Trim Galore version: 0.3.7
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC'
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length before a sequence gets removed: 20 bp
+
+
+cutadapt version 1.1
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_singles
+Maximum error rate: 10.00%
+   Processed reads: 2
+     Trimmed reads: 1 ( 50.0%)
+   Total basepairs:          168 (0.0 Mbp)
+ Trimmed basepairs:            1 (0.0 Mbp) (0.60% of total)
+   Too short reads: 0 (  0.0% of processed reads)
+    Too long reads: 0 (  0.0% of processed reads)
+        Total time:      0.00 s
+     Time per read:      0.32 ms
+
+=== Adapter 1 ===
+
+Adapter 'AGATCGGAAGAGC', length 13, was trimmed 1 times.
+
+Lengths of removed sequences
+length count expected
+1 1 0.5
+
+
+RUN STATISTICS FOR INPUT FILE: ./input_singles
+=============================================
+2 sequences processed in total
+Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%)
+

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/sanger_full_range_report_results2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_report_results2.txt Wed Apr 15 11:32:11 2015 -0400

@@ -0,0 +1,40 @@
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: ./input_mate1
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC'
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+
+
+cutadapt version 1.1
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1
+Maximum error rate: 10.00%
+   Processed reads: 100
+     Trimmed reads: 20 ( 20.0%)
+   Total basepairs:        24894 (0.0 Mbp)
+ Trimmed basepairs:           26 (0.0 Mbp) (0.10% of total)
+   Too short reads: 0 (  0.0% of processed reads)
+    Too long reads: 0 (  0.0% of processed reads)
+        Total time:      0.01 s
+     Time per read:      0.05 ms
+
+=== Adapter 1 ===
+
+Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times.
+
+Lengths of removed sequences
+length count expected
+1 16 25.0
+2 2 6.2
+3 2 1.6
+
+
+RUN STATISTICS FOR INPUT FILE: ./input_mate1
+=============================================
+100 sequences processed in total
+Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%)
+

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/sanger_full_range_results1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_results1.fastqsanger Wed Apr 15 11:32:11 2015 -0400

[

@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876

diff -r eb546ac2aab2 -r 2c1f0fe810f7 test-data/sanger_full_range_results2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_results2.fastqsanger Wed Apr 15 11:32:11 2015 -0400

diff -r eb546ac2aab2 -r 2c1f0fe810f7 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Jul 19 09:49:25 2013 -0400
+++ b/tool_dependencies.xml Wed Apr 15 11:32:11 2015 -0400

@@ -1,26 +1,6 @@
<?xml version="1.0"?>
<tool_dependency>
-    <package name="cutadapt" version="1.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://cutadapt.googlecode.com/files/cutadapt-1.1.tar.gz</action>
-                <action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>cutadapt</source_directory>
-                    <destination_directory>$INSTALL_DIR/cutadapt</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
+    <package name="cutadapt" version="1.8">
+        <repository changeset_revision="980a47047f57" name="package_cutadapt_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
</tool_dependency>
-
-
-

diff -r eb546ac2aab2 -r 2c1f0fe810f7 trim_galore
--- a/trim_galore Fri Jul 19 09:49:25 2013 -0400
+++ b/trim_galore Wed Apr 15 11:32:11 2015 -0400

[

b'@@ -7,7 +7,7 @@\n use File::Basename;\n use Cwd;\n \n-## This program is Copyright (C) 2012-13, Felix Krueger (felix.krueger@babraham.ac.uk)\n+## This program is Copyright (C) 2012-14, Felix Krueger (felix.krueger@babraham.ac.uk)\n \n ## This program is free software: you can redistribute it and/or modify\n ## it under the terms of the GNU General Public License as published by\n@@ -25,7 +25,10 @@\n \n \n ## this script is taking in FastQ sequences and trims them with Cutadapt\n-## last modified on 10 April 2013\n+\n+## last modified on 16 July 2014\n+\n+\n \n ########################################################################\n \n@@ -36,15 +39,15 @@\n \n ########################################################################\n \n-\n-my $trimmer_version = \'0.2.8\';\n+my $trimmer_version = \'0.3.7\';\n my $DOWARN = 1; # print on screen warning and text by default\n BEGIN { $SIG{\'__WARN__\'} = sub { warn $_[0] if $DOWARN } };\n \n-my ($cutoff,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$a2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2) = process_commandline();\n+my ($cutoff,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$a2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2,$three_prime_clip_r1,$three_prime_clip_r2) = process_commandline();\n \n my @filenames = @ARGV;\n \n+\n die "\\nPlease provide the filename(s) of one or more FastQ file(s) to launch Trim Galore!\\n\n USAGE: \'trim_galore [options] <filename(s)>\' or \'trim_galore --help\' for more options\\n\\n" unless (@filenames);\n \n@@ -66,10 +69,6 @@\n $stringency = 1;\n }\n \n-unless (defined $length_cutoff){\n- $length_cutoff = 20;\n-}\n-\n if ($phred_encoding == 64){\n $cutoff += 31;\n }\n@@ -86,24 +85,36 @@\n my $filename = shift;\n \n my $output_filename = (split (/\\//,$filename))[-1];\n- # warn "Here is the outputfile name: $output_filename\\n";\n \n my $report = $output_filename;\n $report =~ s/$/_trimming_report.txt/;\n \n if ($no_report_file) {\n $report = File::Spec->devnull;\n- open (REPORT,\'>\',$report) or die "Failed to write to file: $!\\n";\n+ open (REPORT,\'>\',$report) or die "Failed to write to file \'$report\': $!\\n";\n # warn "Redirecting report output to /dev/null\\n";\n }\n else{\n- open (REPORT,\'>\',$output_dir.$report) or die "Failed to write to file: $!\\n";\n+ open (REPORT,\'>\',$output_dir.$report) or die "Failed to write to file \'$report\': $!\\n";\n warn "Writing report to \'$output_dir$report\'\\n";\n }\n \n warn "\\nSUMMARISING RUN PARAMETERS\\n==========================\\nInput filename: $filename\\n";\n print REPORT "\\nSUMMARISING RUN PARAMETERS\\n==========================\\nInput filename: $filename\\n";\n \n+ if ($validate){ # paired-end mode\n+ warn "Trimming mode: paired-end\\n";\n+ print REPORT "Trimming mode: paired-end\\n";\n+ }\n+ else{\n+ warn "Trimming mode: single-end\\n";\n+ print REPORT "Trimming mode: single-end\\n";\n+ }\n+\n+\n+ warn "Trim Galore version: $trimmer_version\\n";\n+ print REPORT "Trim Galore version: $trimmer_version\\n";\n+\n warn "Quality Phred score cutoff: $phred_score_cutoff\\n";\n print REPORT "Quality Phred score cutoff: $phred_score_cutoff\\n";\n \n@@ -193,6 +204,14 @@\n print REPORT "All Read 2 sequences will be trimmed by $clip_r2 bp from their 5\' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications)\\n";\n }\n \n+ if ($three_prime_clip_r1){\n+ warn "All Read 1 sequences will be trimmed by $three_prime_clip_r1 bp from their 3\' end to avoid poor qualities or biases\\n";\n+ print REPORT "All Read 1 sequences will be trimmed by $three_prime_clip_r1 bp from their 3\' end to avoid poor qualities or biases\\n";\n+ }\n+ if ($three_prime_clip_r2){\n+ warn "All Read 2 sequences will be trimmed by $three_prime_clip_r2 bp from their 3\' end to avoid poor quali'..b' }\n@@ -1066,7 +1179,7 @@\n \t die "Please select a sensible cutoff for when a read pair should be filtered out due to short length (allowed range: 15-100 bp)\\n\\n";\n \t}\n \tunless ($length_read_1 > $length_cutoff){\n-\t die "The single-end unpaired read length needs to be longer than the paired-end cut-off value\\n\\n";\n+\t die "The single-end unpaired read length needs to be longer than the paired-end cut-off value ($length_cutoff bp)\\n\\n";\n \t}\n }\n \n@@ -1075,7 +1188,7 @@\n \t die "Please select a sensible cutoff for when a read pair should be filtered out due to short length (allowed range: 15-100 bp)\\n\\n";\n \t}\n \tunless ($length_read_2 > $length_cutoff){\n-\t die "The single-end unpaired read length needs to be longer than the paired-end cut-off value\\n\\n";\n+\t die "The single-end unpaired read length needs to be longer than the paired-end cut-off value ($length_cutoff bp)\\n\\n";\n \t}\n }\n }\n@@ -1117,8 +1230,21 @@\n }\n }\n \n+ ### Trimming at the 3\' end\n+ if (defined $three_prime_clip_r1){ # trimming 3\' bases of read 1\n+ unless ($three_prime_clip_r1 > 0 and $three_prime_clip_r1 < 100){\n+ die "The 3\' clipping value for read 1 should have a sensible value (> 0 and < read length)\\n\\n";\n+ }\n+ }\n \n- return ($quality,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$adapter2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2);\n+ if (defined $three_prime_clip_r2){ # trimming 3\' bases of read 2\n+ unless ($three_prime_clip_r2 > 0 and $three_prime_clip_r2 < 100){\n+ die "The 3\' clipping value for read 2 should have a sensible value (> 0 and < read length)\\n\\n";\n+ }\n+ }\n+\n+\n+ return ($quality,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$adapter2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2,$three_prime_clip_r1,$three_prime_clip_r2);\n }\n \n \n@@ -1165,9 +1291,9 @@\n option requires \'--paired\' to be specified as well.\n \n \n--s/--stringency <INT> Overlap with adapter sequence required to trim a sequence. Defaults to a\n- very stringent setting of \'1\', i.e. even a single bp of overlapping sequence\n- will be trimmed of the 3\' end of any read.\n+--stringency <INT> Overlap with adapter sequence required to trim a sequence. Defaults to a\n+ very stringent setting of 1, i.e. even a single bp of overlapping sequence\n+ will be trimmed off from the 3\' end of any read.\n \n -e <ERROR RATE> Maximum allowed error rate (no. of errors divided by the length of the matching\n region) (default: 0.1)\n@@ -1205,6 +1331,15 @@\n methylation. Please refer to the M-bias plot section in the Bismark User Guide for\n some examples. Default: OFF.\n \n+--three_prime_clip_R1 <int> Instructs Trim Galore to remove <int> bp from the 3\' end of read 1 (or single-end\n+ reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted\n+ bias from the 3\' end that is not directly related to adapter sequence or basecall quality.\n+ Default: OFF.\n+\n+--three_prime_clip_R2 <int> Instructs Trim Galore to remove <int> bp from the 3\' end of read 2 AFTER\n+ adapter/quality trimming has been performed. This may remove some unwanted bias from\n+ the 3\' end that is not directly related to adapter sequence or basecall quality.\n+ Default: OFF.\n \n \n RRBS-specific options (MspI digested material):\n@@ -1273,7 +1408,7 @@\n Default: 35 bp.\n \n \n-Last modified on 15 July 2013.\n+Last modified on 16 July 2014.\n \n HELP\n exit;\n'

diff -r eb546ac2aab2 -r 2c1f0fe810f7 trim_galore_wrapper.xml
--- a/trim_galore_wrapper.xml Fri Jul 19 09:49:25 2013 -0400
+++ b/trim_galore_wrapper.xml Wed Apr 15 11:32:11 2015 -0400

[

b'@@ -1,62 +1,63 @@\n-<tool id="trim_galore" name="Trim Galore" version="0.2.8.1">\n- \n+<tool id="trim_galore" name="Trim Galore" version="0.3.7.0">\n+ \n <description>adaptive quality and adapter trimmer</description>\n <version_command interpreter="perl">trim_galore --version</version_command>\n <requirements>\n- <requirement type="package" version="1.1">cutadapt</requirement>\n+ <requirement type="package" version="1.8">cutadapt</requirement>\n </requirements>\n- <command interpreter="perl">\n- #from glob import glob\n- #import tempfile, os\n+ <macros>\n+ <macro name="paired_adapter_trimming">\n+ <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3\' end." help="" />\n+ <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off read 1">\n+ <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n+ </param>\n+ <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">\n+ <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n+ </param>\n \n- ##\n- ## Creating a temporary directory where trim_galore will store all result files\n- ##\n+ <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n+ <help>Instructs Trim Galore to remove N bp from the 3\' end of read 1 after adapter/quality trimming has been performed. \n+ This may remove some unwanted bias from the 3\' end that is not directly related to adapter sequence or basecall quality.\n+ (--three_prime_clip_R1)</help>\n+ </param>\n+ <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n+ <help>Instructs Trim Galore to remove N bp from the 3\' end of read 2 after\n+ adapter/quality trimming has been performed. This may remove some unwanted bias from\n+ the 3\' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help>\n+ </param>\n+ </macro>\n+ </macros>\n+ <command>\n+<![CDATA[\n \n- #set $temp_dir = os.path.abspath(tempfile.mkdtemp())\n-\n-\n- ## trim_galore removes .fastq and .fq file extensions of input files. \n- ## That is essential if Galaxy provides links to files (these can have real extensions), but that behaviour is causing an inconsitency in output filenaming.\n- ## Fix: link every file to $TMP without file extension\n+ ## trim_galore removes .fastq and .fq file extensions of input files.\n+ ## This is essential if Galaxy provides links to files (with real extensions)\n+ ## but that behaviour is causing an inconsitency in output filenaming.\n+ ## We work around this by linking every file to cwd without file extension\n \n #if $singlePaired.sPaired == "single":\n- #set $input_singles_tmp_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )\n- #set $input_singles_tmp = $input_singles_tmp_handle.name\n- #silent $input_singles_tmp_handle.close()\n- #silent os.system("ln -s %s %s" % (str($singlePaired.input_singles), $input_singles_tmp))\n+ ln -s "${singlePaired.input_singles}" ./input_singles;\n+ #elif $singlePaired.sPaired == "paired":\n+ ln -s "${singlePaired.input_mate1}" ./input_mate1;\n+ ln -s "${singlePaired.input_mate2}" ./input_mate2;\n #else:\n- '..b'_unpaired\'][\'settingsType\'] == "retain_unpaired_output" and\n+ singlePaired[\'sPaired\'] == "paired"\n+ ))\n+ </filter>\n </data>\n \n <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">\n- <filter>\n+ <filter>\n ((\n params[\'settingsType\'] == "custom" and\n params[\'report\'] == True\n ))\n- </filter>\n+ </filter>\n </data>\n \n </outputs>\n <tests>\n- </tests>\n+ <test>\n+ \n+ <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n+ <param name="sPaired" value="single" />\n+ <param name="settingsType" value="custom" />\n+ <param name="report" value="true" />\n+ <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>\n+ <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="2" />\n+ </test>\n+\n+ <test>\n+ \n+ <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n+ <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ <param name="sPaired" value="paired" />\n+ <param name="settingsType" value="custom" />\n+ <param name="report" value="true" />\n+ <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>\n+ <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>\n+ <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="8" />\n+ </test>\n \n+ <test>\n+ \n+ <param name="input_mate_pairs">\n+ <collection type="paired">\n+ <element name="forward" value="bwa-mem-fastq1.fq" />\n+ <element name="reverse" value="bwa-mem-fastq2.fq" />\n+ </collection>\n+ </param>\n+ <param name="sPaired" value="paired_collection" />\n+ <param name="settingsType" value="custom" />\n+ <param name="report" value="true" />\n+ <param name="retain_unpaired" value="retain_unpaired_output" />\n+\n+ <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="8" />\n+\n+ <output_collection name="trimmed_reads_paired_collection" type="paired">\n+ <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>\n+ <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>\n+ </output_collection>\n+\n+ <output_collection name="trimmed_reads_unpaired_collection" type="paired">\n+ <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>\n+ <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n <help>\n+<![CDATA[\n \n **What it does**\n \n-TrimGalore!_ is a wrapper script that makes use of the publically available \n+TrimGalore_ is a wrapper script that makes use of the publically available\n adapter trimming tool Cutadapt.\n \n+.. _TrimGalore: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\n+\n \n-.. _TrimGalore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\n+It is developed by Felix Krueger at the Babraham Institute.\n \n \n-It is developed by Krueger F at the Babraham Institute.\n-\n-\n- </help>\n+]]>\n+ </help>\n </tool>\n'