# HG changeset patch # User iuc # Date 1612210394 0 # Node ID 8c202e741d6894d128e597719cf59fd08a108a68 # Parent afdfa35a89d95dedd6fed0f52028d0b6956c7caa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae" diff -r afdfa35a89d9 -r 8c202e741d68 macros.xml --- a/macros.xml Tue Jul 14 07:38:24 2020 -0400 +++ b/macros.xml Mon Feb 01 20:13:14 2021 +0000 @@ -7,7 +7,7 @@ - 1.16 + 1.18 0 diff -r afdfa35a89d9 -r 8c202e741d68 test-data/assignTaxonomyAddspecies.tab --- a/test-data/assignTaxonomyAddspecies.tab Tue Jul 14 07:38:24 2020 -0400 +++ b/test-data/assignTaxonomyAddspecies.tab Mon Feb 01 20:13:14 2021 +0000 @@ -1,7 +1,7 @@ Level1 Level2 Level3 Level4 Level5 NA Species TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG Bacteria Bacteroidetes Cytophagia Cytophagales NA NA NA -TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG Bacteria Bacteroidetes Cytophagia Cytophagales Cytophagaceae NA NA -TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG Bacteria Bacteroidetes NA NA NA NA NA +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG Bacteria Bacteroidetes Cytophagia Cytophagales Cytophagaceae Sporocytophaga NA +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG Bacteria Bacteroidetes Cytophagia Cytophagales NA NA NA TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG Bacteria Bacteroidetes Cytophagia Cytophagales NA NA NA TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG Bacteria Bacteroidetes Cytophagia Cytophagales NA NA NA TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA @@ -14,19 +14,19 @@ TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGCCAGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATCACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAACCCGGGGCTCAACCCTGGGAGTGCTTTTGAAACTGTGCGGCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA -TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes NA NA NA NA NA +TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales NA NA NA TACGTATGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCTGGCAAGCCTGATGTGAAATACCGGGGCCCAACCCCGGGGCTGCATTGGGAACTGCCAGGCTGGAGTGCCGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTATGACTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA -TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG Bacteria NA NA NA NA NA NA +TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales NA NA NA TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG Bacteria NA NA NA NA NA NA TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillibacter NA TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnoanaerobaculum NA -TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG Bacteria Firmicutes Bacilli Bacillales NA NA NA +TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG Bacteria Firmicutes NA NA NA NA NA TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG Bacteria Firmicutes NA NA NA NA NA TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae NA NA TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG Bacteria Firmicutes Bacilli Bacillales Bacillaceae_2 Pullulanibacillus NA TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnoanaerobaculum NA TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillibacter NA -TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG Bacteria Firmicutes NA NA NA NA NA +TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG Bacteria NA NA NA NA NA NA diff -r afdfa35a89d9 -r 8c202e741d68 test-data/assignTaxonomyAddspecies_boot.tab --- a/test-data/assignTaxonomyAddspecies_boot.tab Tue Jul 14 07:38:24 2020 -0400 +++ b/test-data/assignTaxonomyAddspecies_boot.tab Mon Feb 01 20:13:14 2021 +0000 @@ -1,32 +1,32 @@ Level1 Level2 Level3 Level4 Level5 NA -TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 98 80 70 70 48 48 -TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG 97 88 76 76 50 48 -TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG 100 82 49 49 42 42 -TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 100 76 73 73 46 46 -TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG 97 82 68 68 33 33 -TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 99 99 99 91 -TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG 96 45 31 31 13 13 -TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 99 92 80 80 49 49 -TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 72 72 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAGACAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGCCTGACTGGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 43 -TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG 100 94 87 87 68 41 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGCGCAAGTCTGGAGTGAAATGCCGGGGCCCAACCCCGGAACTGCTTTGGAAACTGTGCAGCTCGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 57 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 99 82 68 68 42 42 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG 99 89 73 73 54 54 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG 97 81 52 52 38 38 +TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 100 74 74 74 42 42 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG 94 74 65 65 39 39 +TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 84 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG 95 41 17 17 13 13 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 93 74 63 63 41 41 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG 100 100 99 99 61 61 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAGACAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGCCTGACTGGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 39 +TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG 100 90 83 83 64 30 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGCGCAAGTCTGGAGTGAAATGCCGGGGCCCAACCCCGGAACTGCTTTGGAAACTGTGCAGCTCGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 62 TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGCCAGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATCACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 96 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 64 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAACCCGGGGCTCAACCCTGGGAGTGCTTTTGAAACTGTGCGGCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 88 -TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 79 38 38 33 26 -TACGTATGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCTGGCAAGCCTGATGTGAAATACCGGGGCCCAACCCCGGGGCTGCATTGGGAACTGCCAGGCTGGAGTGCCGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 97 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTATGACTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 70 -TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 99 99 99 81 -TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG 100 49 46 46 43 30 -TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG 97 33 27 17 15 15 -TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG 100 99 98 98 70 70 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 50 -TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG 100 66 57 57 35 35 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 99 75 -TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG 100 96 42 42 42 42 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 41 -TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 100 100 98 98 87 52 -TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 100 100 100 100 100 62 -TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG 100 98 98 98 89 89 -TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG 100 53 38 38 38 26 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 58 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAACCCGGGGCTCAACCCTGGGAGTGCTTTTGAAACTGTGCGGCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 92 +TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 79 50 50 40 32 +TACGTATGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCTGGCAAGCCTGATGTGAAATACCGGGGCCCAACCCCGGGGCTGCATTGGGAACTGCCAGGCTGGAGTGCCGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 95 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTATGACTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 77 +TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 79 +TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG 100 61 60 60 48 39 +TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG 99 30 30 27 22 22 +TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG 100 96 94 94 73 73 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 51 +TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG 100 77 47 47 30 30 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 99 99 99 99 80 +TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG 100 96 45 45 45 45 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100 34 +TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 100 99 97 97 90 58 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 100 100 99 99 99 62 +TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG 100 99 99 99 95 95 +TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG 100 42 31 31 31 22 diff -r afdfa35a89d9 -r 8c202e741d68 tools.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools.yml Mon Feb 01 20:13:14 2021 +0000 @@ -0,0 +1,5 @@ +install_tool_dependencies: True +install_repository_dependencies: True +install_resolver_dependencies: True + +tools: [] diff -r afdfa35a89d9 -r 8c202e741d68 topics/metagenomics/metadata.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/topics/metagenomics/metadata.yaml Mon Feb 01 20:13:14 2021 +0000 @@ -0,0 +1,28 @@ +--- +name: "metagenomics" +type: "use" +title: "Metagenomics" +summary: "Metagenomics is a discipline that enables the genomic study of uncultured microorganisms" +edam_ontology: "topic_3174" +docker_image: "quay.io/galaxy/metagenomics-training" + +requirements: + - + type: "internal" + topic_name: introduction + +maintainers: + - bebatut + - shiltemann + +references: + - + authors: "Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD." + title: "Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology" + link: "http://www.schlosslab.org/assets/pdf/2013_kozich.pdf" + summary: "" + - + authors: "Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra" + title: "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences." + link: "https://www.ncbi.nlm.nih.gov/pubmed/25118885" + summary: "" diff -r afdfa35a89d9 -r 8c202e741d68 topics/metagenomics/tutorials/dada2/tutorial.bib --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/topics/metagenomics/tutorials/dada2/tutorial.bib Mon Feb 01 20:13:14 2021 +0000 @@ -0,0 +1,30 @@ + +# This is the bibliography file for your tutorial. +# +# To add bibliography (bibtex) entries here, follow these steps: +# 1) Find the DOI for the article you want to cite +# 2) Go to https://doi2bib.org and fill in the DOI +# 3) Copy the resulting bibtex entry into this file +# +# To cite the example below, in your tutorial.md file +# use {% Batut2018 %} + +@article{Batut2018, + doi = {10.1016/j.cels.2018.05.012}, + url = {https://doi.org/10.1016/j.cels.2018.05.012}, + year = {2018}, + month = jun, + publisher = {Elsevier {BV}}, + volume = {6}, + number = {6}, + pages = {752--758.e1}, + author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and + Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton + and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and + Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and + Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and + Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and + Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning}, + title = {Community-Driven Data Analysis Training for Biology}, + journal = {Cell Systems} +} \ No newline at end of file diff -r afdfa35a89d9 -r 8c202e741d68 topics/metagenomics/tutorials/dada2/tutorial.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/topics/metagenomics/tutorials/dada2/tutorial.md Mon Feb 01 20:13:14 2021 +0000 @@ -0,0 +1,642 @@ +--- +layout: tutorial_hands_on + +title: 16S Microbial Analysis with mothur (extended) +zenodo_link: https://doi.org/10.5281/zenodo.800651 +questions: +- What is the effect of normal variation in the gut microbiome on host health? +objectives: +- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy +- Using a mock community to assess the error rate of your sequencing experiment +- Visualize sample diversity using Krona and Phinch +time_estimation: '' +key_points: +- 16S rRNA gene sequencing analysis results depend on the many algorithms used and + their settings +- Quality control and cleaning of your data is a crucial step in order to obtain optimal + results +- Adding a mock community to serve as a control sample can help you asses the error + rate of your experimental setup +- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations +contributors: +- shiltemann +- bebatut +- tnabtaf + +--- + + +# Introduction +{:.no_toc} + + + +General introduction about the topic and then an introduction of the +tutorial (the questions and the objectives). It is nice also to have a +scheme to sum up the pipeline used during the tutorial. The idea is to +give to trainees insight into the content of the tutorial and the (theoretical +and technical) key concepts they will learn. + +You may want to cite some publications; this can be done by adding citations to the +bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations +must be in bibtex format. If you have the DOI for the paper you wish to cite, you can +get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org). + +With the example you will find in the `tutorial.bib` file, you can add a citation to +this article here in your tutorial like this: +{% raw %} `{% cite Batut2018 %}`{% endraw %}. +This will be rendered like this: {% cite Batut2018 %}, and links to a +[bibliography section](#bibliography) which will automatically be created at the end of the +tutorial. + + +**Please follow our +[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)** + +> ### Agenda +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + +# Title for your first section + +Give some background about what the trainees will be doing in the section. +Remember that many people reading your materials will likely be novices, +so make sure to explain all the relevant concepts. + +## Title for a subsection +Section and subsection titles will be displayed in the tutorial index on the left side of +the page, so try to make them informative and concise! + +# Hands-on Sections +Below are a series of hand-on boxes, one for each tool in your workflow file. +Often you may wish to combine several boxes into one or make other adjustments such +as breaking the tutorial into sections, we encourage you to make such changes as you +see fit, this is just a starting point :) + +Anywhere you find the word "***TODO***", there is something that needs to be changed +depending on the specifics of your tutorial. + +have fun! + +## Get data + +> ### {% icon hands_on %} Hands-on: Data upload +> +> 1. Create a new history for this tutorial +> 2. Import the files from [Zenodo]() or from the shared data library +> +> ``` +> +> ``` +> ***TODO***: *Add the files by the ones on Zenodo here (if not added)* +> +> ***TODO***: *Remove the useless files (if added)* +> +> {% include snippets/import_via_link.md %} +> {% include snippets/import_from_data_library.md %} +> +> 3. Rename the datasets +> 4. Check that the datatype +> +> {% include snippets/change_datatype.md datatype="datatypes" %} +> +> 5. Add to each database a tag corresponding to ... +> +> {% include snippets/add_tag.md %} +> +{: .hands_on} + +# Title of the section usually corresponding to a big step in the analysis + +It comes first a description of the step: some background and some theory. +Some image can be added there to support the theory explanation: + +![Alternative text](../../images/image_name "Legend of the image") + +The idea is to keep the theory description before quite simple to focus more on the practical part. + +***TODO***: *Consider adding a detail box to expand the theory* + +> ### {% icon details %} More details about the theory +> +> But to describe more details, it is possible to use the detail boxes which are expandable +> +{: .details} + +A big step can have several subsections or sub steps: + + +## Sub-step with **dada2_plotComplexity** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_plotQualityProfile** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_filterAndTrim** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_filterAndTrim** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_plotComplexity** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_plotQualityProfile** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **Unzip Collection** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **Unzip Collection** {% icon tool %} with the following parameters: +> - {% icon param-file %} *"Input Paired Dataset"*: `paired_output` (output of **dada2_filterAndTrim** {% icon tool %}) +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_learnErrors** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_learnErrors** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_learnErrors** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_learnErrors** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_dada** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_dada** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_dada** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_dada** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_mergePairs** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_mergePairs** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_makeSequenceTable** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_removeBimeraDenovo** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_seqCounts** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_seqCounts** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_assignTaxonomyAddspecies** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + + +## Re-arrange + +To create the template, each step of the workflow had its own subsection. + +***TODO***: *Re-arrange the generated subsections into sections or other subsections. +Consider merging some hands-on boxes to have a meaningful flow of the analyses* + +# Conclusion +{:.no_toc} + +Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the +pipeline used. \ No newline at end of file diff -r afdfa35a89d9 -r 8c202e741d68 topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga Mon Feb 01 20:13:14 2021 +0000 @@ -0,0 +1,798 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "dada2 for paired data (imported from uploaded file)", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 200, + "top": 613 + }, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "b1f16224-49d2-4b7a-a37d-3d93c54f679f", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "dada2_plotComplexity", + "errors": null, + "id": 1, + "input_connections": { + "batch_cond|paired_cond|reads": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "dada2: plotComplexity", + "outputs": [ + { + "name": "output_fwd", + "type": "pdf" + }, + { + "name": "output_rev", + "type": "pdf" + } + ], + "position": { + "left": 499, + "top": 178.5 + }, + "post_job_actions": { + "HideDatasetActionoutput_fwd": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_fwd" + }, + "HideDatasetActionoutput_rev": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_rev" + } + }, + "tool_id": "dada2_plotComplexity", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"kmerSize\": \"\\\"2\\\"\", \"n\": \"\\\"100000\\\"\", \"window\": \"\\\"\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"by\": \"\\\"5\\\"\", \"bins\": \"\\\"100\\\"\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "4f226c7b-9ba8-4b48-8d48-899cf345b660", + "workflow_outputs": [ + { + "label": null, + "output_name": "output_fwd", + "uuid": "52b4da66-504c-4fbe-8487-d6c0613ab6ae" + }, + { + "label": null, + "output_name": "output_rev", + "uuid": "3785a6f5-da8a-4232-b2ab-4f9f4c0732f6" + } + ] + }, + "2": { + "annotation": "", + "content_id": "dada2_plotQualityProfile", + "errors": null, + "id": 2, + "input_connections": { + "batch_cond|paired_cond|reads": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "dada2: plotQualityProfile", + "outputs": [ + { + "name": "output_fwd", + "type": "pdf" + }, + { + "name": "output_rev", + "type": "pdf" + } + ], + "position": { + "left": 496, + "top": 364 + }, + "post_job_actions": { + "HideDatasetActionoutput_fwd": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_fwd" + }, + "HideDatasetActionoutput_rev": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_rev" + } + }, + "tool_id": "dada2_plotQualityProfile", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"n\": \"\\\"500000\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"aggregate\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "f6e0a2ea-a639-48d9-ae3c-c1ec2bab93e5", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "dada2_filterAndTrim", + "errors": null, + "id": 3, + "input_connections": { + "paired_cond|reads": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "dada2: filterAndTrim", + "outputs": [ + { + "name": "paired_output", + "type": "input" + }, + { + "name": "outtab", + "type": "tabular" + } + ], + "position": { + "left": 485, + "top": 612 + }, + "post_job_actions": { + "HideDatasetActionouttab": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outtab" + }, + "HideDatasetActionpaired_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "paired_output" + } + }, + "tool_id": "dada2_filterAndTrim", + "tool_state": "{\"trim\": \"{\\\"trimLeft\\\": \\\"0\\\", \\\"trimRight\\\": \\\"0\\\", \\\"truncLen\\\": \\\"0\\\", \\\"truncQ\\\": \\\"2\\\"}\", \"__page__\": null, \"rmPhiX\": \"\\\"true\\\"\", \"rmlowcomplex\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"filter\": \"{\\\"maxEE\\\": \\\"\\\", \\\"maxLen\\\": \\\"\\\", \\\"maxN\\\": \\\"0\\\", \\\"minLen\\\": \\\"20\\\", \\\"minQ\\\": \\\"0\\\"}\", \"seprev_cond\": \"{\\\"__current_case__\\\": 0, \\\"seprev_select\\\": \\\"no\\\"}\", \"output_statistics\": \"\\\"true\\\"\", \"orientFwd\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "353103fd-afc3-4fe0-a4a3-8dca75b59107", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "dada2_plotComplexity", + "errors": null, + "id": 4, + "input_connections": { + "batch_cond|paired_cond|reads": { + "id": 3, + "output_name": "paired_output" + } + }, + "inputs": [], + "label": null, + "name": "dada2: plotComplexity", + "outputs": [ + { + "name": "output_fwd", + "type": "pdf" + }, + { + "name": "output_rev", + "type": "pdf" + } + ], + "position": { + "left": 840, + "top": 179.5 + }, + "post_job_actions": { + "HideDatasetActionoutput_fwd": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_fwd" + }, + "HideDatasetActionoutput_rev": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_rev" + } + }, + "tool_id": "dada2_plotComplexity", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"kmerSize\": \"\\\"2\\\"\", \"n\": \"\\\"100000\\\"\", \"window\": \"\\\"\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"by\": \"\\\"5\\\"\", \"bins\": \"\\\"100\\\"\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "9c6c20be-b9d8-4645-a2d6-3ecc5bc33f4a", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "dada2_plotQualityProfile", + "errors": null, + "id": 5, + "input_connections": { + "batch_cond|paired_cond|reads": { + "id": 3, + "output_name": "paired_output" + } + }, + "inputs": [], + "label": null, + "name": "dada2: plotQualityProfile", + "outputs": [ + { + "name": "output_fwd", + "type": "pdf" + }, + { + "name": "output_rev", + "type": "pdf" + } + ], + "position": { + "left": 842.5, + "top": 364.5 + }, + "post_job_actions": { + "HideDatasetActionoutput_fwd": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_fwd" + }, + "HideDatasetActionoutput_rev": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_rev" + } + }, + "tool_id": "dada2_plotQualityProfile", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"n\": \"\\\"500000\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"aggregate\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "b5234046-b9a9-4801-8994-496173c3ab2b", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "__UNZIP_COLLECTION__", + "errors": null, + "id": 6, + "input_connections": { + "input": { + "id": 3, + "output_name": "paired_output" + } + }, + "inputs": [], + "label": null, + "name": "Unzip Collection", + "outputs": [ + { + "name": "forward", + "type": "input" + }, + { + "name": "reverse", + "type": "input" + } + ], + "position": { + "left": 841, + "top": 636 + }, + "post_job_actions": { + "HideDatasetActionforward": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "forward" + }, + "HideDatasetActionreverse": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "reverse" + } + }, + "tool_id": "__UNZIP_COLLECTION__", + "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "41ab27fe-f07d-4653-b4b5-e77408957a9a", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "dada2_learnErrors", + "errors": null, + "id": 7, + "input_connections": { + "fls": { + "id": 6, + "output_name": "forward" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool dada2: learnErrors", + "name": "fls" + } + ], + "label": null, + "name": "dada2: learnErrors", + "outputs": [ + { + "name": "errors", + "type": "dada2_errorrates" + }, + { + "name": "plot", + "type": "pdf" + } + ], + "position": { + "left": 1152, + "top": 445 + }, + "post_job_actions": { + "HideDatasetActionerrors": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "errors" + }, + "HideDatasetActionplot": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "plot" + } + }, + "tool_id": "dada2_learnErrors", + "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"err_in\\\": \\\"false\\\", \\\"err_out\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"fls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"nbases\": \"\\\"8\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0.0\\\", \\\"randomize\\\": \\\"false\\\"}\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "e8c86ffd-118c-44f6-a58d-5c1704bb6ed6", + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "dada2_learnErrors", + "errors": null, + "id": 8, + "input_connections": { + "fls": { + "id": 6, + "output_name": "reverse" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool dada2: learnErrors", + "name": "fls" + } + ], + "label": null, + "name": "dada2: learnErrors", + "outputs": [ + { + "name": "errors", + "type": "dada2_errorrates" + }, + { + "name": "plot", + "type": "pdf" + } + ], + "position": { + "left": 1109, + "top": 871 + }, + "post_job_actions": { + "HideDatasetActionerrors": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "errors" + }, + "HideDatasetActionplot": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "plot" + } + }, + "tool_id": "dada2_learnErrors", + "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"err_in\\\": \\\"false\\\", \\\"err_out\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"fls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"nbases\": \"\\\"8\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0.0\\\", \\\"randomize\\\": \\\"false\\\"}\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "2cbc5056-7cc7-4e3e-a283-959a261ca4c5", + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "dada2_dada", + "errors": null, + "id": 9, + "input_connections": { + "batch_cond|derep": { + "id": 6, + "output_name": "forward" + }, + "err": { + "id": 7, + "output_name": "errors" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool dada2: dada", + "name": "batch_cond" + }, + { + "description": "runtime parameter for tool dada2: dada", + "name": "err" + } + ], + "label": null, + "name": "dada2: dada", + "outputs": [ + { + "name": "data_collection", + "type": "input" + } + ], + "position": { + "left": 1424.5, + "top": 585.5 + }, + "post_job_actions": {}, + "tool_id": "dada2_dada", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"err\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "b51bcd73-c8f0-4c39-8a23-9a5baa0a6b4f", + "workflow_outputs": [ + { + "label": null, + "output_name": "data_collection", + "uuid": "8b97daeb-3389-4140-929d-593c5d8bba3a" + } + ] + }, + "10": { + "annotation": "", + "content_id": "dada2_dada", + "errors": null, + "id": 10, + "input_connections": { + "batch_cond|derep": { + "id": 6, + "output_name": "reverse" + }, + "err": { + "id": 8, + "output_name": "errors" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool dada2: dada", + "name": "batch_cond" + }, + { + "description": "runtime parameter for tool dada2: dada", + "name": "err" + } + ], + "label": null, + "name": "dada2: dada", + "outputs": [ + { + "name": "data_collection", + "type": "input" + } + ], + "position": { + "left": 1413.5, + "top": 803.5 + }, + "post_job_actions": {}, + "tool_id": "dada2_dada", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"err\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "188c4ee7-3fb7-4dc7-8efd-30fb38c0d679", + "workflow_outputs": [ + { + "label": null, + "output_name": "data_collection", + "uuid": "7dfc0db1-2376-440c-ac0b-3f9932f063db" + } + ] + }, + "11": { + "annotation": "", + "content_id": "dada2_mergePairs", + "errors": null, + "id": 11, + "input_connections": { + "dadaF": { + "id": 9, + "output_name": "data_collection" + }, + "dadaR": { + "id": 10, + "output_name": "data_collection" + }, + "derepF": { + "id": 6, + "output_name": "forward" + }, + "derepR": { + "id": 6, + "output_name": "reverse" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "dadaR" + }, + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "derepR" + }, + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "dadaF" + }, + { + "description": "runtime parameter for tool dada2: mergePairs", + "name": "derepF" + } + ], + "label": null, + "name": "dada2: mergePairs", + "outputs": [ + { + "name": "merged", + "type": "dada2_mergepairs" + } + ], + "position": { + "left": 1691, + "top": 652.5 + }, + "post_job_actions": {}, + "tool_id": "dada2_mergePairs", + "tool_state": "{\"__page__\": null, \"dadaF\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"derepR\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"maxMismatch\": \"\\\"0\\\"\", \"trimOverhang\": \"\\\"false\\\"\", \"minOverlap\": \"\\\"12\\\"\", \"justConcatenate\": \"\\\"false\\\"\", \"dadaR\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"derepF\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "8a74535a-c7a2-4c24-a907-8cb791b779bf", + "workflow_outputs": [ + { + "label": null, + "output_name": "merged", + "uuid": "887453f1-44ea-4882-8b94-91a3b02eaa0d" + } + ] + }, + "12": { + "annotation": "", + "content_id": "dada2_makeSequenceTable", + "errors": null, + "id": 12, + "input_connections": { + "samples": { + "id": 11, + "output_name": "merged" + } + }, + "inputs": [], + "label": null, + "name": "dada2: makeSequenceTable", + "outputs": [ + { + "name": "stable", + "type": "dada2_sequencetable" + }, + { + "name": "plot_output", + "type": "pdf" + } + ], + "position": { + "left": 1999, + "top": 694 + }, + "post_job_actions": { + "HideDatasetActionplot_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "plot_output" + }, + "HideDatasetActionstable": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable" + } + }, + "tool_id": "dada2_makeSequenceTable", + "tool_state": "{\"orderBy\": \"\\\"abundance\\\"\", \"plot\": \"\\\"true\\\"\", \"__page__\": null, \"filter_cond\": \"{\\\"__current_case__\\\": 0, \\\"filter_select\\\": \\\"no\\\"}\", \"samples\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "3cd64745-bb03-4bfa-b425-a16db0888967", + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "dada2_removeBimeraDenovo", + "errors": null, + "id": 13, + "input_connections": { + "unqs": { + "id": 12, + "output_name": "stable" + } + }, + "inputs": [], + "label": null, + "name": "dada2: removeBimeraDenovo", + "outputs": [ + { + "name": "stable_uniques", + "type": "dada2_uniques" + }, + { + "name": "stable_mergepairs", + "type": "dada2_mergepairs" + }, + { + "name": "stable_sequencetable", + "type": "dada2_sequencetable" + } + ], + "position": { + "left": 2299, + "top": 640 + }, + "post_job_actions": { + "HideDatasetActionstable_mergepairs": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable_mergepairs" + }, + "HideDatasetActionstable_sequencetable": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable_sequencetable" + }, + "HideDatasetActionstable_uniques": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "stable_uniques" + } + }, + "tool_id": "dada2_removeBimeraDenovo", + "tool_state": "{\"unqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"method\": \"\\\"consensus\\\"\", \"__page__\": null}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "4c001b98-d20d-4255-96ee-2b9829aa815b", + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "dada2_seqCounts", + "errors": null, + "id": 14, + "input_connections": { + "inrep_0|input": { + "id": 3, + "output_name": "outtab" + }, + "inrep_1|input": { + "id": 9, + "output_name": "data_collection" + }, + "inrep_2|input": { + "id": 10, + "output_name": "data_collection" + }, + "inrep_4|input": { + "id": 12, + "output_name": "stable" + }, + "inrep_5|input": { + "id": 13, + "output_name": "stable_sequencetable" + } + }, + "inputs": [], + "label": null, + "name": "dada2: sequence counts", + "outputs": [ + { + "name": "counts", + "type": "tabular" + } + ], + "position": { + "left": 2616, + "top": 320 + }, + "post_job_actions": { + "HideDatasetActioncounts": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "counts" + } + }, + "tool_id": "dada2_seqCounts", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"inrep\": \"[{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"filt\\\"}, {\\\"__index__\\\": 1, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised fwd\\\"}, {\\\"__index__\\\": 2, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised rev\\\"}, {\\\"__index__\\\": 3, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"merged\\\"}, {\\\"__index__\\\": 4, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"tabled\\\"}, {\\\"__index__\\\": 5, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"nochim\\\"}]\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "cbdb7105-6e81-418e-98fb-7f36df117fb5", + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "dada2_assignTaxonomyAddspecies", + "errors": null, + "id": 15, + "input_connections": { + "seqs": { + "id": 13, + "output_name": "stable_sequencetable" + } + }, + "inputs": [], + "label": null, + "name": "dada2: assignTaxonomy and addSpecies", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 2623, + "top": 688 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "dada2_assignTaxonomyAddspecies", + "tool_state": "{\"__page__\": null, \"tryRC\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"addSpecies_cond\": \"{\\\"__current_case__\\\": 1, \\\"addSpecies_select\\\": \\\"TRUE\\\", \\\"allowMultiple_cond\\\": {\\\"__current_case__\\\": 0, \\\"allowMultiple\\\": \\\"FALSE\\\"}, \\\"speciesreference_cond\\\": {\\\"__current_case__\\\": 0, \\\"speciesrefFasta\\\": \\\"test_buildid\\\", \\\"speciesreference_select\\\": \\\"builtin\\\"}, \\\"tryRC\\\": \\\"false\\\"}\", \"reference_cond\": \"{\\\"__current_case__\\\": 0, \\\"refFasta\\\": \\\"test_buildid\\\", \\\"reference_select\\\": \\\"builtin\\\"}\", \"outputBootstraps\": \"\\\"false\\\"\", \"minBoot\": \"\\\"50\\\"\", \"seqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.12+galaxy0", + "type": "tool", + "uuid": "babc7594-ae73-4818-919f-561836c45c17", + "workflow_outputs": [] + } + }, + "tags": [], + "uuid": "a4ba74bb-5a8a-403d-885c-822bbe9d6e03", + "version": 1 +} \ No newline at end of file