# HG changeset patch
# User peterjc
# Date 1416570072 18000
# Node ID 0996169ac2e86eb646dc4f4ce67c3f8853c38298
Uploaded v0.0.2, previously only on the TestToolShed
diff -r 000000000000 -r 0996169ac2e8 test-data/NC_010642.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_010642.fna Fri Nov 21 06:41:12 2014 -0500
@@ -0,0 +1,245 @@
+>gi|187250362|ref|NC_010642.1| Panthera tigris mitochondrion, complete genome
+GGGTTAATGACTAATCAGCCCATGATCACACATAACTGTGGTGTCATGCATTTGGTATTTTTAATTTTTA
+GGGGGTCGAACTTGCTATGACTCAGCTATGACCTAAAGGTCCCGACTCAGTCAAATATAATGTAGCTGGA
+CTTATTCTCTATGCGGGGGTTCCACACGTACAACAAACAAGGTGTTATTCAGTCAATGGTCACAGGACAT
+ATACTTAAATTCCTATTGTTCCACAGGACACGGCATGCGCGCACCCACGTATACGCGTACACGTATACAC
+GTATACACGTACACACGTACACACGTACACACGTACACACGTACACACGTATACACGTATACACGTATAC
+ACGTATACACGTATACACGTATACACGTATACACGTATACACGTATACACGTATACACGTACACACGTAC
+ACACGTACACACGTACACACGTATACACGTATACACGTATACACGTATACACGTATACGCGTACACGTAC
+ACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGT
+ACACACGTACACACGTACACACGTACACACGTACACACGTATACACGTATACACGTATACACGTATACAC
+ATGCAAACTTTTTTGATTTAGTAAATAATTAGCTTAACCAAACCCCCCTTACCCCCCGTTAATCTTATTT
+ATTATAGTACGTGTTTATTTCTGTCTTGCCAAACCCCAAAAACAAGACTAAACCCGTATCTAGGCACAAG
+GCCTAAGATTAACGTTTACAAACTCTACCAACCCCATCATTACCAATTATTAATACTAAATCATAACTTC
+GTTCGCAGTTATCTATAGATACGACAACCCGATCTCTAATTCGTCCCTATCGAACAATATTTACATACCC
+AACAACCCTATGTCTTGGTTAATGTAGCTTAAATATATTAAAGCAAGGCACTGAAAATGCCTAGATGGGC
+CGCCAGGCTCCATAAACATAAAGGTTTGGTCCTAGCCTTTCCATTAGTTGTTAATAAAATTACACATGCA
+AGCCTCCGCATCCCGGTGAAAATGCCCTCTAAATCACCCAGTGATCCAAAGGAGCCGGTATCAAGTACAC
+AACCATTGTAGCTCATGACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTGATAAAAATTAAGCC
+ATGAATGAAAGTTCGACTAAGCTATATTAAATTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATA
+CGATTAACCCAAACTAATAGACCCACGGCGTAAAGCGTGTTACAGAAAAAAGTATACTAAAGTTAAGCCT
+TAACTAGGCTGTAAAAAGCCACAGTTAACGTAAAAATACAGCACGAAAGTAACTTTAATATTTCTGACCA
+CACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTAGATAGTTAACC
+CAAACAAAACTATCCGCCAGAGAACTACTAGCAACAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATA
+TCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACCCCGATAAACCTCACCATCTCTTGCTAATTCAGCC
+TATATACCGCCATCTTCAGCAAACCCTAAAAAGGAAGAAAAGTAAGCACAAGTATCTTAACATAAAAAAG
+TTAGGTCAAGGTGTAGCCCATGAGATGGGGAAGTAATGGGCTACATTTTCTATAACTAGAACATCCACGA
+AAATCCTTATGAAATTAAGTATTAAAGGAGGATTTAGTAGTAAATTCGAGAATAGAGAGCTCGATTGAAT
+CGGGCCATGAAGCACGCACACACCGCCCGTCACCCTCCTCAAGTGATTAGACCCCAAAGAAACCTATTCA
+AACCACTACACCCACAAGAGGAGACAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGATAACA
+AGATGTAGCTTAAACAAAGCATCTGGCCTACACCCAGAAGATTTCATATTAAACTGACCATCTTGAGCTA
+GAGCTAGCCCAACTACCCATAAACACAACTAACATTAGAAAGTAAAACAAAACATTTAGTTACTCTAAAA
+AGTATAGGAGATAGAAATTTAACTCGGCGCTATAGAAAAAGTACCGCAAGGGAATGATGAAAGAAAAAAC
+TAAAAGCACTATACAGCAAAGATTACCCCTTGTACCTTTTGCATAATGAATTAGCTAGAATAACCTAACA
+AAGAGAACTTCAGCTAGGCCCCCCGAAACCAGACGAGCTACCCATAAACAATCTATTACAGGATGAACTC
+GTCTATGTTGCAAAATAGTGAGAAGATTTATGGGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTG
+GTTGCCCAGAACAGAATCTTAGTTCAGCTTTAAACTTACCTCAAAAACCCTAAAATTCCAATGTAAGTTT
+AAAATATAGTCTAAAAAGGTACAGCTTTTTAGAATCTAGGATACAGCCTTAATTAGAGAGTAAGCATATA
+ACACAAACCATAGTTGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACAATCAAAACATC
+TCAATGTCAAAAAACGCAACCAACTCCTAATCTAAAACTGGGCTAATCTATTTAACAATAGAAGCAATAA
+TGCTAATATGAGTAACAAGAAATACTTCTCCCGCGCATAAGCTTATATCAGAACGGATAACCACTGATAG
+TTAACAACAAGATATATATAACCTAACTACAAGCAAAATATCAGACTAATTGTTAACCCAACACAGGCAT
+GCAATTTAGGGAAAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAGCCCCGCCTGTTTACCAAAAA
+CATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCCAGTGACATTAGTTAAACGGCCGCGGTAT
+CCTGACCGTGCAAAGGTAGCATAATCATTTGTTCCTTAAATAGGGACTTGTATGAATGGCCACACGAGGG
+CTTTACTGTCTCTTACTTCCAATCCGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATACGACAATAAGA
+CGAGAAGACCCTGTGGAGCTTTAATTAATCGACCCAAAGAGACCTTAATAACCAACCGACAGGAACAACA
+GACCTCTGCCATGGGCCGACAATTTAGGTTGGGGTGACCTCGGAGAATAAAACAACCTCCGAGTGATTTA
+AATCTAGACTGACCAGTCGAAAGTATTACATCACTTATTGATCCAAAGCTTGATCAACGGAACAAGTTAC
+CCCAGGGATAACAGCGCAATCCTATTTCAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGA
+TCAGGACATCCCGATGGTGCAGCAGCTATCAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCT
+GAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTATTAAATAATTTCTCCCAGTACGAAAGGACAAG
+AGAAATAAGGCCCACTTTACCAAAGCGCCTTTAACCAAATAGATGATATAATCTCAATCTAAACAGTTTA
+TCTAAACATATCACCCGTAGAGCTCGGGTTTGTTAGGGTGGCAGAGCCCGGCAATTGCATAAAACTTAAG
+CTTTTACTATCAGAGGTTCAACTCCTCTCCCTAACAGCATGTTTATAATCAATATTCTCTCATTAATTAT
+CCCTATTCTCTTCGCCGTAGCCTTCCTAACCCTAGTTGAACGTAAAGTACTGGGCTACATACAACTCCGT
+AAAGGACCAAACGTCGTAGGACCATACGGCCTACTTCAGCCTATTGCAGACGCCATGAAACTCTTCACTA
+AAGAACCCCTCCGACCCCTCACATCCTCCACATTCATATTCATCACAGCACCCATCCTAGCTCTTACACT
+AGCCCTAACCATATGAATCCCACTGCCCATACCATACCCACTCATTAACATAAACTTAGGAGTGCTATTT
+ATACTAGCTATGTCCAGCCTAGCTGTTTACTCCATTCTATGATCAGGATGGGCTTCAAACTCAAAATATG
+CCCTAATCGGAGCCCTACGAGCCGTAGCCCAAACAATCTCATATGAAGTCACATTAGCTATCATTCTCTT
+ATCAGTACTACTAATAAATGGATCCTTCACATTAGCTGCACTAATTACCACCCAAGAATACATCTGGCTC
+ATCATCCCTGCATGACCCCTAGCCATAATATGATTCATCTCCACACTAGCAGAAACCAACCGAGCTCCAT
+TTGATCTAACAGAAGGAGAATCAGAACTCGTTTCCGGATTCAACGTAGAATACGCAGCAGGCCCCTTTGC
+CCTATTTTTTCTAGCAGAATACGCTAATATTATCATAATAAACATCCTCACAACAATCTTATTTTTCGGA
+GCATTCCATAATCCCTATATACCAGAACTATATACTATCAACTTCACTGTAAAAACCCTAATTCTAACAA
+CCACCTTCCTATGGATCCGAGCATCTTATCCACGATTCCGATATGACCAATTAATGCACCTCCTATGAAA
+AAACTTCCTACCCCTTACTCTAGCCCTATGCATATGACACGTCTCCCTACCCATCATTACAGCAAGCATT
+CCACCCCAAACATAAGAAATATGTCTGACAAAAGAATTACTTTGATAGAGTAAAACATAGAGGTTTAAGC
+CCTCTTATTTCTAGAATTATAGGAATCGAACCTAATCCTAAGAATCCAAAAATCTTCGTGCTACCAATAT
+TACACCACATTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTACAC
+CCTTCCCATACTAATCAAACCCCCTATCCTCACCATCATTATACTAACCGTTATCTCAGGAACTATAATC
+GTAATAACAACTTCTCACTGACTTATAGTCTGAATTGGCTTCGAAATAAACCTATTAGCTATTATTCCCA
+TCCTCATGAAAAAATATAACCCACGAGCCATAGAAGCAGCCACAAAATACTTCCTGACACAAGCAACCGC
+TTCAATACTCCTAATAATAGGAATTATCATCAACCTGCTGCACTCAGGACAATGAACCGTATCAAAAGAC
+CTCAACCCCATGGCATCCATTATAATAACAACCGCCTTAGCAGTAAAACTAGGACTAGCCCCATTCCACT
+TCTGAGTGCCCGAAGTTACACAAGGAATCTCCTTGTCTTCAGGCCTGATCCTACTCACATGACAAAAAAT
+CGCACCACTATCAATTCTTTACCAAATTTCACCCACCATTAACCCCAACCTACTCCTAGCAATAGCCATT
+ATATCAGTTATAATCGGAGGCTGAGGGGGACTTAACCAAACCCAGCTACGAAAAATCATAGCATACTCCT
+CAATCGCCCATATAGGTTGAATAACAGCCATCATAATATATAGCCCCACAATAATAATTTTAAACCTGAC
+TATCTATATCATTATAACACTAACCACTTTCATGTTACTCATATACAACTCCACCACAACAACATTATCC
+TTATCACAAACATGAAACAAAACGCCCCTGATCACCTCACTTATCCTACTGCTAATAATGTCTCTGGGCG
+GCCTCCCCCCACTCTCTGGCTTCATCCCAAAATGAATAATCATTCAAAAACTAACCAAAAATGAAATAAT
+CATAATACCCACACTACTAGCCATAACAGCACTACTTAACCTGTACTTCTACATACGACTAACATATACC
+ACTGCACTAACTATATTCCCCTCAAACAACTGTATAAAAATAAAATGACGGTTCAAATGCACAAAAAAAA
+TAATCTTTTTACCCCCCTTAATCGTAATGTCCACCATGCTACTCCCACTCACACCAATACTATCCGTCCT
+AGATTAGAAAGTTTAGGTTAAACTAGACCAAGAGCCTTCAAAGCTCTAAGTAAGCCCTATAGAATTAACT
+TCTGCATACCTATTAACTCTAAGGACTGGAAGAATCTATCTTACATCAATTGACTGCAAATCAAACACTT
+TAATTAAGCTAAGCCCTTACTAGATTGGTGGGCCCTAACCCCACGAAATTTTAGTTAACAGCTAAATACC
+CTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCTGGAAAAAAAAGGCGGGAGAAGCCCCGGCAGCGT
+CAAGCTGCTTCTTTGAATTTGCAATTCAATATGACATTCACTACAGGACTTGGTAAAAAGAGGGTTAGAA
+CCTCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATAAACCGCTGACTA
+TTTTCAACCAATCACAAGGATATTGGAACTCTTTACCTTTTATTTGGCGCCTGGGCTGGTATAGTGGGGA
+CTGCCCTCAGTCTCCTAATTCGAGCCGAACTGGGTCAACCTGGCACACTACTAGGAGATGACCAAATTTA
+TAATGTAGTAGTTACTGCCCATGCCTTTGTGATAATCTTTTTTATAGTAATGCCTATTATAATTGGAGGA
+TTCGGAAACTGGCTAGTTCCGTTAATAATCGGAGCCCCCGATATGGCATTCCCTCGAATGAATAACATAA
+GCTTCTGACTCCTTCCCCCATCCTTCCTACTTCTGCTCGCATCGTCTATGGTAGAAGCTGGGGCAGGAAC
+TGGGTGGACAGTATACCCACCCCTAGCTGGCAACCTAGCCCATGCAGGAGCATCCGTGGATCTAACTATT
+TTTTCACTACACCTAGCAGGCGTCTCCTCAATCTTAGGTGCTATTAATTTTATTACTACTATTATTAATA
+TAAAACCGCCCGCTATGTCCCAATACCAAACACCCCTGTTTGTTTGATCGGTTCTAATTACTGCTGTGTT
+GCTACTTCTATCACTGCCAGTTTTAGCAGCAGGCATCACCATGCTACTGACAGATCGAAATCTAAATACC
+ACATTTTTTGATCCTGCCGGGGGAGGAGACCCCATCTTATATCAACACCTATTCTGATTCTTCGGTCACC
+CAGAAGTCTATATCTTAATCCTGCCCGGGTTTGGAATAATTTCACATATTGTCACCTACTACTCAGGCAA
+AAAAGAACCTTTTGGCTACATGGGGATAGTCTGAGCCATAATGTCAATTGGCTTTCTGGGCTTTATCGTA
+TGGGCCCATCACATGTTTACTGTAGGGATAGATGTGGATACACGAGCATACTTTACGTCAGCTACTATAA
+TTATCGCTATTCCTACTGGGGTAAAAGTATTTAGCTGATTGGCCACTCTTCACGGGGGTAATATTAAATG
+GTCTCCCGCTATACTATGGGCTTTGGGATTCATTTTCCTATTCACCGTAGGGGGCTTAACAGGAATTGTA
+CTAGCAAACTCCTCATTGGATATTGTCCTTCACGACACATACTACGTAGTAGCCCACTTCCACTACGTCT
+TGTCAATAGGAGCAGTATTTGCTATTATAGGGGGCTTCGTTCACTGATTCCCCTTATTCTCAGGGTATAC
+TCTTGATAATACTTGGGCAAAAGTTCATTTTACGATCATGTTCGTAGGTGTCAATATAACGTTTTTCCCT
+CAGCATTTCCTAGGCCTGTCTGGGATGCCTCGACGTTATTCTGACTATCCAGACGCGTATACAACTTGAA
+ACACAATCTCCTCAATAGGCTCTTTTATTTCACTAACAGCAGTAATATTAATAGTCTTTATAATGTGAGA
+AGCTTTCGCATCAAAGCGAGAAGTAGCCACAGTGGAACTAACCACAACTAATCTCGAATGACTTCACGGA
+TGTCCTCCTCCGTATCACACATTTGAAGAGCCAGCCTACGTGCTGTTAAAATAAGAAAGGAAGGAATCGA
+ACCTCCTTAGACTGGTTTCAAGCCAATACCATAACCACTATGTCTTTCTCAATTAAGAAGTATTAGTAAA
+ATAATTACATAACTTTGTCAAAGTTAAATTATAGGTTTAAGCCCTATGTGCTTCCATGGCATACCCCTTC
+CAACTAGGTTTTCAAGATGCTACATCCCCCATTATAGAAGAGCTTTTACACTTCCATGATCATACATTAA
+TAATTGTATTCCTAATTAGCTCCCTAGTCCTCTACATTATCTCATTAATACTGACAACTAAACTTACGCA
+TACAAGCACAATAGATGCCCAAGAAGTAGAAACTATCTGAACCATTTTACCAGCCATCATCTTAATTCTC
+ATTGCCCTGCCTTCCTTACGAATTCTCTATATAATAGATGAGATTAATAATCCCTCCCTCACTGTAAAGA
+CTATAGGACATCAGTGATACTGAAGTTATGAGTACACCGACTATGAGGACCTAAGCTTCGACTCCTACAT
+AATCCCCACTCAAGAGTTAAAGCCCGGAGAGCTCCGACTACTAGAAGTTGATAACCGAGTAGTGTTGCCA
+ATAGAAGTGACTATTCGCATGTTAGTCTCATCAGAGGACGTACTGCACTCGTGAGCCATCCCATCCCTGG
+GCCTAAAAACTGACGCTATCCCAGGCCGACTAAACCAAACAACCCTAATAGGCACACGGCCTGGGCTATA
+TTATGGTCAGTGCTCAGAAATCTGCGGCTCAAATCACAGTTTTATGCCCATTGTCCTTGAACTAGTCCCG
+CTGTCATATTTCGAAAAATGATCTGCATCTATGCTGTAATTTCACTAAGAAGCTAAATTAGCGTTAACCT
+TTTAAGTTAAAAACTGGGAGTTCAAACCTCCCCTTAGTGACATGCCACAGTTAGACACATCAACCTGATT
+TATTACTATTATTTCAATAATCATGACACTGTTCGTTATATTTCAACTAAAAATCTCAAAACATCTGTAC
+CCATCAAGCCCAGAACCCAAATCTACAGCTGCATTAAAACAGCCGAGTCCCTGAGAAAAAAAATGAACGA
+AAATCTATTCACCTCTTTTACTACCCCAACAATAATAGGACTGCCTGTTGTTGTGTTAATCGTTATGTTC
+CCCAGCATTCTATTTCCCTCGCCTAACCGACTAATTAATAACCGCCTAGTCTCACTCCAACAATGATTAG
+TACAACTTACATTAAAGCAAATACTGATTACCCACAATTACAAAGGACAAACCTGGGCCCTAATACTTAT
+GTCTCTCATTTTATTTATTGGGTCAACAAATCTGCTAGGTCTACTACCTCACTCATTTACTCCAACTACC
+CAATTATCAATAAACCTAGGCATAGCCATCCCCTTGTGAGCCGGCACCGTAATCACTGGATTCCGTCACA
+AAACTAAAGCATCCTTGGCCCACTTTCTACCACAAGGAACACCAGTCCCCTTAATCCCTATGCTCGTAAT
+TATCGAAACTATCAGCCTTTTTATCCAGCCCGTAGCCCTAGCCGTACGACTCACAGCTAATATTACTGCA
+GGCCATTTATTAATACACCTAATCGGAGGAGCTGCTTTAGCCCTAACAAATATTAGTGCCCCTACTGCTT
+TAATTACCTTTATCATCCTCATCCTACTGACAATTCTTGAATTCGCTGTAGCTCTAATCCAAGCCTATGT
+TTTTACCCTACTTGTGAGCCTGTATTTACATGATAATACTTAATGACCCACCAAACCCACGCATATCACA
+TGGTTAATCCCAGCCCATGGCCACTTACAGGGGCCCTTTCGGCCCTACTAATAACCTCAGGCCTGGCTAT
+ATGATTTCACTATAACTCAATACTACTATTAACTCTAGGAATAACCACTAACCTATTGACTATATACCAA
+TGGTGACGAGACATCATTCGGGAGAGCACATTCCAAGGCCACCACACACCCATTGTTCAAAAAGGCCTCC
+GATACGGAATAATCCTTTTCATCATCTCAGAAGTATTCTTCTTCGCAGGTTTTTTCTGGGCCTTCTATCA
+CTCAAGCCTGGCCCCGACCCCCGAATTGGGAGGATGCTGGCCACCAACAGGTATTATTCCCCTAAACCCC
+CTAGAAGTCCCACTACTCAATACTTCTGTGCTCTTAGCTTCCGGAGTGTCAATCACCTGAGCCCATCATA
+GCCTAATAGAAGGAAATCGAAAACACATGCTCCAAGCACTATTTATTACAATCTCCCTAGGAGTCTATTT
+TACCCTCCTCCAAGCCTCTGAGTACTATGAAACATCATTTACAATCTCGGACGGAGTTTATGGGTCCACC
+TTTTTCATAGCCACAGGGTTCCACGGACTACACGTAATTATTGGCTCTACCTTCCTAATCGTATGTTTCT
+TGCGCCAACTAAAATACCACTTCACATCGAGCCACCATTTTGGATTCGAAGCCGCTGCTTGATATTGACA
+TTTCGTAGACGTGGTTTGACTGTTCTTATACGTTTCCATTTATTGATGAGGATCCTATTCCCTTAGTATC
+AACAAGTACAGTTGACTTCCAATCAACCAGTTTCGGTATAATCCGAAAGGGAATAATAAACATAATACTC
+GCTCTACTCACCAACACACTTCTATCCACACTACTTGTACTCATCGCGTTCTGACTACCCCAACTAAACA
+CCTATGCAGAAAAAGCAAGTCCTTATGAATGTGGATTTGACCCCATAGGATCCGCTCGCCTGCCCTTCTC
+CATAAAATTCTTCCTAGTAGCTATCACATTCTTGCTATTCGACCTAGAAATTGCACTACTGCTCCCTCTT
+CCCTGAGCCTCACAAACAAACAAACTGTCAACCATGCTTATCACAGCCCTTCTACTAATCTCCCTATTAG
+CCGCAAGCCTAGCCTACGAGTGAACCCAAAAAGGATTAGAATGAACTGAATATGATAATTAGTTTAAACT
+AAAACAAATGATTTCGACTCATTAGATTGTAGCTTACCCTATAATTATCAAATGTCCATAGTCTATGTTA
+ACATCTTCCTGGCTTTCATCGTATCACTCATAGGACTATTAATGTACCGATCCCACTTAATATCCTCCCT
+TCTATGCCTAGAAGGCATAATACTATCCCTATTTATTATGATAACCATGGCAGTTCTAAACAATCACTTT
+ACACTAGCTAGCATGACCCCCATTATCCTGCTAGTATTTGCAGCCTGCGAGGCAGCACTGGGCTTGTCCC
+TACTAGTAATGGTATCAAATACATATGGTACCGACTATGTACAAAACCTAAACCTCTTGCAATGCTAAAA
+ATTATTATCCCCACTGCCATACTCATACCAATAACATGATTATCAAAACCCAGCATAATCTGAATTAACT
+CAACCACCTATAGTTTTCTGATCAGCCTTGTTAGCCTGTCCTACTTAAATCAACTAGGCGACAACAGCCT
+AAATCTCTCATTACTATTTTTCTCAGACTCACTCTCTGCACCCCTACTAGTATTAACAACATGACTCTTA
+CCACTAATGCTCATGGCTAGTCAATCACACCTGTCAAAAGAGACCCTAGCCCGAAAAAAACTATACATTA
+CAATACTTATTATCCTACAACTCCTCTTAATTATAACATTCACCGCTACAGAACTGATTATATTCTACAT
+TCTATTCGAAGCTACATTAATCCCTACTCTTATTATTATCACTCGATGAGGCAATCAAACAGAGCGACTA
+AACGCTGGTCTGTACTTTCTATTCTACACCCTGGTAGGCTCACTACCCCTCCTAGTCGCACTACTATACA
+TCCAAAACACAACAGGAACTCTGAACTTCCTAATTATTCAATACTGAGCCAAACCAATTTCAGCCACCTG
+ATCTAATATCTTTCTCTGACTAGCATGCATAATAGCATTCATAGTAAAAATACCTCTATATGGGCTCCAC
+CTGTGACTACCAAAAGCACATGTCGAAGCTCCCATTGCCGGCTCAATAGTCCTTGCTGCTGTACTGTTGA
+AGCTAGGAGGATATGGAATGATACGCATTACAATCCTACTCAACCCCACAACAAACCAAATGGCATACCC
+CTTCATAATGCTATCCCTATGGGGAATAATTATAACAAGCTCTATTTGTCTACGCCAGACAGACCTAAAA
+TCCCTAATCGCATATTCATCCGTAAGCCATATGGCCCTAGTAATCGTGGCCGTACTAATTCAAACACCTT
+GGAGTTACATAGGAGCCACAGCTCTTATAATCGCCCACGGACTAACTTCCTCAGTGCTATTTTGCCTTGC
+AAACTCAAACTACGAACGAATCCATAGCCGAACAATAATTCTCGCACGAGGCCTACAAACCATCCTCCCC
+CTAATAGCTGCTTGATGACTACTGGCCAGCCTCGCAAACCTGGCCCTACCTCCTACTATTAACCTAATTG
+CAGAGCTATTTGTAGTAGTGGCCTCCTTTTCATGATCTAACATAACCATTACTCTCATGGGCACAAATAT
+CATCATCACAGCCCTATATACCCTCTACATACTCATTACAACCCAACGAGGCAAATATACACACCACATT
+AAAAACATCAATCCATCATTCACACGAGAAAATGCCCTAATAACACTTCATCTGCTCCCACTTTTTCTCT
+TATCTCTCAACCCCAAAATCGTACTAGGTCCTATTTACTGTAAATATAGTTTAATAAAAACATTAGATTG
+TGAATCTAATAATAGAAGTGCAAATCTTCCTATTTAAACGAAAAAGTATGCAAGAGCTGCTAACTCATGC
+CCCCACGTATAAAAACGTGGCTTTTTCAACTTTTATAGGATAGAAGTAATCCATTGGTCTTAGGAGCCAA
+AAAATTGGTGCAACTCCAAATAAAAGTAATAAACCTACTTACCTCCTCTATACTCACTGCGATATTTATC
+CTACTCCTACCTATCATTACATCCAACACTCAATTATATAAAAGTAACCTATACCCTCACTATGTAAAAA
+CCACAATCTCTTACGCCTTTACCATTAGTATAATCCCAGCCATAATATTCATTTCCTCCGGACAAGAGAT
+AACCATCTCAAACTGATGTTGACTATCAATTCAAACCCTTAAATTATCACTAAGCTTCAAACTAGATTAT
+TTCTCGATCATCTTCATCCCAGTAGCACTTTTCGTTACATGGTCGATCATAGAATTCTCAATGTGATACA
+TACACACAGATCCCTATATTAACCAGTTCTTTAAGTACCTCCTTATATTCCTAATCACTATAATGATCTT
+AGTGACCGCCAATAATCTATTTCAGCTGTTTATTGGATGGGAGGGAGTAGGAATTATATCTTTCCTACTT
+ATCGGATGATGATATGGTCGAGCAGACGCAAACACTGCCGCCCTGCAAGCAATTCTCTACAACCGTATTG
+GTGATGTAGGATTTATCATGGCCATAGCATGATTCCTTACCAACCTAAATGCATGAAACCTCCAACAAAT
+CTTTATCACTCAACATGAAAGCCTGAATATGCCATTACTAGGACTCCTCCTAGCCGCCACAGGCAAGTCC
+GCCCAATTTGGCCTACACCCATGATTGCCATCAGCCATAGAAGGTCCAACTCCCGTCTCCGCCCTACTCC
+ACTCAAGCACAATAGTTGTAGCCGGAGTCTTCTTATTAATCCGCTTCCACCCACTCATAGAACAAAATAA
+AGCCATACAAACCCTCACTCTATGCCTGGGGGCCATCACAACCCTATTCACAGCCATCTGTGCCCTCACA
+CAAAATGATATTAAAAAAATTGTTGCTTTCTCAACTTCAAGCCAATTAGGCCTGATAATCGTTACTATCG
+GAATTAACCAACCCTACCTTGCATTCCTGCATATCTGCACACACGCATTTTTTAAAGCCATATTATTCAT
+GTGCTCCGGATCAATTATCCACAGTCTAAACGACGAGCAAGATATTCGAAAAATAGGCGGACTATATAAA
+CCAATACCCTTTACTACCACCTCCCTTATTATCGGAAGCCTCGCATTAACAGGCATGCCATTCCTAACAG
+GCTTTTACTCCAAAGACCTAATCATCGAGACAGCCAATACGTCGTATACCAACGCCTGAGCCCTATTGGT
+CACTCTCATTGCTACATCCCTCACAGCCGCCTATAGTACTCGAATCATATTCTTTGCACTCCTGGGGCAA
+CCCCGATTCAACTCCCTAAGCCCAATCAATGAAAACAACCCCCACCTCATCAACTCCATTAAACGTCTCT
+TAATTGGAAGCATTTTTGCAGGATACTTGATCTCCCATAACATCCCCCCAACGACCATCCCACAAATGAC
+CATACCCTGCCACCTAAAACTAACTGCTCTCGCCATGACCATCATAGGCTTTATCCTGGCATTAGAGCTT
+AACCTCGTGGCTAAAAACTTAAAATTTAAATACCCCTCAAATCTTTTTAAGTTTTCTAACCTCCTCGGGT
+ACTTTCCAATCGTAATTCACCGCCTCCCATCGATAATAAGCCTAACCATAAGCCAAAAATCCGCATCGAT
+ACTATTAGATATAATCTGGCTAGAAAATGTAATACCAAAATCCATCTCCCACTTCCAAATAAAAATATCA
+ACCGCCGTATCTAATCAGAAGGGACTAGTTAAGCTCTACTTCCTATCCTTCATAATCACCCTGACCCTTA
+GCCTACTCTTACTTAGTTTCCACGAGTAACCTCTATAATCACCAATACACCAATAAGCAAAGACCAACCA
+GTGACAACCACTAGCCAGGTTCCATAACTATACAGTGCTGCAATTCCTATGGCCTCCTCACTAAAAAACC
+CCGAGTCACCCGTATCATAGATCACTCAATCACCCGCACCATTAAACTTAAACACAACCTCAACCTCATC
+TTCCTTTAAAATATAGCAAGCAGTCAACAACTCCGCTAATACCCCCGTAATAAACGCACCTAATACGGCT
+TTATTAGATGTCCACGCCTCGGGGTAGGGCTCAGTAGCCATAGCTGTAGTGTACCCAAACACCACAAGCA
+TGCCCCCCAAATAAATTAAAAAAACTATTAAACCTAAAAATGACCCCCCAAAATTCAATACAATACCGCA
+ACCAACACCACCAGCCACAATCAATCCAAGCCCACCATAAATAGGAGAAGGCTTTGAAGAAAAACTCACA
+AAGCTCACCACGAAAATTGTACTTAAAATAAATACAATGTATGTTATCATAATTCTCACATGGATTCTAA
+CCACGACCAATGATATGAAAAACCATCGTTGTATTTCAACTATAAGAACTTAATGACCAACATTCGAAAA
+TCACACCCCCTTATCAAAATTATTAATCACTCATTTATTGACCTACCCGCCCCATCCAATATTTCAGCAT
+GATGAAACTTTGGCTCCTTACTAGGGGTGTGCTTAATCTTACAAATCCTCACTGGCCTCTTTCTAGCCAT
+ACACTACACATCAGACACAATAACCGCTTTCTCATCAGTTACCCACATTTGCCGCGACGTAAACTACGGC
+TGGATTATCCGATATCTACATGCCAACGGAGCCTCCATATTCTTTATCTGTCTATACATGCACGTAGGAC
+GAGGAATATACTACGGCTCCTACACCTTCTCAAAAACATGAAATATCGGGATTGTGCTATTGTTTACGGT
+CATGGCTACAGCCTTCATAGGATATGTCTTACCATGAGGACAAATATCATTCTGAGGGGCAACCGTAATC
+ACCAACCTCCTGTCAGCAATCCCATATATTGGGACCGACCTAGTAGAGTGAATCTGAGGGGGTTTCTCAG
+TAGACAAAGCTACCCTGACACGATTCTTTGCCTTCCACTTCATCCTTCCGTTTATCGTCTCAGCCCTAGC
+AGCAGTCCACCTCCTATTCCTTCACGAAACAGGATCCAATAACCCCTCAGGAATGGTGTCCGACTCAGAC
+AAAATCCCATTCCACCCATACTACACAATTAAAGATATCTTAGGCCTCTTAGTACTAATCCTAACCCTCA
+CACTACTCGTCCTATTCTCACCAGACCTATTAGGAGACCCTGATAACTACATCCCCGCCAACCCCCTAAA
+TACCCCTCCCCATATTAAGCCCGAATGGTATTTCCTATTCGCATACGCAATCCTCCGATCTATTCCCAAT
+AAACTAGGAGGAGTTCTAGCCCTAGTCTTATCCATCTTAATCTTAGCCACTATCCCTGCCCTCCACACAT
+CCAAACAACGAGGAATAATGTTTCGACCGCTAAGCCAATGCTTATTCTGACTCTTAGTGGCAGACCTTCT
+AACCCTAACATGAATTGGTGGCCAACCTGTAGAACACCCCTTTATTGCCATCGGCCAACTAGCCTCTATC
+CTATACTTCTTCATCCTCCTAGTCTTAATCCCCATCTCAGGCATTATTGAAAACCGCCTCCTTAAATGAA
+GAGTCTTCGTAGTATATAAATTACTTTGGTCTTGTAAACCAAAAAAGGAGAATATGTACTCTCCCTAAGA
+CTTCAAGGAAGAAGCAATAGCCCCACCATCAGCACCCAAAGCTGAAATTCTTTCTTAAACTATTCCTTGC
+CAATACCAAAAAACAACCCCATGACTTTCATAATTCATATATTGCATATACCCGTACTGTGCTTGCCCAG
+TATGTCCTCATCCCCACAAAAAATAAGTGAAAAAATCCTCAATCCCCGTTAATACAGAACACACAACACG
+AAATAACCTGTTAACTACCGGACCCCCCCCCTCCCCCCGTTAACACATTACGTAGGGCATACTATGTATA
+TCGGGCATTAATCGCCTGTCCCCATGAATATTAAGCATGTACAGTAGTTTATATATTTTACATAAGGCAT
+ACTATGTATATCGTGCATTAATCCCTTGTCCCCATGAATATTAAGCATGTACAGTAGTTCATATATATTA
+CATAAAACATAATAGTGCTTAATCGTGCATATTCATGATTTAAAACAGTTCTTTCATGGATCTCAACTAT
+CCGAAAAAGCTTAATCACCTGGCCTCGAAAAACCAACAACCCTTGCTCGAGCGTGTACCTCTTCTCGCTC
+CGGGCCCATTTCAACGTGGGGGTGTCTATAGTGAAACTATACCTGGCATCTGGTTCTTACTTCAGGGTCA
+TGACATTCTTAAATCCAATCCTTCAACTTTCTCAAATAGGACATCTCGAT
+
diff -r 000000000000 -r 0996169ac2e8 tools/clc_assembly_cell/README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clc_assembly_cell/README.rst Fri Nov 21 06:41:12 2014 -0500
@@ -0,0 +1,126 @@
+Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
+==========================================================
+
+This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+CLC Assembly Cell is the commercial command line assembly suite from CLCbio.
+It uses SIMD instructions to parallelize and accelerate their assembly
+algorithms, and is also very memory efficient making it an appealing choice
+for complex genomes where the RAM requirements exclude other popular tools.
+
+For more information:
+http://www.clcbio.com/products/clc-assembly-cell/
+
+You can download the CLC Assembly Cell User Manual here, currently v4.2
+http://www.clcbio.com/files/usermanuals/CLC_Assembly_Cell_User_Manual.pdf
+
+There is also an online manual here:
+http://clcsupport.com/clcassemblycell/current/index.php?manual=Introduction.html
+
+There is currently a free trial download here:
+http://www.clcbio.com/?action=transfer_user&productVersion=4.2&productID=6982&productName=CLC+Assembly+Cell&nonce=db842e3f95
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+
+This Galaxy wrapper was written and tested using CLC Assembly Cell
+version 4.10.86742
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and
+install the wrapper from the Galaxy Tool Shed. However, you will need to
+manually install the CLC Assembly Cell software, and setup the environment
+variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries
+(and in particular, the ``clc_assembler`` binary). For example:
+
+$ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/
+
+
+Manual Installation
+===================
+
+First install the CLC Assembly Cell sortware as described above.
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a ``tools/clcbio/`` folder:
+
+* clc_assembler.xml (Galaxy tool definition)
+* clc_mapper.xml (Galaxy tool definition)
+* README.rst (this file)
+
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
+the tools. Just all these line, for example next to other assembly tools::
+
+
+
+
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then run::
+
+ $ ./run_tests.sh -id clc_assembler
+ $ ./run_tests.sh -id clc_mapper
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1 - Initial public release.
+v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable.
+ - Enable and fixed the tests.
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on this itHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+ $ tar -czf clcbio.tar.gz tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/tool_dependencies.xml test-data/NC_010642.fna
+
+Check this worked::
+
+ $ tar -tzf clcbio.tar.gz
+ tools/clc_assembly_cell/README.rst
+ tools/clc_assembly_cell/clc_assembler.xml
+ tools/clc_assembly_cell/clc_mapper.xml
+ tools/clc_assembly_cell/tool_dependencies.xml
+ test-data/NC_010642.fna
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+NOTE: This is the licence for the Galaxy Wrapper only. The CLCbio tools are
+commercial, and are available and licenced separately.
diff -r 000000000000 -r 0996169ac2e8 tools/clc_assembly_cell/clc_assembler.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clc_assembly_cell/clc_assembler.xml Fri Nov 21 06:41:12 2014 -0500
@@ -0,0 +1,133 @@
+
+ Assembles reads giving a FASTA file
+
+ clc_assembler
+
+ \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version
+ \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
+#for $rg in $read_group
+##--------------------------------------
+#if str($rg.segments.type) == "paired"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2"
+#end if
+##--------------------------------------
+#if str($rg.segments.type) == "interleaved"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename"
+#end if
+##--------------------------------------
+#if str($rg.segments.type) == "none"
+-p no -q
+#for $f in $rg.segments.filenames
+"$f"
+#end for
+#end if
+##--------------------------------------
+#end for
+-m $min_contig_len
+-o "$out_fasta"
+--cpus \${GALAXY_SLOTS:-4}
+-v | grep -v "^Progress: "
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Runs the ``clc_assembler`` tool giving a FASTA output file. You would then
+typically map the same set of reads onto this assembly using ``cls_mapper``
+to any perform downstream analysis using the mapped reads.
+
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite this wrapper as:
+
+Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
+http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+
+
diff -r 000000000000 -r 0996169ac2e8 tools/clc_assembly_cell/clc_mapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clc_assembly_cell/clc_mapper.xml Fri Nov 21 06:41:12 2014 -0500
@@ -0,0 +1,169 @@
+
+ Maps reads giving a SAM/BAM file
+
+ clc_mapper
+ clc_cas_to_sam
+ samtools
+ samtools
+
+ \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version
+ echo Mapping reads with clc_mapper...
+&& \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper
+#for $ref in $references
+#if str($ref.ref_type)=="circular"
+-d -z "$ref.ref_file"
+#else
+-d "$ref.ref_file"
+#end if
+#end for
+#for $rg in $read_group
+##--------------------------------------
+#if str($rg.segments.type) == "paired"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2"
+#end if
+##--------------------------------------
+#if str($rg.segments.type) == "interleaved"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename"
+#end if
+##--------------------------------------
+#if str($rg.segments.type) == "none"
+-p no -q
+#for $f in $rg.segments.filenames
+"$f"
+#end for
+#end if
+##--------------------------------------
+#end for
+-o "temp_job.cas"
+--cpus \${GALAXY_SLOTS:-4}
+## TODO - filtering out the progress lines seems to mess up the multiple commands
+## | grep -v "^Progress: "
+##===========================================
+## TODO - I've required all the input in Sanger FASTQ format (or FASTA) so can
+## use the offset 33, rather then the CLCbio default of 64 which is only for
+## obsolete Illumina FASTQ files. Really need this option per input file...
+&& echo Converting CAS file to BAM with clc_cas_to_sam...
+&& /mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_cas_to_sam --cas "temp_job.cas" -o "temp_job.bam" --no-progress --qualityoffset 33
+&& rm "temp_job.cas"
+##===========================================
+&& echo Sorting BAM file with samtools...
+&& samtools sort "temp_job.bam" "temp_sorted"
+&& mv "temp_sorted.bam" "$out_bam"
+&& echo Indexing BAM file with samtools...
+&& samtools index "$out_bam"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Runs the CLCbio tool ``clc_mapper`` which produces a proprietary binary
+CAS format file, which is immediately processed using ``clc_cas_to_sam``
+to generate a self-contained standard BAM file, which is then sorted
+and indexed using ``samtools``.
+
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite this wrapper as:
+
+Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
+http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+
+
diff -r 000000000000 -r 0996169ac2e8 tools/clc_assembly_cell/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clc_assembly_cell/tool_dependencies.xml Fri Nov 21 06:41:12 2014 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+