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author matthias
date Sun, 05 May 2019 12:28:14 -0400
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ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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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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3 - filterAndTrim
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4 - derep
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5 - learnErrors
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6 - dada
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7 - mergePairs
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8 - makeSequenceTable
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9 - removeBimeraDenovo
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ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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11 Datatypes
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12 =========
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ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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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.
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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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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ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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18 - dada2_derep (Rdata: named list see docs for derep-class)
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19 - dada2_dada (Rdata: named list, see docs for dada-class)
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20 - dada2_errorrates (Rdata: named list, see docs for learnErrors)
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21 - dada2_mergepairs (Rdata: named list, see docs for mergePairs)
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ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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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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25 - dada2_uniques
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26 -- in R a named integer vector (names are the unique sequences)
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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)
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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28 - dada2_sequencetable
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29 -- in R a named integer matrix (rows = samples, columns = unique sequences)
ea57169fd0d0 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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30 -- in Galaxy written as a table (rows = unique sequences, columns = samples)
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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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35 TODOs
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36 =====
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38 - implememt getUniques tool to view intermediate results?
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39 - implement tests for cached reference data