Galaxy |

Changeset 0:ce4aec98949d (2019-11-08)

Next changeset 1:6b4ddc3b64bd (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_dada.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 ce4aec98949d README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Nov 08 18:48:34 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 ce4aec98949d dada2_dada.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dada2_dada.xml Fri Nov 08 18:48:34 2019 -0500

[

b'@@ -0,0 +1,166 @@\n+<tool id="dada2_dada" name="dada2: dada" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">\n+ <description>Remove sequencing errors</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ <expand macro="version_command"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $batch_cond.batch_select == "no"\n+ mkdir output &&\n+ #end if\n+ Rscript \'$dada2_script\' \\${GALAXY_SLOTS:-1}\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="dada2_script"><![CDATA[\n+library(ggplot2, quietly=T)\n+library(dada2, quietly=T)\n+\n+args <- commandArgs(trailingOnly = TRUE)\n+nthreads <- as.integer(args[1])\n+\n+derep <- c()\n+#if $batch_cond.batch_select == "no"\n+#for $d in $batch_cond.derep:\n+derep <- c(derep, \'$d\')\n+#end for\n+#else\n+derep <- c(derep, \'$batch_cond.derep\')\n+#end if\n+\n+err <- readRDS(\'$err\')\n+\n+#if $batch_cond.batch_select == "yes":\n+pool <- F\n+#else\n+ #if $batch_cond.pool == "TRUE"\n+pool <- T\n+ #else if $batch_cond.pool == "FALSE"\n+pool <- F\n+ #else\n+pool <- \'pseudo\'\n+ #end if\n+#end if\n+\n+## the Galaxy wrapper does not implement the arguments\n+## - errorEstimationFunction = $errfoo, \n+## - selfConsist = $selfconsist\n+## since they are probably not relevant for the end user\n+dada_result <- dada(derep, err,\n+ pool = pool, multithread = nthreads)\n+\n+#if $batch_cond.batch_select == "no":\n+ #if len($batch_cond.derep) > 1:\n+ for( id in names(dada_result) ){\n+ saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep=".")))\n+ }\n+ #else\n+ #for $d in $batch_cond.derep:\n+ saveRDS(dada_result, file=file.path("output" ,paste(\'$d.element_identifier\', "dada2_dada", sep=".")))\n+ #end for\n+ #end if\n+#else\n+ saveRDS(dada_result, file=\'$dada\')\n+#end if\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="batch_cond">\n+ <param name="batch_select" type="select" label="Process samples in batches" help="process samples jointly (default) or in independent jobs (see also below)">\n+ <option value="no">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="yes">\n+ <param argument="derep" type="data" format="fastq,fastq.gz" label="Reads" help="despite the parameter name the sequences don\'t need to be dereplicated "/>\n+ </when>\n+ <when value="no">\n+ <param argument="derep" type="data" multiple="true" format="fastq,fastq.gz" label="Reads" help="despite the parameter name the sequences don\'t need to be dereplicated "/>\n+ <param argument="pool" type="select" label="Pool samples">\n+ <option value="FALSE">process samples individually</option>\n+ <option value="TRUE">pool samples</option>\n+ <option value="pseudo">pseudo pooling between individually processed samples</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ <param argument="err" type="data" format="dada2_errorrates" label="Error rates"/>\n+ \n+ </inputs>\n+ <outputs>\n+ <data name="dada" format="dada2_dada">\n+ <filter>batch_cond[\'batch_select\']=="yes"</filter>\n+ </data>\n+ <collection name="data_collection" type="list">\n+ <discover_datasets pattern="(?P<name>.+)\\.dada2_dada" format="dada2_dada" directory="output" />\n+ <filter>batch_cond[\'batch_select\']=="no"</filter>\n+ </collection>\n+ </outputs>\n+ <tests>\n+ \n+ <'..b'/>\n+ </output_collection>\n+ </test>\n+ \n+ <test>\n+ <param name="batch_cond|batch_select" value="yes"/>\n+ <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />\n+ <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" />\n+ <output name="dada" value="dada_F3D0_R1.Rdata" ftype="dada2_dada" />\n+ </test>\n+ \n+ <test>\n+ <param name="batch_cond|batch_select" value="no"/>\n+ <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />\n+ <param name="batch_cond|pool" value="pseudo"/>\n+ <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" />\n+ <output_collection name="data_collection" type="list">\n+ <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Description\n+...........\n+\n+The dada function takes as input amplicon sequencing reads and returns the inferred\n+composition of the sample (or samples). Put another way, dada removes all sequencing errors to\n+reveal the members of the sequenced community.\n+\n+Usage\n+.....\n+\n+**Input:**\n+\n+- A number of fastq(.gz) files (given as collection or multiple data sets)\n+- An dada2_errorrates data set computed with learnErrors\n+\n+You can decide to compute the data jointly or in batches.\n+\n+- Jointly (Process "samples in batches"=no): A single Galaxy job is started that processes all fastq data sets jointly. You may chose different pooling strategies: if the started dada job processes the samples individually, pooled, or pseudo pooled.\n+- In batches (Process "samples in batches"=yes): A separate Galaxy job is started for earch fastq data set. This is equivalent to joint processing and choosing to process samples individually.\n+\n+While the single dada job (in case of joint processing) can use multiple cores on one compute node, batched processing distributes the work on a number of jobs (equal to the number of input fastq data sets) where each can use multiple cores. Hence, if you intend to or need to process the data sets individually, batched processing is more efficient -- in particular if Galaxy has access to a larger number of compute resources.\n+\n+A typical use case of individual processing of the samples are large data sets for which the pooled strategy needs to much time or memory. Pseudo-pooling is recommended for those interested in detecting singleton ASVs in their samples\n+\n+\n+**Output**: a data set of type dada2_dada (which is a RData file containing the output of dada2\'s dada function).\n+\n+The output of this tool can serve as input for *dada2: mergePairs*, *dada2: removeBimeraDinovo*, and "dada2: makeSequenceTable"\n+\n+Details\n+.......\n+\n+Briefly, dada implements a statistical test for the notion that a specific sequence was seen too many times to have been caused by amplicon errors from currently inferred sample sequences. Overly abundant sequences are used as the seeds of new partitions of sequencing reads, and the final set of partitions is taken to represent the denoised composition of the sample. A more detailed explanation of the algorithm is found in the dada2 puplication (see below) and https://doi.org/10.1186/1471-2105-13-283. dada depends on a parametric error model of substitutions. Thus the quality of its sample inference is affected by the accuracy of the estimated error rates. All comparisons between sequences performed by dada depend on pairwise alignments. This step is the most computationally intensive part of the algorithm, and two alignment heuristics have been implemented in dada for speed: A kmer-distance screen and banded Needleman-Wunsch alignmemt.\n+\n+@HELP_OVERVIEW@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n'

diff -r 000000000000 -r ce4aec98949d macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Nov 08 18:48:34 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 ce4aec98949d static/images/pairpipe.png

Binary file static/images/pairpipe.png has changed

diff -r 000000000000 -r ce4aec98949d static/images/pairpipe.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/pairpipe.svg Fri Nov 08 18:48:34 2019 -0500

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diff -r 000000000000 -r ce4aec98949d test-data/assignTaxonomyAddspecies_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assignTaxonomyAddspecies_F3D0.tab Fri Nov 08 18:48:34 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 ce4aec98949d 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 18:48:34 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 ce4aec98949d test-data/dada2_species.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_species.loc Fri Nov 08 18:48:34 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 ce4aec98949d test-data/dada2_taxonomy.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_taxonomy.loc Fri Nov 08 18:48:34 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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diff -r 000000000000 -r ce4aec98949d test-data/filterAndTrim_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filterAndTrim_F3D0.tab Fri Nov 08 18:48:34 2019 -0500

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+ reads.in reads.out
+Unnamed Collection 250 249

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diff -r 000000000000 -r ce4aec98949d test-data/filterAndTrim_single_filters_F3D0_R1.fq.gz

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diff -r 000000000000 -r ce4aec98949d test-data/gentest.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.R Fri Nov 08 18:48:34 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 ce4aec98949d test-data/gentest.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.sh Fri Nov 08 18:48:34 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

diff -r 000000000000 -r ce4aec98949d test-data/learnErrors_F3D0_R1.Rdata

Binary file test-data/learnErrors_F3D0_R1.Rdata has changed

diff -r 000000000000 -r ce4aec98949d test-data/learnErrors_F3D0_R1.pdf

Binary file test-data/learnErrors_F3D0_R1.pdf has changed

diff -r 000000000000 -r ce4aec98949d test-data/learnErrors_F3D0_R2.Rdata

Binary file test-data/learnErrors_F3D0_R2.Rdata has changed

diff -r 000000000000 -r ce4aec98949d test-data/learnErrors_F3D0_R2.pdf

Binary file test-data/learnErrors_F3D0_R2.pdf has changed

diff -r 000000000000 -r ce4aec98949d test-data/makeSequenceTable_F3D0.pdf

Binary file test-data/makeSequenceTable_F3D0.pdf has changed

diff -r 000000000000 -r ce4aec98949d test-data/makeSequenceTable_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeSequenceTable_F3D0.tab Fri Nov 08 18:48:34 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 ce4aec98949d test-data/mergePairs_F3D0.Rdata

Binary file test-data/mergePairs_F3D0.Rdata has changed

diff -r 000000000000 -r ce4aec98949d test-data/mergePairs_F3D0_nondefault.Rdata

Binary file test-data/mergePairs_F3D0_nondefault.Rdata has changed

diff -r 000000000000 -r ce4aec98949d test-data/qualityProfile.pdf

Binary file test-data/qualityProfile.pdf has changed

diff -r 000000000000 -r ce4aec98949d test-data/reference.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fa Fri Nov 08 18:48:34 2019 -0500

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

diff -r 000000000000 -r ce4aec98949d test-data/reference_species.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference_species.fa Fri Nov 08 18:48:34 2019 -0500

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

diff -r 000000000000 -r ce4aec98949d test-data/removeBimeraDenovo_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/removeBimeraDenovo_F3D0.tab Fri Nov 08 18:48:34 2019 -0500

diff -r 000000000000 -r ce4aec98949d 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 18:48:34 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 ce4aec98949d 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 18:48:34 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 ce4aec98949d test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata

Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed

diff -r 000000000000 -r ce4aec98949d 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 18:48:34 2019 -0500

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

diff -r 000000000000 -r ce4aec98949d 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 18:48:34 2019 -0500

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

diff -r 000000000000 -r ce4aec98949d 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 18:48:34 2019 -0500

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

diff -r 000000000000 -r ce4aec98949d 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 18:48:34 2019 -0500

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

diff -r 000000000000 -r ce4aec98949d 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 18:48:34 2019 -0500

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

diff -r 000000000000 -r ce4aec98949d 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 18:48:34 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 ce4aec98949d 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 18:48:34 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 ce4aec98949d 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 18:48:34 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 ce4aec98949d 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 18:48:34 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>