Mercurial > repos > matthias > dada2_learnerrors
annotate README.md @ 12:a17407e12071 draft default tip
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit df2dfeb75f88b326f567cab8df4e6c4a7f2e548c
| author | matthias |
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| date | Tue, 15 Oct 2019 07:24:12 -0400 |
| parents | ef3ebaa70032 |
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| rev | line source |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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1 Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html. |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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2 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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3 - filterAndTrim |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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4 - derep |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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5 - learnErrors |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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6 - dada |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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7 - mergePairs |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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8 - makeSequenceTable |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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9 - removeBimeraDenovo |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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10 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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11 Datatypes |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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12 ========= |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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13 |
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ef3ebaa70032
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit a54770771e567c7ad8a9dd75cc4689c3935ef11c
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14 The dada2 Galaxy wrappers use a few extra data types to ensure that only inputs of the correct type can be used, these datatypes are available from Galaxy release 19.05, for earlier releases they need to be added manually. |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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15 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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16 For the outputs of derep, dada, learnErrors, and mergePairs the following datatypes are used that derive from Rdata (which contains the named list that is returned from the corresponding dada function): |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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17 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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18 - dada2_derep (Rdata: named list see docs for derep-class) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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19 - dada2_dada (Rdata: named list, see docs for dada-class) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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20 - dada2_errorrates (Rdata: named list, see docs for learnErrors) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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21 - dada2_mergepairs (Rdata: named list, see docs for mergePairs) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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22 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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23 For the outputs of makeSequenceTable and removeBimeraDenovo the following data types are used which derive from tabular: |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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24 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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25 - dada2_uniques |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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26 -- in R a named integer vector (names are the unique sequences) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents:
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27 -- in Galaxy written as a table (each row corresponding to a unique sequence, column 1: the sequence, column 2: the count) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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28 - dada2_sequencetable |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents:
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29 -- in R a named integer matrix (rows = samples, columns = unique sequences) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
parents:
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30 -- in Galaxy written as a table (rows = unique sequences, columns = samples) |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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31 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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32 Note the difference between the R and Galaxy representations! The main motivation is that the dada2_sequencetable is analogous to OTU tables as produced for instance by qiime (and it seemed natural to extend this to the uniques which are essentially a sequencetables of single samples). |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
matthias
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33 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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34 |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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35 TODOs |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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36 ===== |
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9aeea74a1fc9
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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37 |
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ef3ebaa70032
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit a54770771e567c7ad8a9dd75cc4689c3935ef11c
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38 - implement getUniques tool to view intermediate results? |