| Next changeset 1:4d89978c6188 (2019-12-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" |
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README.md dada2_assignTaxonomyAddspecies.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 |
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| diff -r 000000000000 -r 18517edb4733 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Nov 08 18:50:24 2019 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 18517edb4733 dada2_assignTaxonomyAddspecies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dada2_assignTaxonomyAddspecies.xml Fri Nov 08 18:50:24 2019 -0500 |
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| b'@@ -0,0 +1,232 @@\n+<tool id="dada2_assignTaxonomyAddspecies" name="dada2: assignTaxonomy and addSpecies" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">\n+ <description>Learn Error rates</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+ Rscript \'$dada2_script\' \\${GALAXY_SLOTS:-1}\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="dada2_script"><![CDATA[\n+@READ_FOO@\n+\n+library(dada2, quietly=T)\n+\n+args <- commandArgs(trailingOnly = TRUE)\n+nthreads <- as.integer(args[1])\n+\n+seqs <- $read_data($seqs)\n+\n+#if $reference_cond.reference_select == "history"\n+ref <- \'$reference_cond.refFasta\'\n+tl <- \'$reference_cond.taxLevels\'\n+#else\n+ref <- \'$reference_cond.refFasta.fields.path\'\n+tl <- \'$reference_cond.refFasta.fields.taxlevels\'\n+#end if\n+tl <- strsplit(tl, ",")[[1]]\n+\n+taxa <- assignTaxonomy(seqs, ref, minBoot = $minBoot, tryRC = $tryRC,\n+ outputBootstraps = $outputBootstraps,\n+ taxLevels = tl, multithread = nthreads, verbose=T)\n+\n+#if $outputBootstraps\n+ boot <- taxa\\$boot\n+ taxa <- taxa\\$tax\n+#end if\n+\n+#if $addSpecies_cond.addSpecies_select == "TRUE"\n+ #if $addSpecies_cond.allowMultiple_cond.allowMultiple == "num"\n+ aM <- $addSpecies_cond.allowMultiple_cond.num\n+ #else\n+ aM <- $addSpecies_cond.allowMultiple_cond.allowMultiple\n+ #end if\n+ #if $addSpecies_cond.speciesreference_cond.speciesreference_select == "history"\n+ ref <- \'$addSpecies_cond.speciesreference_cond.speciesrefFasta\'\n+ #else\n+ ref <- \'$addSpecies_cond.speciesreference_cond.speciesrefFasta.fields.path\'\n+ #end if\n+ taxa <- addSpecies(taxa, ref, allowMultiple = aM, tryRC = $addSpecies_cond.tryRC)\n+#end if\n+write.table(taxa, file = \'$output\', quote = F, sep = "\\t", row.names = T, col.names = NA)\n+\n+#if $outputBootstraps\n+ write.table(boot, file = \'$bootstraps\', quote = F, sep = "\\t", row.names = T, col.names = NA)\n+#end if\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="seqs" type="data" format="@DADA_UNIQUES@,dada2_sequencetable,dada2_uniques" label="sequences to be assigned" help=""/>\n+ <conditional name="reference_cond">\n+ <param name="reference_select" type="select" label="Select a reference dataset your history or use a built-in?">\n+ <option value="builtin">Use a built-in reference</option>\n+ <option value="history">Use reference data from the history</option>\n+ </param>\n+ <when value="builtin">\n+ <param name="refFasta" type="select" label="Select reference data set" help="If a reference data set of interest is not listed, contact the Galaxy administrators">\n+ <options from_data_table="dada2_taxonomy">\n+ <filter type="sort_by" column="2"/>\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="refFasta" type="data" format="fasta,fasta.gz" label="Reference data set" />\n+ <param argument="taxLevels" type="text" label="Names of the taxonomic levels in the data set" help="comma separated list" />\n+ </when>\n+ </conditional>\n+ <param argument="minBoot" type="integer" value="50" min="0" label="Minimum bootstrap confidence" help="for assigning a\n+taxonomic level"/>\n+ <param argument="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/>\n+ <param argument="outputBootstraps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Out'..b'ies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />\n+ <param name="addSpecies_cond|allowMultiple" value="TRUE"/>\n+ <param name="addSpecies_cond|tryRC" value="TRUE" />\n+ <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" compare="sim_size" />\n+ <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" compare="sim_size" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Description\n+...........\n+\n+This tool implements dada2\'s assignTaxonomy and assignSpecies functions.\n+\n+- assignTaxonomy assigns taxonomy to the sequence variants. The DADA2 package provides a native implementation of the naive Bayesian classifier method for this purpose (see Wang et al. 2007, kmer size 8 and 100 bootstrap replicates). The assignTaxonomy function takes as input a set of sequences to be classified and a training set of reference sequences with known taxonomy, and outputs taxonomic assignments with at least minBoot bootstrap confidence. Properly formatted reference files for several popular taxonomic databases are available http://benjjneb.github.io/dada2/training.html\n+- assignSpecies makes species level assignments based on exact matching between ASVs and sequenced reference strains. Recent analysis suggests that exact matching (or 100% identity) is the only appropriate way to assign species to 16S gene fragments. Currently, species-assignment training fastas are available for the Silva and RDP 16S databases.\n+\n+Usage\n+.....\n+\n+**Input**\n+\n+- A list of sequences contained in the results of removeBimeraDenovo or sequenceTable (note that also the results of dada, and mergePairs are accepted).\n+- Reference data bases for taxonomic and species/genus level assignment. Several cached data bases can be chosen (ask your Galaxy admin if they are missing). For using custom data bases see below.\n+\n+**Output**\n+\n+- A table containing the assigned taxonomies exceeding the minBoot level of bootstrapping confidence. Rows correspond to the provided sequences, columns to the taxonomic levels. NA indicates that the sequence was not consistently classified at that level at the minBoot threshold.\n+- Optionally two columns for the genus and species taxonomic levels can be added. NA indicates that the sequence was not classified at that level.\n+- If outputBootstraps checked, a table containing the assigned taxonomies (named "taxa") and the bootstrap values (named "boot") will be returned.\n+\n+@HELP_OVERVIEW@\n+\n+Custom Reference data sets\n+..........................\n+\n+For ** taxonomy assignment ** the following is needed:\n+\n+- a reference fasta data base\n+- a comma separated list of taxonomic ranks present in the reference data base\n+\n+The reference fasta data base for taxonomic assignment (fasta or compressed fasta) needs to encode the taxonomy corresponding to each sequence in the fasta header lines in the following fashion (note, the second sequence is not assigned down to level 6):\n+\n+::\n+\n+ >Level1;Level2;Level3;Level4;Level5;Level6;\n+ ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC\n+ >Level1;Level2;Level3;Level4;Level5;\n+ CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC\n+\n+The list of required taxonomic ranks could be for instance: "Kingdom,Phylum,Class,Order,Family,Genus"\n+\n+The reference data base for ** species assignment ** is a fasta file (or compressed fasta file), with the id line formatted as follows:\n+\n+::\n+\n+ >ID Genus species\n+ ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC\n+ >ID Genus species\n+ CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC\n+\n+\n+ ]]></help>\n+ <expand macro="citations">\n+ <citation type="doi">10.1128/AEM.00062-07</citation>\n+ </expand>\n+</tool>\n+\n+\n' |
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| diff -r 000000000000 -r 18517edb4733 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Nov 08 18:50:24 2019 -0500 |
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| @@ -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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| @@ -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 |
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| @@ -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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| @@ -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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| @@ -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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| @@ -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') |
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| @@ -0,0 +1,8 @@ + +conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-dada2@1.12 bioconductor-dada2=1.12 +conda activate bioconductor-dada2@1.12 + +Rscript gentest.R + +# remove files only needed for test generation +rm learnErrors_F3D0_R2.pdf dada_F3D0_R2.Rdata |
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| b |
| diff -r 000000000000 -r 18517edb4733 test-data/makeSequenceTable_F3D0.pdf |
| b |
| Binary file test-data/makeSequenceTable_F3D0.pdf has changed |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/makeSequenceTable_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/makeSequenceTable_F3D0.tab Fri Nov 08 18:50:24 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 18517edb4733 test-data/mergePairs_F3D0.Rdata |
| b |
| Binary file test-data/mergePairs_F3D0.Rdata has changed |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/mergePairs_F3D0_nondefault.Rdata |
| b |
| Binary file test-data/mergePairs_F3D0_nondefault.Rdata has changed |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/qualityProfile.pdf |
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| Binary file test-data/qualityProfile.pdf has changed |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Fri Nov 08 18:50:24 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>A;B;C;D;E; +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>A;B;C;F;G; +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/reference_species.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_species.fa Fri Nov 08 18:50:24 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>IDA GenusA speciesA +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>IDB GenusB speciesB +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/removeBimeraDenovo_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0.tab Fri Nov 08 18:50:24 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 18517edb4733 test-data/removeBimeraDenovo_F3D0_dada_uniques.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0_dada_uniques.tab Fri Nov 08 18:50:24 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 18517edb4733 test-data/removeBimeraDenovo_F3D0_derep_uniques.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0_derep_uniques.tab Fri Nov 08 18:50:24 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 18517edb4733 test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata |
| b |
| Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/seqCounts_F3D0_dadaF.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_dadaF.tab Fri Nov 08 18:50:24 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples dadaF +dada_F3D0_R1.Rdata 189 |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/seqCounts_F3D0_filter.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_filter.tab Fri Nov 08 18:50:24 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples filter reads.in filter reads.out +filterAndTrim_F3D0.tab 250 249 |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/seqCounts_F3D0_merge.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_merge.tab Fri Nov 08 18:50:24 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples merge +mergePairs_F3D0.Rdata 66 |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/seqCounts_F3D0_nochim.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_nochim.tab Fri Nov 08 18:50:24 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples nochim +V1 66 |
| b |
| diff -r 000000000000 -r 18517edb4733 test-data/seqCounts_F3D0_seqtab.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_seqtab.tab Fri Nov 08 18:50:24 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples seqtab +V1 66 |
| b |
| diff -r 000000000000 -r 18517edb4733 tool-data/dada2_species.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dada2_species.loc.sample Fri Nov 08 18:50:24 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 18517edb4733 tool-data/dada2_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dada2_taxonomy.loc.sample Fri Nov 08 18:50:24 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 18517edb4733 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 08 18:50:24 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 18517edb4733 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Nov 08 18:50:24 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> |
