|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus commit 5d67d705695dfee875bda85aa02ddf38924790a7 |
|
added:
test-data/output1.fasta test-data/reference.fasta test-data/sample1.vcf tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample vcftools_consensus.xml |
| b |
| diff -r 000000000000 -r 79f5d34da277 test-data/output1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.fasta Fri Nov 25 07:30:19 2016 -0500 |
| b |
| b'@@ -0,0 +1,168 @@\n+>Chromosome\n+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT\n+AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG\n+ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT\n+GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC\n+CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC\n+GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT\n+ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG\n+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC\n+GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC\n+GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT\n+TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG\n+GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG\n+GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC\n+AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG\n+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC\n+GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC\n+CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC\n+ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC\n+ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC\n+GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC\n+GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC\n+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG\n+GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC\n+AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC\n+CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC\n+ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC\n+TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC\n+CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG\n+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC\n+TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT\n+TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATAACACCCGCATAA\n+CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC\n+TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCGTTC\n+GTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTCATCGTGAGGT\n+GAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT\n+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGC\n+CCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTT\n+CCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTG\n+GAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGC\n+CCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTT\n+CGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCG\n+GATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC\n+GGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGG\n+TTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGT\n+CGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAG\n+CGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGG\n+ATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCG\n+AGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACG\n+TGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG\n+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGAC\n+GAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACC\n+CAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTA\n+CGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGG\n+GTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGC\n+CGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCGTCATTTGGGG\n+CTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT\n+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACG\n+ACGTTAGGTTCGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGT\n+GCGGTGATCTCCACGATCGTGGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATC\n+GCCACGGGGCGAGTCAACAAAGCGCGATTGAATCGATCATCGGTCCGAAGTACACGTGAT\n+GTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGGATCTGGGGTTGGTTCGTGGG\n+GATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAGGCCTGCGATC\n+GCTGCGGTACGAGCCGAATATGAGAGGGTGTTGCGCCAGCGGACGGCGTTATTGAAGTCC\n+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGAC\n'..b'TCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGG\n+CACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGA\n+CCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT\n+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAA\n+GTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCA\n+CTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGC\n+GCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGA\n+CATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGA\n+ACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGAT\n+GTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA\n+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCA\n+CGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGA\n+TGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCC\n+GCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCA\n+GCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGG\n+GCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGG\n+TGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCG\n+TCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGA\n+GGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGA\n+TGTCTAACGCAACCCTGCGTTCGATTGCAAACGAGGAATAGATGACAGACACGACGTTGC\n+CGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCCAGCAGGAGATGCAGCGCA\n+GCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACG\n+GGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGG\n+ACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGC\n+ACGGCGACGCGTCGATCTACGACACCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCT\n+ACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGA\n+TGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACG\n+AGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTAC\n+CCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAA\n+CCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGA\n+ATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGG\n+ACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTG\n+GCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTA\n+CCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGA\n+TCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTA\n+GCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGG\n+TGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAG\n+CGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTG\n+ACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGC\n+GAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCAC\n+TGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACA\n+TCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGG\n+AACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAG\n+ACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCG\n+TGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCG\n+ACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCA\n+AGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTG\n+CGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGA\n+TCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGG\n+CCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAAC\n+GCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCA\n+CTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCG\n+GAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGG\n+CCGACGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCG\n+ACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATA\n+TCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGA\n+CGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCG\n+GTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGA\n+TTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCG\n+CGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGG\n+GCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATG\n+CCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAATCAGGCTCGCCCGACGACGATG\n+CGGATCGCGTAGCGATCTGAGGAGGAATCGGGCAGCTAGGCTCGGCAGCCGGGTACGAGT\n+GTTAGGAGTCGGGGTGACTGCACCGAACGAGCCGGGGGCGCTCAGCAAGGGCGACGGCCC\n+GAATGCGGATGGCTTGGTCGACCGTGGGGGCGCACATCGG\n' |
| b |
| diff -r 000000000000 -r 79f5d34da277 test-data/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fasta Fri Nov 25 07:30:19 2016 -0500 |
| b |
| b'@@ -0,0 +1,168 @@\n+>Chromosome\n+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT\n+AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG\n+ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT\n+GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC\n+CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC\n+GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT\n+ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG\n+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC\n+GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC\n+GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT\n+TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG\n+GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG\n+GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC\n+AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG\n+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC\n+GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC\n+CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC\n+ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC\n+ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC\n+GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC\n+GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC\n+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG\n+GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC\n+AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC\n+CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC\n+ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC\n+TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC\n+CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG\n+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC\n+TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT\n+TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAA\n+CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC\n+TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCATTC\n+GTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTCATCGTGAGGT\n+GAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT\n+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGC\n+CCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTT\n+CCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTG\n+GAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGC\n+CCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTT\n+CGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCG\n+GATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC\n+GGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGG\n+TTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGT\n+CGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAG\n+CGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGG\n+ATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCG\n+AGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACG\n+TGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG\n+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGAC\n+GAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACC\n+CAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTA\n+CGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGG\n+GTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGC\n+CGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCGTCATTTGGGG\n+CTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT\n+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACG\n+ACGTTAGGTTCGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGT\n+GCGGTGATCTCCACGATCGTGGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATC\n+GCCACGGGGCGAGTCAACAAAGCGCGATTGAATCGATCATCGGTCCGAAGTACACGTGAT\n+GTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGGATCTGGGGTTGGTTCGTGGG\n+GATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAGGCCTGCGATC\n+GCTGCGGTACGAGCCGAATATGAGAGGGTGTTGCGCCAGCGGACGGCGTTATTGAAGTCC\n+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGAC\n'..b'TCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGG\n+CACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGA\n+CCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT\n+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAA\n+GTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCA\n+CTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGC\n+GCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGA\n+CATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGA\n+ACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGAT\n+GTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA\n+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCA\n+CGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGA\n+TGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCC\n+GCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCA\n+GCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGG\n+GCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGG\n+TGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCG\n+TCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGA\n+GGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGA\n+TGTCTAACGCAACCCTGCGTTCGATTGCAAACGAGGAATAGATGACAGACACGACGTTGC\n+CGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCGAGCAGGAGATGCAGCGCA\n+GCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACG\n+GGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGG\n+ACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGC\n+ACGGCGACGCGTCGATCTACGACAGCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCT\n+ACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGA\n+TGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACG\n+AGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTAC\n+CCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAA\n+CCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGA\n+ATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGG\n+ACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTG\n+GCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTA\n+CCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGA\n+TCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTA\n+GCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGG\n+TGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAG\n+CGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTG\n+ACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGC\n+GAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCAC\n+TGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACA\n+TCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGG\n+AACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAG\n+ACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCG\n+TGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCG\n+ACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCA\n+AGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTG\n+CGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGA\n+TCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGG\n+CCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAAC\n+GCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCA\n+CTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCG\n+GAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGG\n+CCGGCGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCG\n+ACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATA\n+TCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGA\n+CGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCG\n+GTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGA\n+TTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCG\n+CGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGG\n+GCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATG\n+CCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAATCAGGCTCGCCCGACGACGATG\n+CGGATCGCGTAGCGATCTGAGGAGGAATCGGGCAGCTAGGCTCGGCAGCCGGGTACGAGT\n+GTTAGGAGTCGGGGTGACTGCACCGAACGAGCCGGGGGCGCTCAGCAAGGGCGACGGCCC\n+GAATGCGGATGGCTTGGTCGACCGTGGGGGCGCACATCGG\n' |
| b |
| diff -r 000000000000 -r 79f5d34da277 test-data/sample1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.vcf Fri Nov 25 07:30:19 2016 -0500 |
| [ |
| b'@@ -0,0 +1,98 @@\n+##fileformat=VCFv4.1\n+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:35:17 SAST 2015",Epoch=1433669717749,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2997_878#L6-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GVC'..b')\n+##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive)\n+##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive)\n+##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive)\n+##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive)\n+##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive)\n+##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive)\n+##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive)\n+##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive)\n+##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive)\n+##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive)\n+##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive)\n+##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive)\n+##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive)\n+##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive)\n+##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive)\n+##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive)\n+##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive)\n+##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive)\n+##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive)\n+##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive)\n+##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive)\n+##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive)\n+##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive)\n+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">\n+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">\n+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">\n+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">\n+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">\n+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">\n+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">\n+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">\n+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">\n+##contig=<ID=Chromosome,length=10000>\n+##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t./R_2997_878#L6-_.R\n+Chromosome\t1849\t.\tC\tA,<NON_REF>\t4546\t.\tDP=129;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,129,0:129:99:4576,0,4576:0,0,56,73\n+Chromosome\t1977\t.\tA\tG,<NON_REF>\t1957\t.\tDP=54;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,54,0:54:99:1987,0,1987:0,0,13,41\n+Chromosome\t4013\t.\tT\tC,<NON_REF>\t2397\t.\tDP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,66,0:66:99:2427,0,2427:0,0,31,35\n+Chromosome\t7362\t.\tG\tC,<NON_REF>\t2519\t.\tDP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,68,0:68:99:2549,0,2549:0,0,28,40\n+Chromosome\t7585\t.\tG\tC,<NON_REF>\t1295\t.\tDP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,36,0:36:99:1325,0,1325:0,0,26,10\n+Chromosome\t9304\t.\tG\tA,<NON_REF>\t1945\t.\tDP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,58,0:58:99:1975,0,1975:0,0,23,35\n' |
| b |
| diff -r 000000000000 -r 79f5d34da277 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Nov 25 07:30:19 2016 -0500 |
| b |
| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
| b |
| diff -r 000000000000 -r 79f5d34da277 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 25 07:30:19 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 79f5d34da277 vcftools_consensus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools_consensus.xml Fri Nov 25 07:30:19 2016 -0500 |
| [ |
| @@ -0,0 +1,78 @@ +<tool id="vcftools_consensus" name="Consensus" version="0.1.11"> + <description>Apply VCF variants to a fasta file to create consensus sequence</description> + + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="1.3.2">htslib</requirement> + <requirement type="package" version="0.1.11">vcftools</requirement> + </requirements> + + <stdio> + <!--<regex match=".*" source="both" level="log" description="tool progress"/>--> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command> + <![CDATA[ + ln -s '${variants}' variants.vcf && + vcf-sort variants.vcf | bgzip -c > variants.sorted.vcf.gz && + + tabix -p vcf variants.sorted.vcf.gz && + + #if $ref_genome_source.index_source == 'history': + ln -s '${ref_genome_source.ref_file}' reference.fasta && + samtools faidx reference.fasta && + #end if + + cat + #if $ref_genome_source.index_source == 'builtin' + '${ ref_genome_source.reference_genome.fields.path }' + #else + reference.fasta + #end if + | vcf-consensus variants.sorted.vcf.gz > '${output}' + ]]> + </command> + <inputs> + <conditional name="ref_genome_source"> + <param name="index_source" type="select" label="Reference genome source"> + <option value="builtin">Built-in genome</option> + <option value="history">History</option> + </param> + <when value="builtin"> + <param name="reference_genome" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="2" type="sort_by" /> + <validator message="No suitable reference genomes found" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Reference genome" /> + </when> + </conditional> + <param name="variants" label="Datasets containing Variants" type="data" format="vcf" /> + </inputs> + + <outputs> + <data name="output" format="fasta"/> + </outputs> + + <tests> + <test> + <param name="index_source" value="history" /> + <param ftype="fasta" name="ref_file" value="reference.fasta" /> + <param ftype="vcf" name="variants" value="sample1.vcf" /> + <output name="output" ftype="fasta" file="output1.fasta" /> + </test> + </tests> + + <help> + Please see the VCFtools `documentation`__ for help and further information. + + .. __: http://vcftools.sourceforge.net/docs.html + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr330</citation> + </citations> +</tool> |