# HG changeset patch
# User matthias
# Date 1557074381 14400
# Node ID caa2bdb8a4313aaaa863e1eeed9d7cd71fe59725
# Parent 02ac909ff0f555fda239f170c9b24398c5e20aec
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
diff -r 02ac909ff0f5 -r caa2bdb8a431 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Sun May 05 12:39:41 2019 -0400
@@ -0,0 +1,39 @@
+Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html.
+
+- filterAndTrim
+- derep
+- learnErrors
+- dada
+- mergePairs
+- makeSequenceTable
+- removeBimeraDenovo
+
+Datatypes
+=========
+
+The dada2 Galaxy wrappers use a few extra data types to ensure that only inputs of the correct type can be used.
+
+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):
+
+- dada2_derep (Rdata: named list see docs for derep-class)
+- dada2_dada (Rdata: named list, see docs for dada-class)
+- dada2_errorrates (Rdata: named list, see docs for learnErrors)
+- dada2_mergepairs (Rdata: named list, see docs for mergePairs)
+
+For the outputs of makeSequenceTable and removeBimeraDenovo the following data types are used which derive from tabular:
+
+- dada2_uniques
+-- in R a named integer vector (names are the unique sequences)
+-- in Galaxy written as a table (each row corresponding to a unique sequence, column 1: the sequence, column 2: the count)
+- dada2_sequencetable
+-- in R a named integer matrix (rows = samples, columns = unique sequences)
+-- in Galaxy written as a table (rows = unique sequences, columns = samples)
+
+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).
+
+
+TODOs
+=====
+
+- implememt getUniques tool to view intermediate results?
+- implement tests for cached reference data
diff -r 02ac909ff0f5 -r caa2bdb8a431 dada2_assignTaxonomyAddspecies.xml
--- a/dada2_assignTaxonomyAddspecies.xml Mon Apr 29 09:53:04 2019 -0400
+++ b/dada2_assignTaxonomyAddspecies.xml Sun May 05 12:39:41 2019 -0400
@@ -152,9 +152,9 @@
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@@ -175,11 +175,11 @@
**Input**
- A list of sequences contained in the results of removeBimeraDenovo or sequenceTable (note that also the results of derep, dada, and mergePairs are accepted).
-- Reference data bases for taxonomic and species/genus level assignment. Several chached data bases can be chosen (ask your Galaxy admin if they are missing). For using custom data bases see below.
+- Reference data bases for taxonomic and species/genus level assignment. Several cached data bases can be chosen (ask your Galaxy admin if they are missing). For using custom data bases see below.
**Output**
-- A table containing the assigned taxonomies exceeding the minBoot level of bootstrapping confidence. Rows correspond to the provided sequences, columns to the taxonomic levels. NA indicates that the sequence was not consistently classified at that level at the minBoot threshhold.
+- A table containing the assigned taxonomies exceeding the minBoot level of bootstrapping confidence. Rows correspond to the provided sequences, columns to the taxonomic levels. NA indicates that the sequence was not consistently classified at that level at the minBoot threshold.
- Optionally two columns for the genus and species taxonomic levels can be added. NA indicates that the sequence was not classified at that level.
- If outputBootstraps checked, a table containing the assigned taxonomies (named "taxa") and the bootstrap values (named "boot") will be returned.
diff -r 02ac909ff0f5 -r caa2bdb8a431 macros.xml
--- a/macros.xml Mon Apr 29 09:53:04 2019 -0400
+++ b/macros.xml Sun May 05 12:39:41 2019 -0400
@@ -25,23 +25,44 @@
dada2_derep,dada2_dada,dada2_mergepairs
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@@ -63,9 +84,9 @@
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