Galaxy |

Changeset 0:d26cea4b4cc4 (2019-11-08)

Next changeset 1:4cc834cce4fb (2019-12-05)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"

added:
README.md
dada2_seqCounts.xml
macros.xml
static/images/pairpipe.png
static/images/pairpipe.svg
test-data/F3D0_S188_L001_R1_001.fastq.gz
test-data/F3D0_S188_L001_R2_001.fastq.gz
test-data/assignTaxonomyAddspecies_F3D0.tab
test-data/assignTaxonomyAddspecies_F3D0_boot.tab
test-data/complexity.pdf
test-data/dada2_species.loc
test-data/dada2_taxonomy.loc
test-data/dada_F3D0_R1.Rdata
test-data/dada_F3D0_R2.Rdata
test-data/derepFastq_F3D0_R1.Rdata
test-data/derepFastq_F3D0_R2.Rdata
test-data/filterAndTrim_F3D0.tab
test-data/filterAndTrim_F3D0_R1.fq.gz
test-data/filterAndTrim_F3D0_R2.fq.gz
test-data/filterAndTrim_single_F3D0_R1.fq.gz
test-data/filterAndTrim_single_filters_F3D0_R1.fq.gz
test-data/filterAndTrim_single_trimmers_F3D0_R1.fq.gz
test-data/gentest.R
test-data/gentest.sh
test-data/learnErrors_F3D0_R1.Rdata
test-data/learnErrors_F3D0_R1.pdf
test-data/learnErrors_F3D0_R2.Rdata
test-data/learnErrors_F3D0_R2.pdf
test-data/makeSequenceTable_F3D0.pdf
test-data/makeSequenceTable_F3D0.tab
test-data/mergePairs_F3D0.Rdata
test-data/mergePairs_F3D0_nondefault.Rdata
test-data/qualityProfile.pdf
test-data/reference.fa
test-data/reference_species.fa
test-data/removeBimeraDenovo_F3D0.tab
test-data/removeBimeraDenovo_F3D0_dada_uniques.tab
test-data/removeBimeraDenovo_F3D0_derep_uniques.tab
test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata
test-data/seqCounts_F3D0_dadaF.tab
test-data/seqCounts_F3D0_filter.tab
test-data/seqCounts_F3D0_merge.tab
test-data/seqCounts_F3D0_nochim.tab
test-data/seqCounts_F3D0_seqtab.tab
tool-data/dada2_species.loc.sample
tool-data/dada2_taxonomy.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test

diff -r 000000000000 -r d26cea4b4cc4 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,57 @@
+Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html.
+
+- filterAndTrim
+- learnErrors
+- dada
+- mergePairs
+- makeSequenceTable
+- removeBimeraDenovo
+
+Installation
+============
+
+The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases.
+In order to run the tools you may either upgrade Galaxy or execute the following two steps:
+
+1. `find GALAXY_ROOT/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ -name "dada2_*xml" -exec sed -i -e 's/profile="19.09"/profile="YOUR_RELEASE"/' {} ;` (replace GALAXY_ROOT and YOUR_RELEASE appropriately)
+2. insert the following lines in `config/datatypes.xml` (just before the line `</registration>`):
+```
+    <datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
+```
+
+Datatypes
+=========
+
+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.
+
+For the outputs of 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_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).
+
+Test data
+=========
+
+Test data for `dada2_seqCounts` is generated using planemo's `--update_test_data` argument and manual
+inspection of the test files. In addition a run of the pipeline (using collections) is executed
+manually using `planemo serve` making sure that the entries of the tables are generated in a useful way.
+
+In order to have the Collection unzip tool available use `planemo s --galaxy_root GALAXY_ROOT  --extra_tools GALAXY_ROOT/lib/galaxy/tools/`
+
+All test other test data is generated using the shell script (`gentest.sh`) in test-data

diff -r 000000000000 -r d26cea4b4cc4 dada2_seqCounts.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dada2_seqCounts.xml Fri Nov 08 18:50:51 2019 -0500

[

@@ -0,0 +1,156 @@
+<tool id="dada2_seqCounts" name="dada2: sequence counts" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript '$dada2_script'
+    ]]></command>
+    <configfiles>
+        <configfile name="dada2_script"><![CDATA[
+@READ_FOO@
+library(dada2, quietly=T)
+
+getN <- function(x){ sum(getUniques(x)) }
+
+df <- NULL
+#for $i, $rep in enumerate($inrep)
+    samples = list()
+    #for $s in $rep.input:
+        ## for collection input assume identifiers are sample names
+        #if $s.ext in ["tabular", "dada2_dada", "dada2_mergepairs"]
+            sample_name <- '$s.element_identifier'
+            samples[[sample_name]] <- $read_data( $s )
+        #else
+            samples <- $read_data( $s )
+        #end if
+        #if $s.ext == "tabular"
+            tabular <- T
+        #else
+            tabular <- F
+        #end if
+    #end for
+
+    #if str($rep.name) == ""
+        dname <- '$str(i)'
+    #else
+        dname <- '$rep.name'
+    #end if
+
+    if( tabular ){
+        tdf <- NULL
+        for( n in names( samples ) ){
+            if(is.null(tdf)){
+                tdf <- samples[[n]]
+            }else{
+                tdf <- rbind(tdf, samples[[n]])
+            }
+        }
+        names(tdf) <- paste( dname, names(tdf) )
+        tdf <- cbind( data.frame(samples=names( samples )), tdf)
+    }else{
+        if(is.null(names(samples))){
+            tdf <- data.frame( samples = row.names(samples) )
+        }else{
+            tdf <- data.frame( samples = names(samples) )
+        }
+        t <- tryCatch({
+            sapply(samples, getN)
+        },
+        error=function(cond) {
+            rowSums(samples)
+        })
+        tdf[[ dname ]] <- t
+    }
+    if(is.null(df)){
+        df <- tdf
+    }else{
+        df <- merge( df, tdf, by="samples", all=T, no.dups=T)
+    }
+#end for
+write.table(df, "$counts", quote=F, sep="\t", row.names = F, col.names = T)
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <repeat name="inrep" title="data sets" min="1">
+            <param name="input" type="data" multiple="true" format="tabular,@DADA_UNIQUES@,dada2_sequencetable,dada2_uniques" label="Dataset(s)"/>
+            <param name="name" type="text" value="" optional="true" label="name"/>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="counts" format="tabular" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="filterAndTrim_F3D0.tab" ftype="tabular"/>
+                <param name="name" value="filter"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_filter.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="dada_F3D0_R1.Rdata" ftype="dada2_dada"/>
+                <param name="name" value="dadaF"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_dadaF.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs"/>
+                <param name="name" value="merge"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_merge.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable"/>
+                <param name="name" value="seqtab"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_seqtab.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="removeBimeraDenovo_F3D0.tab" ftype="dada2_sequencetable"/>
+                <param name="name" value="nochim"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_nochim.tab" ftype="tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Description
+...........
+
+Get the counts of sequences per sample for the different stages of the dada pipeline.
+
+Usage
+.....
+
+**Inputs:**
+
+Any number of results of dada2 steps in the following form:
+- a collection of results from dada, or mergePairs; or the collection of statistics from filterAndTrim (the identifiers of the collection elements are used as sample names)
+- the result of makeSequenceTable or removeBimeraDenovo
+
+**Output:**
+
+A table containing the number of sequences per sample (rows) for each input (columns)
+
+Details
+.......
+
+For results from
+
+- dada, and mergePairs the sum of the result of dada2's getUniques function is used
+- makeSequenceTable, and removeBimeraDenovo R's rowSums function is used
+
+@HELP_OVERVIEW@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>

diff -r 000000000000 -r d26cea4b4cc4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Nov 08 18:50:51 2019 -0500

[

@@ -0,0 +1,131 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@DADA2_VERSION@">1.12</token>
+    <token name="@WRAPPER_VERSION@">0</token>
+
+    <xml name="version_command">
+        <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+        ]]></version_command>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <regex match="Error: cannot allocate" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+            <regex match="'Calloc' could not allocate memory" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+        </stdio>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nmeth.3869</citation>
+            <yield/>
+        </citations>
+    </xml>
+
+    <token name="@DADA_UNIQUES@">dada2_dada,dada2_mergepairs</token>
+
+    
+    <token name="@READ_FOO@"><![CDATA[
+    read.uniques <- function ( fname ) {
+         p <- read.table(fname, header=F, sep="\t")
+         n <-x[,2]
+         names(n)<-x[,1]
+    }
+    #def read_data($dataset)
+        #if $dataset.is_of_type('dada2_sequencetable')
+            t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ))
+        #else if $dataset.is_of_type('dada2_uniques')
+            read.uniques('$dataset')
+        #else if $dataset.is_of_type('tabular')
+            read.table('$dataset', header=T, sep="\t", row.names=1)
+        #else
+            readRDS('$dataset')
+        #end if
+    #end def
+    ]]></token>
+    
+    <token name="@WRITE_FOO@"><![CDATA[
+write.data <- function( data, fname, type ){
+    if( type == 'dada2_uniques'){
+        write.table(data, file = fname, quote = F, sep = "\t", row.names = T, col.names = F)
+    }else if( type== 'dada2_sequencetable'){
+        write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA)
+    }else{
+        saveRDS(data, file=fname)
+    }
+}
+    ]]></token>
+
+    <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
+        <conditional name="paired_cond">
+            <param name="paired_select" type="select" label="Paired reads">
+                <option value="paired">paired - in a data set pair</option>
+                <option value="separate">paired - in two separate data sets</option>
+                <option value="single">single</option>
+            </param>
+            <when value="paired">
+                <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
+            </when>
+            <when value="separate">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
+                <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
+            </when>
+            <when value="single">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
+            </when>
+        </conditional>
+    </xml>
+
+    
+    <xml name="trimmers">
+        <section name="trim" title="Trimming parameters">
+            <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
+            <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>
+            <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
+            <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
+        </section>
+    </xml>
+    <xml name="filters">
+        <section name="filter" title="Filtering parameters">
+            <param argument="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/>
+            <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
+            <param argument="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/>
+            <param argument="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/>
+            <param argument="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/>
+        </section>
+    </xml>
+
+    <xml name="errorEstimationFunction">
+        <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function">
+            <option value="loessErrfun">loess: Use a loess fit to estimate error rates from transition counts</option>
+            <option value="noqualErrfun">noqual: Estimate error rates for each type of transition while ignoring quality scores.</option>
+            <option value="PacBioErrfun">PacBio: Estimate error rates from transition counts in PacBio CCS data.</option>
+        </param>
+    </xml>
+    <token name="@HELP_OVERVIEW@"><![CDATA[
+Overview
+........
+
+The intended use of the dada2 tools for paired sequencing data is shown in the following image.
+
+.. image:: pairpipe.png
+
+For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.
+
+More information may be found on the dada2 homepage:: https://benjjneb.github.io/dada2/index.html (in particular tutorials) or the documentation of dada2's R package https://bioconductor.org/packages/release/bioc/html/dada2.html (in particular the pdf which contains the full documentation of all parameters)
+    ]]></token>
+</macros>

diff -r 000000000000 -r d26cea4b4cc4 static/images/pairpipe.png

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diff -r 000000000000 -r d26cea4b4cc4 test-data/assignTaxonomyAddspecies_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assignTaxonomyAddspecies_F3D0.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,8 @@
+ Level1 Level2 Level3 Level4 Level5 Species
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG A B C D E NA
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG A B C D E NA
+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG A B C D E NA
+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG A B C D E NA
+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG A B C D E NA
+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG A B C D E NA
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG A B C D E NA

diff -r 000000000000 -r d26cea4b4cc4 test-data/assignTaxonomyAddspecies_F3D0_boot.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assignTaxonomyAddspecies_F3D0_boot.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,8 @@
+ Level1 Level2 Level3 Level4 Level5
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 100 100 100 100 100
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 100 100 100 100 100
+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100
+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100
+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100
+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 100 100 100 100 100
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 100 100 100 100 100

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diff -r 000000000000 -r d26cea4b4cc4 test-data/dada2_species.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_species.loc Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,10 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of dada2 reference data sets for species assignment, using three
+# tab separated columns:
+#
+# <unique_build_id> <display_name> <fasta_file_path>
+#
+# Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html
+#
+# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
+test_buildid test_displayname ${__HERE__}/reference_species.fa

diff -r 000000000000 -r d26cea4b4cc4 test-data/dada2_taxonomy.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_taxonomy.loc Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,10 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of dada2 reference data sets for taxonomy assignment, using three
+# tab separated columns:
+#
+# <unique_build_id> <display_name> <fasta_file_path> <taxlevels>
+#
+# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
+#
+# taxlevels is a comma separated list of taxonomy levels
+test_buildid test_displayname ${__HERE__}/reference.fa Level1,Level2,Level3,Level4,Level5

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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filterAndTrim_F3D0.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,2 @@
+ reads.in reads.out
+Unnamed Collection 250 249

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diff -r 000000000000 -r d26cea4b4cc4 test-data/gentest.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.R Fri Nov 08 18:50:51 2019 -0500

[

@@ -0,0 +1,99 @@
+library(dada2, quietly=T)
+library(ggplot2, quietly=T)
+
+fwd <- c('F3D0_S188_L001_R1_001.fastq.gz')
+rev <- c('F3D0_S188_L001_R2_001.fastq.gz')
+
+sample.names <- c('F3D0_S188_L001')
+
+names(fwd) <- sample.names
+names(rev) <- sample.names
+
+
+filt.fwd <- c('filterAndTrim_F3D0_R1.fq.gz')
+filt.rev <- c('filterAndTrim_F3D0_R2.fq.gz')
+
+ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev)
+
+# In the test no name can be given to the collection
+rownames(ftout) <- c( 'Unnamed Collection' )
+write.table(ftout, "filterAndTrim_F3D0.tab", quote=F, sep="\t", col.names=NA)
+
+# Plot quality profile (just for one file, Galaxy compares with sim_size)
+
+qp <- plotQualityProfile(fwd)
+ggsave('qualityProfile.pdf', qp, width = 20,height = 15,units = c("cm"))
+
+# Plot complexity (just for one file, Galaxy compares with sim_size)
+
+cp <- plotComplexity(fwd)
+ggsave('complexity.pdf', cp, width = 20,height = 15,units = c("cm"))
+
+
+# learn Errors
+err.fwd <- learnErrors(filt.fwd)
+saveRDS(err.fwd, file='learnErrors_F3D0_R1.Rdata')
+plot <- plotErrors(err.fwd)
+ggsave('learnErrors_F3D0_R1.pdf', plot, width = 20,height = 15,units = c("cm"))
+
+err.rev <- learnErrors(filt.fwd)
+saveRDS(err.rev, file='learnErrors_F3D0_R2.Rdata')
+plot <- plotErrors(err.rev)
+ggsave('learnErrors_F3D0_R2.pdf', plot, width = 20,height = 15,units = c("cm"))
+
+# dada
+dada.fwd <- dada(filt.fwd, err.fwd)
+saveRDS(dada.fwd, file="dada_F3D0_R1.Rdata")
+dada.rev <- dada(filt.rev, err.rev)
+saveRDS(dada.rev, file="dada_F3D0_R2.Rdata")
+
+# merge pairs
+merged <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev)
+saveRDS(merged, file='mergePairs_F3D0.Rdata')
+
+# make sequence table
+seqtab <- makeSequenceTable(merged)
+write.table(t(seqtab), file="makeSequenceTable_F3D0.tab", quote=F, sep="\t", row.names = T, col.names = NA)
+
+reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
+df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
+pdf( 'makeSequenceTable_F3D0.pdf' )
+ggplot(data=df, aes(x=length, y=count)) +
+ geom_col() +
+ theme_bw()
+bequiet <- dev.off()
+
+# remove bimera
+seqtab.nochim <- removeBimeraDenovo(seqtab)
+write.table(t(seqtab), file="removeBimeraDenovo_F3D0.tab", quote=F, sep="\t", row.names = T, col.names = NA)
+
+# assign taxonomy/species
+tl <- 'Level1,Level2,Level3,Level4,Level5'
+tl <- strsplit(tl, ",")[[1]]
+
+taxa <- assignTaxonomy(seqtab.nochim, 'reference.fa', outputBootstraps = T, taxLevels=c('Level1','Level2','Level3','Level4','Level5'))
+
+taxa$tax <- addSpecies(taxa$tax, 'reference_species.fa')
+write.table(taxa$tax, file = 'assignTaxonomyAddspecies_F3D0.tab', quote = F, sep = "\t", row.names = T, col.names = NA)
+
+write.table(taxa$boot, file = 'assignTaxonomyAddspecies_F3D0_boot.tab', quote = F, sep = "\t", row.names = T, col.names = NA)
+
+
+
+## Generate extra test data for parameter testing
+
+filterAndTrim(fwd, c('filterAndTrim_single_F3D0_R1.fq.gz'), rm.phix = T, orient.fwd = 'TACGG')
+
+filterAndTrim(fwd, c('filterAndTrim_single_trimmers_F3D0_R1.fq.gz'), truncQ = 30, truncLen = 2, trimLeft = 150, trimRight = 2)
+
+filterAndTrim(fwd, c('filterAndTrim_single_filters_F3D0_R1.fq.gz'), maxLen = 255, minLen = 60, maxN = 100, minQ = 13, maxEE = 1)
+
+
+merged_nondef <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev, minOverlap = 8, maxMismatch = 1, justConcatenate = TRUE, trimOverhang = TRUE)
+saveRDS(merged_nondef, file='mergePairs_F3D0_nondefault.Rdata')
+
+rb.dada.fwd <- removeBimeraDenovo(dada.fwd)
+write.table(rb.dada.fwd, file = 'removeBimeraDenovo_F3D0_dada_uniques.tab', quote = F, sep = "\t", row.names = T, col.names = F)
+
+rb.merged <- removeBimeraDenovo(merged, method="pooled")
+saveRDS(rb.merged, file='removeBimeraDenovo_F3D0_mergepairs.Rdata')

diff -r 000000000000 -r d26cea4b4cc4 test-data/gentest.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.sh Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,8 @@
+
+conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-dada2@1.12 bioconductor-dada2=1.12
+conda activate bioconductor-dada2@1.12
+
+Rscript gentest.R
+
+# remove files only needed for test generation
+rm learnErrors_F3D0_R2.pdf dada_F3D0_R2.Rdata

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diff -r 000000000000 -r d26cea4b4cc4 test-data/learnErrors_F3D0_R2.Rdata

Binary file test-data/learnErrors_F3D0_R2.Rdata has changed

diff -r 000000000000 -r d26cea4b4cc4 test-data/learnErrors_F3D0_R2.pdf

Binary file test-data/learnErrors_F3D0_R2.pdf has changed

diff -r 000000000000 -r d26cea4b4cc4 test-data/makeSequenceTable_F3D0.pdf

Binary file test-data/makeSequenceTable_F3D0.pdf has changed

diff -r 000000000000 -r d26cea4b4cc4 test-data/makeSequenceTable_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeSequenceTable_F3D0.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,8 @@
+ V1
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 22
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 18
+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 11
+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 5
+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 5
+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 3
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 2

diff -r 000000000000 -r d26cea4b4cc4 test-data/mergePairs_F3D0.Rdata

Binary file test-data/mergePairs_F3D0.Rdata has changed

diff -r 000000000000 -r d26cea4b4cc4 test-data/mergePairs_F3D0_nondefault.Rdata

Binary file test-data/mergePairs_F3D0_nondefault.Rdata has changed

diff -r 000000000000 -r d26cea4b4cc4 test-data/qualityProfile.pdf

Binary file test-data/qualityProfile.pdf has changed

diff -r 000000000000 -r d26cea4b4cc4 test-data/reference.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fa Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,4 @@
+>A;B;C;D;E;
+ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
+>A;B;C;F;G;
+CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC

diff -r 000000000000 -r d26cea4b4cc4 test-data/reference_species.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference_species.fa Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,4 @@
+>IDA GenusA speciesA
+ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
+>IDB GenusB speciesB
+CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC

diff -r 000000000000 -r d26cea4b4cc4 test-data/removeBimeraDenovo_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/removeBimeraDenovo_F3D0.tab Fri Nov 08 18:50:51 2019 -0500

diff -r 000000000000 -r d26cea4b4cc4 test-data/removeBimeraDenovo_F3D0_dada_uniques.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/removeBimeraDenovo_F3D0_dada_uniques.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,18 @@
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG 22
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG 20
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG 16
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG 19
+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACA 5
+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA 5
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG 17
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA 25
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAG 9
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACA 4
+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGAAGACAAGTCAGATGTGAAATCCCGCGGCTCAACCGCGGAACTGCATTTGAAACTGTTTTTCTTGAGTACCGGAGAGGTCATCGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATGACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACA 10
+TACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGTAGGCGGGAAGCCAAGTCAGCTGTGAAAACTACGGGCTTAACCTGTAGACTGCAGTTGAAACTGGCTTTCTTGAGTGAAGTAGAGGTTGGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCGGTGGCGAAGGCGGCCAACTGGGCTTTAACTGACGCTGAGGCTCGAAAGTGTGGGGAGCAAACA 2
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAG 9
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGGGCGCAGACGGCCATGGCAAGCCCGGTGTGAAAGGCAGGGGCATAACCCCTGGACTGCACTGGGAACTGTCAGGCTGGAGTGCCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGCGGCGAAGGCGGCTTACTGGACGGCAACTGACGTTGAGGCCCGAAAGCGTGGGGAGCGAA 2
+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA 15
+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACA 3
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACA 2
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGTCAAGTCAGCGGTAAAAATTCCGGGCTCAACCCGGTCCCGCCGTTGAAACTGGCGAACTCGAGAGGGAGAGAAGTAGGCGGAATGCGCAGTGTAGCGGTGAAATGCATAGATATTGCGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCTCCTGTCTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG 4

diff -r 000000000000 -r d26cea4b4cc4 test-data/removeBimeraDenovo_F3D0_derep_uniques.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/removeBimeraDenovo_F3D0_derep_uniques.tab Fri Nov 08 18:50:51 2019 -0500

b'@@ -0,0 +1,2304 @@\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t451\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t373\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t347\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAG\t327\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\t273\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t215\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t169\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACA\t127\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACA\t115\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAG\t113\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAATGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t80\n+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\t78\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGGATGCCAAGTCAGCGGTCAAATTTCGGGGCTCAACCCCGACCTGCCGTTGAAACTGGTGTCCTAGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\t71\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\t68\n+TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAG\t59\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGCAAGTCTGAAGTGAAAGGCGGGGGCTCAACCCCCGGACTGCTTTGGAAACTGTATGACTGGAGTGCAGG'..b'CGAGGCTCAACCACGGGAGTGCATTGGAAACTGGCGAGCTGGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGCAACTGACGCTGAGGCTCGCAAGCGTGGGGAGCCACCA\t1\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGTGGCAGGGCAAGTCAGATGTGAAAACCCGGGGCTCAACTCCGGGATTGCATTTGAAACTGTCCGGCTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACA\t1\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCCTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCGGGTACTGCTTTTGAAACTGTAGGGCTTGAGGGAAGTAGAGGCAGCCGGAATTCCCGGGGTAGCGGGGAAATGCGAGGGGTTCGGGAGGACCACCAGTGGCGAAGGGGGCCTGCGGGGCGTTAACTGAGGCTGAGGAACGAAAGCGTGGGGAGCAAAAG\t1\n+TACGTATGGTGCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t1\n+TAGGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t1\n+TAGGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACA\t1\n+TATGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t1\n+TATGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAATGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t1\n+TATGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAG\t1\n+TATGTATGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCAGGGCAAGCCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGGAACTGCCCCGCTCGAGTGCCGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGTACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAA\t1\n+TCCCGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t1\n+TCCGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGGGTGGGTATCGAACAG\t1\n+TCCTTCGCCCGCACGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t1\n+TGCGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGGATGCCAAGTCAGCGGTCAAATTTCGGGGCTCAACCCCGACCTGCCGTTGAAACTGGGGTCCTAGAGTGGGCGAGAAGGATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTCATGCACGAAAGCGGGGGTATCGAACAG\t1\n+TGCGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t1\n+TTCGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTATGTAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGGACTGCTTTGGAAACTGTGTAACTGGAGTACAGGAGGGGCAGGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGCGGCGAAGGCGGCCTGCTGGACTGAAACTGACGTTGAGGCTCGAAAGCGTGGGGGGCAACCG\t1\n'

diff -r 000000000000 -r d26cea4b4cc4 test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata

Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed

diff -r 000000000000 -r d26cea4b4cc4 test-data/seqCounts_F3D0_dadaF.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_F3D0_dadaF.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,2 @@
+samples dadaF
+dada_F3D0_R1.Rdata 189

diff -r 000000000000 -r d26cea4b4cc4 test-data/seqCounts_F3D0_filter.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_F3D0_filter.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,2 @@
+samples filter reads.in filter reads.out
+filterAndTrim_F3D0.tab 250 249

diff -r 000000000000 -r d26cea4b4cc4 test-data/seqCounts_F3D0_merge.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_F3D0_merge.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,2 @@
+samples merge
+mergePairs_F3D0.Rdata 66

diff -r 000000000000 -r d26cea4b4cc4 test-data/seqCounts_F3D0_nochim.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_F3D0_nochim.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,2 @@
+samples nochim
+V1 66

diff -r 000000000000 -r d26cea4b4cc4 test-data/seqCounts_F3D0_seqtab.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_F3D0_seqtab.tab Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,2 @@
+samples seqtab
+V1 66

diff -r 000000000000 -r d26cea4b4cc4 tool-data/dada2_species.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dada2_species.loc.sample Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,9 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of dada2 reference data sets for species assignment, using three
+# tab separated columns:
+#
+# <unique_build_id> <display_name> <fasta_file_path>
+#
+# Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html
+#
+# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html

diff -r 000000000000 -r d26cea4b4cc4 tool-data/dada2_taxonomy.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dada2_taxonomy.loc.sample Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,9 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of dada2 reference data sets for taxonomy assignment, using three
+# tab separated columns:
+#
+# <unique_build_id> <display_name> <fasta_file_path> <taxlevels>
+#
+# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
+#
+# taxlevels is a comma separated list of taxonomy levels

diff -r 000000000000 -r d26cea4b4cc4 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="dada2_species" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/dada2_species.loc" />
+    </table>
+    <table name="dada2_taxonomy" comment_char="#">
+        <columns>value, name, path, taxlevels</columns>
+        <file path="tool-data/dada2_taxonomy.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r d26cea4b4cc4 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Nov 08 18:50:51 2019 -0500

@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="dada2_species" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/dada2_species.loc" />
+    </table>
+    <table name="dada2_taxonomy" comment_char="#">
+        <columns>value, name, path, taxlevels</columns>
+        <file path="${__HERE__}/test-data/dada2_taxonomy.loc" />
+    </table>
+</tables>