commit/galaxy-central: guerler: Bowtie2: Added quotation marks to group selection and added basic tool test
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f02a75ce05b7/ Changeset: f02a75ce05b7 User: guerler Date: 2013-08-07 20:17:43 Summary: Bowtie2: Added quotation marks to group selection and added basic tool test Affected #: 4 files diff -r f54e602ca23310b8a237af1388d7bc2a37047d34 -r f02a75ce05b71457845c0e5f56f409047a841967 test-data/bowtie2/phix_genome.fasta --- /dev/null +++ b/test-data/bowtie2/phix_genome.fasta @@ -0,0 +1,78 @@ +>gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174, complete genome +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA \ No newline at end of file diff -r f54e602ca23310b8a237af1388d7bc2a37047d34 -r f02a75ce05b71457845c0e5f56f409047a841967 test-data/bowtie2/phix_mapped.bam Binary file test-data/bowtie2/phix_mapped.bam has changed diff -r f54e602ca23310b8a237af1388d7bc2a37047d34 -r f02a75ce05b71457845c0e5f56f409047a841967 test-data/bowtie2/phix_reads.fastq --- /dev/null +++ b/test-data/bowtie2/phix_reads.fastq @@ -0,0 +1,260 @@ +@HWI-EAS210R_0001:4:10:890:1882#0/1 +AATCTCATCTCTCTTTTTGCGTTCTGCTTCAATATCTG ++HWI-EAS210R_0001:4:10:890:1882#0/1 +fcceeggggggggggggffghggggggggggggggggg +@HWI-EAS210R_0001:4:10:890:1010#0/1 +GTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGA ++HWI-EAS210R_0001:4:10:890:1010#0/1 +gggggggggggggghgggggggggfggggggggggggg +@HWI-EAS210R_0001:4:10:890:1780#0/1 +GAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTAT ++HWI-EAS210R_0001:4:10:890:1780#0/1 +ggfhggggggggggggggggghgggggfggggggdggg +@HWI-EAS210R_0001:4:10:890:1348#0/1 +TTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT ++HWI-EAS210R_0001:4:10:890:1348#0/1 +ggggggggggggggggggggggggghfggeggggggdg +@HWI-EAS210R_0001:4:10:890:1707#0/1 +AAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCC ++HWI-EAS210R_0001:4:10:890:1707#0/1 +gfgfgfgggggggfggeggggffgcgggdfggfggdgg +@HWI-EAS210R_0001:4:10:890:1527#0/1 +CGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC ++HWI-EAS210R_0001:4:10:890:1527#0/1 +gggggggggggggggggggggggggggggggggggggg +@HWI-EAS210R_0001:4:10:890:781#0/1 +CGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCAT ++HWI-EAS210R_0001:4:10:890:781#0/1 +gggggggggggggggggggggggggggggggghggggg +@HWI-EAS210R_0001:4:10:890:568#0/1 +GTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT ++HWI-EAS210R_0001:4:10:890:568#0/1 +gggggggfgggggggggggggggggggggggggggggg +@HWI-EAS210R_0001:4:10:890:1365#0/1 +CCAACATAAACATTATTGCCCGGCGTACGAGGAAGGAC ++HWI-EAS210R_0001:4:10:890:1365#0/1 +eggggdggfghggggggggghgfgfegghfggfgggge +@HWI-EAS210R_0001:4:10:890:161#0/1 +GTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCT ++HWI-EAS210R_0001:4:10:890:161#0/1 +ggggfg_gggfegggfgeggaefefdbfddeedgcgg` +@HWI-EAS210R_0001:4:10:890:1920#0/1 +TTTATCAATACCATGAAAAATATCAACCACACCAGAAG ++HWI-EAS210R_0001:4:10:890:1920#0/1 +gggggggggggggggggggggffggggggggggggggg +@HWI-EAS210R_0001:4:10:890:61#0/1 +GTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCA ++HWI-EAS210R_0001:4:10:890:61#0/1 +eede[egfggfggggggggggggegggggfgggggggg +@HWI-EAS210R_0001:4:10:890:1284#0/1 +AAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA ++HWI-EAS210R_0001:4:10:890:1284#0/1 +gggggggggggggggggggggggggggggggggggggg +@HWI-EAS210R_0001:4:10:890:208#0/1 +CAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC ++HWI-EAS210R_0001:4:10:890:208#0/1 +gggeggggggggggggggggggggggggggggddgggg +@HWI-EAS210R_0001:4:10:890:859#0/1 +CAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGC ++HWI-EAS210R_0001:4:10:890:859#0/1 +ggggcgggggggggggdgfggggggggfggggghgggh +@HWI-EAS210R_0001:4:10:890:1947#0/1 +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGAT ++HWI-EAS210R_0001:4:10:890:1947#0/1 +ggggggggggggggggggeggggggggggggfgfgggg +@HWI-EAS210R_0001:4:10:890:416#0/1 +AATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTG ++HWI-EAS210R_0001:4:10:890:416#0/1 +eggggggggggdcgggggfggfgggggfcgfggggggg +@HWI-EAS210R_0001:4:10:890:654#0/1 +GCAGCAAGGTCCATATCTGACTTTTTGTTAACGTATTT ++HWI-EAS210R_0001:4:10:890:654#0/1 +ggggghggggghggggghgfggggfgdfffgggggggg +@HWI-EAS210R_0001:4:10:890:269#0/1 +CTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGG ++HWI-EAS210R_0001:4:10:890:269#0/1 +eecaadggggggggggggggggdgg\ffffgggggggg +@HWI-EAS210R_0001:4:10:890:657#0/1 +TACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGG ++HWI-EAS210R_0001:4:10:890:657#0/1 +ggggghggggffgggfggggggfggfggggfffgfggg +@HWI-EAS210R_0001:4:10:890:1449#0/1 +TTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTA ++HWI-EAS210R_0001:4:10:890:1449#0/1 +ggggggggggggggggfgggghgggggggggggghhfh +@HWI-EAS210R_0001:4:10:890:305#0/1 +CACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATA ++HWI-EAS210R_0001:4:10:890:305#0/1 +gggegggfgggfggggggdgggdggfgffggggggfhg +@HWI-EAS210R_0001:4:10:890:1190#0/1 +AATAAGCAATGACGGCAGCAATAAACTCAACAGGAGCA ++HWI-EAS210R_0001:4:10:890:1190#0/1 +bbecb_gggggggggggggggggggcgggfVgggeggg +@HWI-EAS210R_0001:4:10:890:1586#0/1 +ATTAGCTGTACCATACTCAGGCACACAAAAATACTGAT ++HWI-EAS210R_0001:4:10:890:1586#0/1 +eggWgaa^O[\`[\_]J_^][`W`\]K^BBBBBBBBBB +@HWI-EAS210R_0001:4:10:890:617#0/1 +AAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGG ++HWI-EAS210R_0001:4:10:890:617#0/1 +gggggggggggggggggggggggggggggggggggggg +@HWI-EAS210R_0001:4:10:890:1562#0/1 +GTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATC ++HWI-EAS210R_0001:4:10:890:1562#0/1 +hggffggggdgggggaageef`Waegggbgggcgddgg +@HWI-EAS210R_0001:4:10:890:1410#0/1 +CATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACAT ++HWI-EAS210R_0001:4:10:890:1410#0/1 +\geedggfffcd\gd`\edeggY_Zda`gggXgadeeg +@HWI-EAS210R_0001:4:10:890:465#0/1 +AGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCG ++HWI-EAS210R_0001:4:10:890:465#0/1 +gggggfgggggggfgggeggggbgggggagf^ffefea +@HWI-EAS210R_0001:4:10:890:1323#0/1 +ATGACAAGTAAAGGACGGTTGTCAGCGTCATAAGAGGT ++HWI-EAS210R_0001:4:10:890:1323#0/1 +gggggggfggdggggggggggggggggggggfgghggg +@HWI-EAS210R_0001:4:10:890:1064#0/1 +TTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAA ++HWI-EAS210R_0001:4:10:890:1064#0/1 +gggggggcegggfgfggfgfgggdgggggghfggggdf +@HWI-EAS210R_0001:4:10:890:637#0/1 +ATAGTGCCATGCTCAGGAACAAAGAAACGCGGCACAGA ++HWI-EAS210R_0001:4:10:890:637#0/1 +ggggggggggggggggggeggggggfddgggcgggggd +@HWI-EAS210R_0001:4:10:890:1825#0/1 +TCCATCTGAATGCAATGAAGAAAACCACCATTACCAGC ++HWI-EAS210R_0001:4:10:890:1825#0/1 +gggggggghgggffgggggegggffgghgggggggggg +@HWI-EAS210R_0001:4:10:890:1697#0/1 +ACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCAT ++HWI-EAS210R_0001:4:10:890:1697#0/1 +eecaadeffedeggcabebeagggdecL_aNTTTTeg_ +@HWI-EAS210R_0001:4:10:890:1479#0/1 +ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCC ++HWI-EAS210R_0001:4:10:890:1479#0/1 +ggggggggggggggggggggfggggggggghgbgggfg +@HWI-EAS210R_0001:4:10:890:1838#0/1 +ATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGAT ++HWI-EAS210R_0001:4:10:890:1838#0/1 +ggfgfggfggggggfgggggggaggggfegfhggdggg +@HWI-EAS210R_0001:4:10:890:988#0/1 +CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACC ++HWI-EAS210R_0001:4:10:890:988#0/1 +ggghggfggggggegghgfggfgggggggggggggggg +@HWI-EAS210R_0001:4:10:890:1902#0/1 +CTTCCTCGTACGCCGGGCAATAATGTTTATGTTGGTTT ++HWI-EAS210R_0001:4:10:890:1902#0/1 +gggggggegggggggggggggggggggggfgggggggg +@HWI-EAS210R_0001:4:10:890:1983#0/1 +TTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAA ++HWI-EAS210R_0001:4:10:890:1983#0/1 +ffdfbaQa_c_Y\]Yeceeeege_gYR^VS]ZW[\Lcc +@HWI-EAS210R_0001:4:10:890:1058#0/1 +GCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAA ++HWI-EAS210R_0001:4:10:890:1058#0/1 +ggggdgggggggggggggggggggggggggggfggggg +@HWI-EAS210R_0001:4:10:890:287#0/1 +GTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCA ++HWI-EAS210R_0001:4:10:890:287#0/1 +ggggggfcggggg^fbe``egggggggdgg`dddfggg +@HWI-EAS210R_0001:4:10:890:335#0/1 +AAGAGGTTTTACCTCCAAATGAAGAAATAACATCATGG ++HWI-EAS210R_0001:4:10:890:335#0/1 +`^_``Q[cccggfgggggggbddg\dXdbegggddfg` +@HWI-EAS210R_0001:4:10:891:149#0/1 +TTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAG ++HWI-EAS210R_0001:4:10:891:149#0/1 +ggggghgggggghggggggggggggfgggggggffggg +@HWI-EAS210R_0001:4:10:891:445#0/1 +ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACT ++HWI-EAS210R_0001:4:10:891:445#0/1 +gggggggddggggggggggggggggggggggggggggg +@HWI-EAS210R_0001:4:10:891:1476#0/1 +GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCG ++HWI-EAS210R_0001:4:10:891:1476#0/1 +ggegggffghhggfhggfgeggffgggffggagfggfg +@HWI-EAS210R_0001:4:10:891:323#0/1 +TGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGT ++HWI-EAS210R_0001:4:10:891:323#0/1 +gggcgfefghgggghgfgfgggggggggegaaeeagge +@HWI-EAS210R_0001:4:10:891:69#0/1 +CTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTAC ++HWI-EAS210R_0001:4:10:891:69#0/1 +gggefgggfgafP_Vdbacbgegebd`fbaeggaggQd +@HWI-EAS210R_0001:4:10:891:1379#0/1 +GACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAAT ++HWI-EAS210R_0001:4:10:891:1379#0/1 +gggggggggggggggggggggggggggggfgefggggg +@HWI-EAS210R_0001:4:10:891:608#0/1 +CTTATGCTAATTTGCATACTGACCAAGAACGTGATTAC ++HWI-EAS210R_0001:4:10:891:608#0/1 +ggggggggggggggggggggggggfggggggggggggg +@HWI-EAS210R_0001:4:10:891:1831#0/1 +GTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTA ++HWI-EAS210R_0001:4:10:891:1831#0/1 +ggggggggggggggggghggggggggghgggggfgggg +@HWI-EAS210R_0001:4:10:891:412#0/1 +TAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACG ++HWI-EAS210R_0001:4:10:891:412#0/1 +gggggggggggggggggggggggggggggggggggggg +@HWI-EAS210R_0001:4:10:891:346#0/1 +AATTCATCCATTAACTTCTCATCAACATATACAAACTC ++HWI-EAS210R_0001:4:10:891:346#0/1 +^W][_b^be_cRgaggdgdgbL_^_\ZN\R]]`W]cYe +@HWI-EAS210R_0001:4:10:891:174#0/1 +AGTGGAGGCCTCCAGCAATCTTGAACACTCATCCTTAA ++HWI-EAS210R_0001:4:10:891:174#0/1 +ggggggggggggggggggggggcgggggfgggghghcg +@HWI-EAS210R_0001:4:10:891:1415#0/1 +ACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATC ++HWI-EAS210R_0001:4:10:891:1415#0/1 +gggggggggggdghgggggggggggggggggggggggg +@HWI-EAS210R_0001:4:10:891:705#0/1 +TTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTC ++HWI-EAS210R_0001:4:10:891:705#0/1 +gfgggggggggfgggggggggggfgddgggggggeggg +@HWI-EAS210R_0001:4:10:891:1398#0/1 +GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAA ++HWI-EAS210R_0001:4:10:891:1398#0/1 +ebehggdhdfgffdda`e\ecgfggedgegeggdfdfg +@HWI-EAS210R_0001:4:10:891:971#0/1 +TAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCCAC ++HWI-EAS210R_0001:4:10:891:971#0/1 +ggfgggghggggggfggfgghggfggggfghggffghg +@HWI-EAS210R_0001:4:10:891:627#0/1 +GTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAA ++HWI-EAS210R_0001:4:10:891:627#0/1 +dfdffaeaaagggg[bgggghgghgggfgg\efefggd +@HWI-EAS210R_0001:4:10:891:1822#0/1 +GAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCA ++HWI-EAS210R_0001:4:10:891:1822#0/1 +gggeggfggegggggdggggghgfgedgggggcfgdcg +@HWI-EAS210R_0001:4:10:891:1103#0/1 +AAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGA ++HWI-EAS210R_0001:4:10:891:1103#0/1 +ggeggfggggggggghggggggggggfffgdggggggb +@HWI-EAS210R_0001:4:10:891:586#0/1 +TATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC ++HWI-EAS210R_0001:4:10:891:586#0/1 +ggggggggggggegfgggfcgggggffggggggggggg +@HWI-EAS210R_0001:4:10:891:1620#0/1 +TTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCT ++HWI-EAS210R_0001:4:10:891:1620#0/1 +gggggfggggghgggggghcgggdgggegggefgfT`` +@HWI-EAS210R_0001:4:10:891:42#0/1 +CTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTA ++HWI-EAS210R_0001:4:10:891:42#0/1 +ggefggggggfggggfaf_fggggdfggggfaYbfd]b +@HWI-EAS210R_0001:4:10:891:1609#0/1 +GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCATC ++HWI-EAS210R_0001:4:10:891:1609#0/1 +gggghgggghfgghgggggfffggggcgggfdggfggf +@HWI-EAS210R_0001:4:10:891:1028#0/1 +AATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAAT ++HWI-EAS210R_0001:4:10:891:1028#0/1 +gfgggggggdgbggfgegeeggggggggdggegggddg +@HWI-EAS210R_0001:4:10:891:902#0/1 +ATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCG ++HWI-EAS210R_0001:4:10:891:902#0/1 +ggggggfgggggggggggggggggfddggggggggggg diff -r f54e602ca23310b8a237af1388d7bc2a37047d34 -r f02a75ce05b71457845c0e5f56f409047a841967 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -87,10 +87,10 @@ ## read group information #if str($read_group.selection) == "yes": #if $read_group.rgid and $read_group.rglb and $read_group.rgpl and $read_group.rgsm: - --rg-id $read_group.rgid - --rg LB:$read_group.rglb - --rg PL:$read_group.rgpl - --rg SM:$read_group.rgsm + --rg-id "$read_group.rgid" + --rg "LB:$read_group.rglb" + --rg "PL:$read_group.rgpl" + --rg "SM:$read_group.rgsm" #end if #end if @@ -254,6 +254,17 @@ </outputs><tests> + <test> + <!-- basic test on single paired default run --> + <param name="type" value="single"/> + <param name="selection" value="no"/> + <param name="full" value="no"/> + <param name="unaligned_file" value="false"/> + <param name="source" value="history" /> + <param name="input_1" value="bowtie2/phix_reads.fastq" ftype="fastqsanger"/> + <param name="own_file" value="bowtie2/phix_genome.fasta" /> + <output name="output" file="bowtie2/phix_mapped.bam" /> + </test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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