Repository 'dada2_removebimeradenovo'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo

Changeset 0:1937c2b4da7a (2019-11-08)
Next changeset 1:7f8f0e9fcb37 (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_removeBimeraDenovo.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
b
diff -r 000000000000 -r 1937c2b4da7a README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Nov 08 18:49:03 2019 -0500
b
@@ -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 
b
diff -r 000000000000 -r 1937c2b4da7a dada2_removeBimeraDenovo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dada2_removeBimeraDenovo.xml Fri Nov 08 18:49:03 2019 -0500
[
@@ -0,0 +1,115 @@
+<tool id="dada2_removeBimeraDenovo" name="dada2: removeBimeraDenovo" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
+    <description>Remove bimeras from collections of unique sequences</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[
+library(dada2, quietly=T)
+@READ_FOO@
+@WRITE_FOO@
+
+unqs <- $read_data($unqs)
+
+seqtab.nochim <- removeBimeraDenovo(unqs, method = "$method")
+
+## - output is data.frame (mergepairs) or sequencetable (if this was the input)
+##   in the former case the (multi item) list is stored as RDS
+##   in the latter case the named int matrix is stored as tabular (rows=samples, columns=ASVs)
+## - otherwise uniques-vector, i.e. a named integer vector
+
+#if $unqs.is_of_type('dada2_dada')
+    write.data( seqtab.nochim, '$stable_uniques', "dada2_uniques" )
+#else if $unqs.is_of_type('dada2_sequencetable')
+    write.data( seqtab.nochim, '$stable_sequencetable', "dada2_sequencetable" )
+#else if $unqs.is_of_type('dada2_mergepairs')
+    write.data( seqtab.nochim, '$stable_mergepairs', "dada2_mergepairs" )
+#end if
+
+## dada input
+if(class(unqs)=="list"){
+    unqssum<-lapply(lapply(unqs, getUniques),sum)
+    outsum<-lapply(seqtab.nochim,sum)
+    mapply(function(X,Y) { 100*X/Y }, X=nonchimsum, Y=unqssum)
+    cat("remaining nonchimeric: ", mapply(function(X,Y) { 100*X/Y }, X=nonchimsum, Y=unqssum), "%")
+}else{
+    cat("remaining nonchimeric: ", 100*sum(getUniques(seqtab.nochim))/sum(getUniques(unqs)), "%")
+}
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="unqs" type="data" format="@DADA_UNIQUES@,dada2_sequencetable" label="sequence table" help=""/>
+        <param argument="method" type="select" label="Method">
+            <option value="consensus">check samples independently for bimeras and make a consensus decision on each sequence variant</option>
+            <option value="pooled">pool samples for bimera identification</option>
+            <option value="per-sample">check samples independently for bimeras and remove (0-out) sequence variants from samples independently</option>
+        </param>
+   </inputs>
+   <outputs>
+        <!-- fix output filters in a later release https://github.com/galaxyproject/galaxy/issues/7464 -->
+        <data name="stable_uniques" format="dada2_uniques" label="${tool.name} on ${on_string}" from_work_dir="nonchim.uniques">
+            <filter>unqs.ext == "dada2_dada"</filter>
+        </data>
+        <data name="stable_mergepairs" format="dada2_mergepairs" label="${tool.name} on ${on_string}" from_work_dir="nonchim.mergepairs">
+            <filter>unqs.ext == "dada2_mergepairs"</filter>
+        </data>
+        <data name="stable_sequencetable" format="dada2_sequencetable" label="${tool.name} on ${on_string}" from_work_dir="nonchim.mergepairs">
+            <filter>unqs.ext == "dada2_sequencetable"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="unqs" ftype="dada2_sequencetable" value="makeSequenceTable_F3D0.tab"/>
+            <output name="stable_sequencetable" value="removeBimeraDenovo_F3D0.tab" ftype="dada2_sequencetable" />
+        </test>
+        <!-- dada input -->
+        <test expect_num_outputs="1">
+            <param name="unqs" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/>
+            <output name="stable_uniques" value="removeBimeraDenovo_F3D0_dada_uniques.tab" ftype="dada2_uniques" />
+        </test>
+        <!-- mergepairs input + non default-->
+        <test expect_num_outputs="1">
+            <param name="unqs" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
+            <param name="method" value="pooled"/>
+            <output name="stable_mergepairs" value="removeBimeraDenovo_F3D0_mergepairs.Rdata" ftype="dada2_mergepairs" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Description
+...........
+
+This tool can be used to remove chimeric sequences, i.e. sequences that can be constructed by combining a left-segment and a right-segment from two more abundant “parent” sequences.. Two methods to identify chimeras are supported: Identification from pooled sequences and identification by consensus across samples.
+
+- from **pooled** sequences: Each sequence is evaluated against a set of "parents" drawn from the sequence collection that are sufficiently more abundant than the sequence being evaluated. Sequences that are bimera are removed, i.e. a two-parent chimera, in which the left side is made up of one parent sequence, and the right-side made up of a second parent sequence.
+- by **consensus**: In short, bimeric sequences are flagged on a sample-by-sample basis. Then, a vote is performed for each sequence across all samples in which it appeared. If the sequence is flagged in a sufficiently high fraction of samples, it is identified as a bimera. A logical vector is returned, with an entry for each sequence in the table indicating whether it was identified as bimeric by this consensus procedure.
+
+Usage
+.....
+
+**Input**
+
+- the results of makeSequenceTable (note that also the results of dada, and mergePairs are accepted)
+
+**Output**
+
+A data set of type:
+- dada2_sequenceTable (resp. dada2_mergepairs) if the input is of type dada2_sequenceTable (resp. dada2_mergepairs)
+- dada2_uniques otherwise
+
+Details
+.......
+
+The frequency of chimeric sequences varies substantially from dataset to dataset, and depends on on factors including experimental procedures and sample complexity. Here chimeras make up about 21% of the merged sequence variants, but when we account for the abundances of those variants we see they account for only about 4% of the merged sequence reads.
+
+Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited. In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline.
+
+@HELP_OVERVIEW@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
b
diff -r 000000000000 -r 1937c2b4da7a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Nov 08 18:49:03 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" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+        ]]></version_command>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <regex match="Error: cannot allocate" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+            <regex match="'Calloc' could not allocate memory" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+        </stdio>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nmeth.3869</citation>
+            <yield/>
+        </citations>
+    </xml>
+
+    <token name="@DADA_UNIQUES@">dada2_dada,dada2_mergepairs</token>
+
+    <!-- function to read dada2 data types
+         - dada, and mergepairs are simply read as RDS
+         - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
+         - uniques is a named integer vector (columns=ASVs, only one rows)-->
+    <token name="@READ_FOO@"><![CDATA[
+    read.uniques <- function ( fname ) {
+         p <- read.table(fname, header=F, sep="\t")
+         n <-x[,2]
+         names(n)<-x[,1]
+    }
+    #def read_data($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>
+    <!-- function to write dada2 data types (the content or the R variable 'out' is written)
+         - dada, and mergepairs are written as RDS
+         - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
+         - uniques is a named integer vector (columns=ASVs, only one rows)-->
+    <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>
+
+    <!-- for filterAndTrim -->
+    <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>
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diff -r 000000000000 -r 1937c2b4da7a test-data/assignTaxonomyAddspecies_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assignTaxonomyAddspecies_F3D0.tab Fri Nov 08 18:49:03 2019 -0500
b
@@ -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
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diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -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 1937c2b4da7a test-data/dada2_species.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_species.loc Fri Nov 08 18:49:03 2019 -0500
b
@@ -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
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diff -r 000000000000 -r 1937c2b4da7a test-data/dada2_taxonomy.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_taxonomy.loc Fri Nov 08 18:49:03 2019 -0500
b
@@ -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 1937c2b4da7a test-data/filterAndTrim_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filterAndTrim_F3D0.tab Fri Nov 08 18:49:03 2019 -0500
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@@ -0,0 +1,2 @@
+ reads.in reads.out
+Unnamed Collection 250 249
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diff -r 000000000000 -r 1937c2b4da7a test-data/filterAndTrim_single_filters_F3D0_R1.fq.gz
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diff -r 000000000000 -r 1937c2b4da7a test-data/filterAndTrim_single_trimmers_F3D0_R1.fq.gz
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Binary file test-data/filterAndTrim_single_trimmers_F3D0_R1.fq.gz has changed
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diff -r 000000000000 -r 1937c2b4da7a test-data/gentest.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.R Fri Nov 08 18:49:03 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')
b
diff -r 000000000000 -r 1937c2b4da7a test-data/gentest.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.sh Fri Nov 08 18:49:03 2019 -0500
b
@@ -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
b
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diff -r 000000000000 -r 1937c2b4da7a test-data/makeSequenceTable_F3D0.pdf
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Binary file test-data/makeSequenceTable_F3D0.pdf has changed
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diff -r 000000000000 -r 1937c2b4da7a test-data/makeSequenceTable_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeSequenceTable_F3D0.tab Fri Nov 08 18:49:03 2019 -0500
b
@@ -0,0 +1,8 @@
+ V1
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 22
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 18
+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 11
+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 5
+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 5
+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 3
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 2
b
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Binary file test-data/qualityProfile.pdf has changed
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diff -r 000000000000 -r 1937c2b4da7a test-data/reference.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fa Fri Nov 08 18:49:03 2019 -0500
b
@@ -0,0 +1,4 @@
+>A;B;C;D;E;
+ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
+>A;B;C;F;G;
+CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC
b
diff -r 000000000000 -r 1937c2b4da7a test-data/reference_species.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference_species.fa Fri Nov 08 18:49:03 2019 -0500
b
@@ -0,0 +1,4 @@
+>IDA GenusA speciesA
+ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
+>IDB GenusB speciesB
+CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC
b
diff -r 000000000000 -r 1937c2b4da7a test-data/removeBimeraDenovo_F3D0.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/removeBimeraDenovo_F3D0.tab Fri Nov 08 18:49:03 2019 -0500
b
@@ -0,0 +1,8 @@
+ V1
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 22
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 18
+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 11
+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 5
+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 5
+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 3
+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 2
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -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
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
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'
b
diff -r 000000000000 -r 1937c2b4da7a test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata
b
Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -0,0 +1,2 @@
+samples dadaF
+dada_F3D0_R1.Rdata 189
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -0,0 +1,2 @@
+samples filter reads.in filter reads.out
+filterAndTrim_F3D0.tab 250 249
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -0,0 +1,2 @@
+samples merge
+mergePairs_F3D0.Rdata 66
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -0,0 +1,2 @@
+samples nochim
+V1 66
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -0,0 +1,2 @@
+samples seqtab
+V1 66
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -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
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -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
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -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>
b
diff -r 000000000000 -r 1937c2b4da7a 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 18:49:03 2019 -0500
b
@@ -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>