| Previous changeset 3:806fe614ca46 (2020-07-14) Next changeset 5:8daf4564ccda (2021-07-02) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae" |
|
modified:
macros.xml test-data/assignTaxonomyAddspecies.tab test-data/assignTaxonomyAddspecies_boot.tab |
|
added:
tools.yml topics/metagenomics/metadata.yaml topics/metagenomics/tutorials/dada2/tutorial.bib topics/metagenomics/tutorials/dada2/tutorial.md topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga |
| b |
| diff -r 806fe614ca46 -r ac72310b038a macros.xml --- a/macros.xml Tue Jul 14 07:41:26 2020 -0400 +++ b/macros.xml Mon Feb 01 20:20:36 2021 +0000 |
| b |
| @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@DADA2_VERSION@">1.16</token> + <token name="@DADA2_VERSION@">1.18</token> <token name="@WRAPPER_VERSION@">0</token> <xml name="version_command"> |
| b |
| diff -r 806fe614ca46 -r ac72310b038a test-data/assignTaxonomyAddspecies.tab --- a/test-data/assignTaxonomyAddspecies.tab Tue Jul 14 07:41:26 2020 -0400 +++ b/test-data/assignTaxonomyAddspecies.tab Mon Feb 01 20:20:36 2021 +0000 |
| b |
| b'@@ -1,7 +1,7 @@\n \tLevel1\tLevel2\tLevel3\tLevel4\tLevel5\tNA\tSpecies\n TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tCytophagaceae\tNA\tNA\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidetes\tNA\tNA\tNA\tNA\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tCytophagaceae\tSporocytophaga\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n@@ -14,19 +14,19 @@\n TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGCCAGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATCACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAACCCGGGGCTCAACCCTGGGAGTGCTTTTGAAACTGTGCGGCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n-TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tNA\tNA\tNA\tNA\tNA\n+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTA'..b'CATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tNA\tNA\tNA\tNA\tNA\tNA\n TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tOscillibacter\tNA\n TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tLachnoanaerobaculum\tNA\n-TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\tBacteria\tFirmicutes\tBacilli\tBacillales\tNA\tNA\tNA\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\tBacteria\tFirmicutes\tNA\tNA\tNA\tNA\tNA\n TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG\tBacteria\tFirmicutes\tNA\tNA\tNA\tNA\tNA\n TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG\tBacteria\tFirmicutes\tBacilli\tBacillales\tBacillaceae_2\tPullulanibacillus\tNA\n TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tLachnoanaerobaculum\tNA\n TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tOscillibacter\tNA\n-TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tNA\tNA\tNA\tNA\tNA\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG\tBacteria\tNA\tNA\tNA\tNA\tNA\tNA\n' |
| b |
| diff -r 806fe614ca46 -r ac72310b038a test-data/assignTaxonomyAddspecies_boot.tab --- a/test-data/assignTaxonomyAddspecies_boot.tab Tue Jul 14 07:41:26 2020 -0400 +++ b/test-data/assignTaxonomyAddspecies_boot.tab Mon Feb 01 20:20:36 2021 +0000 |
| b |
| b'@@ -1,32 +1,32 @@\n \tLevel1\tLevel2\tLevel3\tLevel4\tLevel5\tNA\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\t98\t80\t70\t70\t48\t48\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\t97\t88\t76\t76\t50\t48\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\t100\t82\t49\t49\t42\t42\n-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t100\t76\t73\t73\t46\t46\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG\t97\t82\t68\t68\t33\t33\n-TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t99\t99\t99\t91\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG\t96\t45\t31\t31\t13\t13\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\t99\t92\t80\t80\t49\t49\n-TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t72\t72\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAGACAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGCCTGACTGGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t43\n-TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\t100\t94\t87\t87\t68\t41\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGCGCAAGTCTGGAGTGAAATGCCGGGGCCCAACCCCGGAACTGCTTTGGAAACTGTGCAGCTCGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t57\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\t99\t82\t68\t68\t42\t42\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\t99\t89\t73\t73\t54\t54\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGA'..b'GAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t95\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTATGACTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t77\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t79\n+TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG\t100\t61\t60\t60\t48\t39\n+TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t99\t30\t30\t27\t22\t22\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t100\t96\t94\t94\t73\t73\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t51\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\t100\t77\t47\t47\t30\t30\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t99\t99\t99\t99\t80\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG\t100\t96\t45\t45\t45\t45\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t34\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG\t100\t99\t97\t97\t90\t58\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG\t100\t100\t99\t99\t99\t62\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t100\t99\t99\t99\t95\t95\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG\t100\t42\t31\t31\t31\t22\n' |
| b |
| diff -r 806fe614ca46 -r ac72310b038a tools.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools.yml Mon Feb 01 20:20:36 2021 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +install_tool_dependencies: True +install_repository_dependencies: True +install_resolver_dependencies: True + +tools: [] |
| b |
| diff -r 806fe614ca46 -r ac72310b038a topics/metagenomics/metadata.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/topics/metagenomics/metadata.yaml Mon Feb 01 20:20:36 2021 +0000 |
| b |
| @@ -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: "" |
| b |
| diff -r 806fe614ca46 -r ac72310b038a 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 20:20:36 2021 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 806fe614ca46 -r ac72310b038a 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 20:20:36 2021 +0000 |
| [ |
| b'@@ -0,0 +1,642 @@\n+---\n+layout: tutorial_hands_on\n+\n+title: 16S Microbial Analysis with mothur (extended)\n+zenodo_link: https://doi.org/10.5281/zenodo.800651\n+questions:\n+- What is the effect of normal variation in the gut microbiome on host health?\n+objectives:\n+- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy\n+- Using a mock community to assess the error rate of your sequencing experiment\n+- Visualize sample diversity using Krona and Phinch\n+time_estimation: \'\'\n+key_points:\n+- 16S rRNA gene sequencing analysis results depend on the many algorithms used and\n+ their settings\n+- Quality control and cleaning of your data is a crucial step in order to obtain optimal\n+ results\n+- Adding a mock community to serve as a control sample can help you asses the error\n+ rate of your experimental setup\n+- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations\n+contributors:\n+- shiltemann\n+- bebatut\n+- tnabtaf\n+\n+---\n+\n+\n+# Introduction\n+{:.no_toc}\n+\n+<!-- This is a comment. -->\n+\n+General introduction about the topic and then an introduction of the\n+tutorial (the questions and the objectives). It is nice also to have a\n+scheme to sum up the pipeline used during the tutorial. The idea is to\n+give to trainees insight into the content of the tutorial and the (theoretical\n+and technical) key concepts they will learn.\n+\n+You may want to cite some publications; this can be done by adding citations to the\n+bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations\n+must be in bibtex format. If you have the DOI for the paper you wish to cite, you can\n+get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org).\n+\n+With the example you will find in the `tutorial.bib` file, you can add a citation to\n+this article here in your tutorial like this:\n+{% raw %} `{% cite Batut2018 %}`{% endraw %}.\n+This will be rendered like this: {% cite Batut2018 %}, and links to a\n+[bibliography section](#bibliography) which will automatically be created at the end of the\n+tutorial.\n+\n+\n+**Please follow our\n+[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)**\n+\n+> ### Agenda\n+>\n+> In this tutorial, we will cover:\n+>\n+> 1. TOC\n+> {:toc}\n+>\n+{: .agenda}\n+\n+# Title for your first section\n+\n+Give some background about what the trainees will be doing in the section.\n+Remember that many people reading your materials will likely be novices,\n+so make sure to explain all the relevant concepts.\n+\n+## Title for a subsection\n+Section and subsection titles will be displayed in the tutorial index on the left side of\n+the page, so try to make them informative and concise!\n+\n+# Hands-on Sections\n+Below are a series of hand-on boxes, one for each tool in your workflow file.\n+Often you may wish to combine several boxes into one or make other adjustments such\n+as breaking the tutorial into sections, we encourage you to make such changes as you\n+see fit, this is just a starting point :)\n+\n+Anywhere you find the word "***TODO***", there is something that needs to be changed\n+depending on the specifics of your tutorial.\n+\n+have fun!\n+\n+## Get data\n+\n+> ### {% icon hands_on %} Hands-on: Data upload\n+>\n+> 1. Create a new history for this tutorial\n+> 2. Import the files from [Zenodo]() or from the shared data library\n+>\n+> ```\n+> \n+> ```\n+> ***TODO***: *Add the files by the ones on Zenodo here (if not added)*\n+>\n+> ***TODO***: *Remove the useless files (if added)*\n+>\n+> {% include snippets/import_via_link.md %}\n+> {% include snippets/import_from_data_library.md %}\n+>\n+> 3. Rename the datasets\n+> 4. Check that the datatype\n+>\n+> {% include snippets/change_datatype.md datatype="datatypes" %}\n+>\n+> 5. Add to each database a tag corresponding to ...\n+>\n+> {% include snippets/add_tag.md %}\n+>\n+{: .hands_on}\n+\n+# Title of the section usually corresponding to a big step in the '..b'+> {: .comment}\n+>\n+{: .hands_on}\n+\n+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n+\n+> ### {% icon question %} Questions\n+>\n+> 1. Question1?\n+> 2. Question2?\n+>\n+> > ### {% icon solution %} Solution\n+> >\n+> > 1. Answer for question1\n+> > 2. Answer for question2\n+> >\n+> {: .solution}\n+>\n+{: .question}\n+\n+## Sub-step with **dada2_makeSequenceTable**\n+\n+> ### {% icon hands_on %} Hands-on: Task description\n+>\n+> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters:\n+>\n+> ***TODO***: *Check parameter descriptions*\n+>\n+> ***TODO***: *Consider adding a comment or tip box*\n+>\n+> > ### {% icon comment %} Comment\n+> >\n+> > A comment about the tool or something else. This box can also be in the main text\n+> {: .comment}\n+>\n+{: .hands_on}\n+\n+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n+\n+> ### {% icon question %} Questions\n+>\n+> 1. Question1?\n+> 2. Question2?\n+>\n+> > ### {% icon solution %} Solution\n+> >\n+> > 1. Answer for question1\n+> > 2. Answer for question2\n+> >\n+> {: .solution}\n+>\n+{: .question}\n+\n+## Sub-step with **dada2_removeBimeraDenovo**\n+\n+> ### {% icon hands_on %} Hands-on: Task description\n+>\n+> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters:\n+>\n+> ***TODO***: *Check parameter descriptions*\n+>\n+> ***TODO***: *Consider adding a comment or tip box*\n+>\n+> > ### {% icon comment %} Comment\n+> >\n+> > A comment about the tool or something else. This box can also be in the main text\n+> {: .comment}\n+>\n+{: .hands_on}\n+\n+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n+\n+> ### {% icon question %} Questions\n+>\n+> 1. Question1?\n+> 2. Question2?\n+>\n+> > ### {% icon solution %} Solution\n+> >\n+> > 1. Answer for question1\n+> > 2. Answer for question2\n+> >\n+> {: .solution}\n+>\n+{: .question}\n+\n+## Sub-step with **dada2_seqCounts**\n+\n+> ### {% icon hands_on %} Hands-on: Task description\n+>\n+> 1. **dada2_seqCounts** {% icon tool %} with the following parameters:\n+>\n+> ***TODO***: *Check parameter descriptions*\n+>\n+> ***TODO***: *Consider adding a comment or tip box*\n+>\n+> > ### {% icon comment %} Comment\n+> >\n+> > A comment about the tool or something else. This box can also be in the main text\n+> {: .comment}\n+>\n+{: .hands_on}\n+\n+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n+\n+> ### {% icon question %} Questions\n+>\n+> 1. Question1?\n+> 2. Question2?\n+>\n+> > ### {% icon solution %} Solution\n+> >\n+> > 1. Answer for question1\n+> > 2. Answer for question2\n+> >\n+> {: .solution}\n+>\n+{: .question}\n+\n+## Sub-step with **dada2_assignTaxonomyAddspecies**\n+\n+> ### {% icon hands_on %} Hands-on: Task description\n+>\n+> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters:\n+>\n+> ***TODO***: *Check parameter descriptions*\n+>\n+> ***TODO***: *Consider adding a comment or tip box*\n+>\n+> > ### {% icon comment %} Comment\n+> >\n+> > A comment about the tool or something else. This box can also be in the main text\n+> {: .comment}\n+>\n+{: .hands_on}\n+\n+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n+\n+> ### {% icon question %} Questions\n+>\n+> 1. Question1?\n+> 2. Question2?\n+>\n+> > ### {% icon solution %} Solution\n+> >\n+> > 1. Answer for question1\n+> > 2. Answer for question2\n+> >\n+> {: .solution}\n+>\n+{: .question}\n+\n+\n+## Re-arrange\n+\n+To create the template, each step of the workflow had its own subsection.\n+\n+***TODO***: *Re-arrange the generated subsections into sections or other subsections.\n+Consider merging some hands-on boxes to have a meaningful flow of the analyses*\n+\n+# Conclusion\n+{:.no_toc}\n+\n+Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the\n+pipeline used.\n\\ No newline at end of file\n' |
| b |
| diff -r 806fe614ca46 -r ac72310b038a 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 20:20:36 2021 +0000 |
| [ |
| b'@@ -0,0 +1,798 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "dada2 for paired data (imported from uploaded file)", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "content_id": null, \n+ "errors": null, \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset Collection"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Input dataset collection", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 613\n+ }, \n+ "tool_id": null, \n+ "tool_state": "{\\"collection_type\\": \\"list:paired\\", \\"name\\": \\"Input Dataset Collection\\"}", \n+ "tool_version": null, \n+ "type": "data_collection_input", \n+ "uuid": "b1f16224-49d2-4b7a-a37d-3d93c54f679f", \n+ "workflow_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "content_id": "dada2_plotComplexity", \n+ "errors": null, \n+ "id": 1, \n+ "input_connections": {\n+ "batch_cond|paired_cond|reads": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "dada2: plotComplexity", \n+ "outputs": [\n+ {\n+ "name": "output_fwd", \n+ "type": "pdf"\n+ }, \n+ {\n+ "name": "output_rev", \n+ "type": "pdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 499, \n+ "top": 178.5\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionoutput_fwd": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_fwd"\n+ }, \n+ "HideDatasetActionoutput_rev": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_rev"\n+ }\n+ }, \n+ "tool_id": "dada2_plotComplexity", \n+ "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\\\\\\"\\"}", \n+ "tool_version": "1.12+galaxy0", \n+ "type": "tool", \n+ "uuid": "4f226c7b-9ba8-4b48-8d48-899cf345b660", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output_fwd", \n+ "uuid": "52b4da66-504c-4fbe-8487-d6c0613ab6ae"\n+ }, \n+ {\n+ "label": null, \n+ "output_name": "output_rev", \n+ "uuid": "3785a6f5-da8a-4232-b2ab-4f9f4c0732f6"\n+ }\n+ ]\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "content_id": "dada2_plotQualityProfile", \n+ "errors": null, \n+ "id": 2, \n+ "input_connections": {\n+ "batch_cond|paired_cond|reads": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "dada2'..b' }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "dada2: sequence counts", \n+ "outputs": [\n+ {\n+ "name": "counts", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 2616, \n+ "top": 320\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActioncounts": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "counts"\n+ }\n+ }, \n+ "tool_id": "dada2_seqCounts", \n+ "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\\\\\\"\\"}", \n+ "tool_version": "1.12+galaxy0", \n+ "type": "tool", \n+ "uuid": "cbdb7105-6e81-418e-98fb-7f36df117fb5", \n+ "workflow_outputs": []\n+ }, \n+ "15": {\n+ "annotation": "", \n+ "content_id": "dada2_assignTaxonomyAddspecies", \n+ "errors": null, \n+ "id": 15, \n+ "input_connections": {\n+ "seqs": {\n+ "id": 13, \n+ "output_name": "stable_sequencetable"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "dada2: assignTaxonomy and addSpecies", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 2623, \n+ "top": 688\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionoutput": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output"\n+ }\n+ }, \n+ "tool_id": "dada2_assignTaxonomyAddspecies", \n+ "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\\\\\\"\\"}", \n+ "tool_version": "1.12+galaxy0", \n+ "type": "tool", \n+ "uuid": "babc7594-ae73-4818-919f-561836c45c17", \n+ "workflow_outputs": []\n+ }\n+ }, \n+ "tags": [], \n+ "uuid": "a4ba74bb-5a8a-403d-885c-822bbe9d6e03", \n+ "version": 1\n+}\n\\ No newline at end of file\n' |