| Next changeset 1:777f9846c56d (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_filterAndTrim.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 cc41546adf56 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Nov 08 18:48:06 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 cc41546adf56 dada2_filterAndTrim.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dada2_filterAndTrim.xml Fri Nov 08 18:48:06 2019 -0500 |
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| b'@@ -0,0 +1,264 @@\n+<tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">\n+ <description>Filter and trim short read data</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 \'$dada2_script\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="dada2_script"><![CDATA[\n+truncQ <- c($trim.truncQ)\n+truncLen <- c($trim.truncLen)\n+trimLeft <- c($trim.trimLeft)\n+trimRight <- c($trim.trimRight)\n+#if str($filter.maxLen) == ""\n+ maxLen <- c(Inf)\n+#else:\n+ maxLen <- c($filter.maxLen)\n+#end if\n+minLen <- c($filter.minLen)\n+maxN <- c($filter.maxN)\n+minQ <- c($filter.minQ)\n+#if str($filter.maxEE) == ""\n+ maxEE <- c(Inf)\n+#else:\n+ maxEE <- c($filter.maxEE)\n+#end if\n+#if $paired_cond.paired_select != "single" and $seprev_cond.seprev_select == "yes"\n+ truncQ <- c(truncQ,$seprev_cond.trim.truncQ)\n+ truncLen <- c(truncLen,$seprev_cond.trim.truncLen)\n+ trimLeft <- c(trimLeft,$seprev_cond.trim.trimLeft)\n+ trimRight <- c(trimRight,$seprev_cond.trim.trimRight)\n+ #if str($seprev_cond.filter.maxLen) == ""\n+ maxLen <- c(maxLen,Inf)\n+ #else:\n+ maxLen <- c(maxLen,$seprev_cond.filter.maxLen)\n+ #end if\n+ minLen <- c(minLen,$seprev_cond.filter.minLen)\n+ maxN <- c(maxN,$seprev_cond.filter.maxN)\n+ minQ <- c(minQ,$seprev_cond.filter.minQ)\n+ #if str($seprev_cond.filter.maxEE) == ""\n+ maxEE <- c(maxEE,Inf)\n+ #else:\n+ maxEE <- c(maxEE,$seprev_cond.filter.maxEE)\n+ #end if\n+#end if\n+\n+fwd <- NULL\n+rev <- NULL\n+filt.fwd <- NULL\n+filt.rev <- NULL\n+#if $paired_cond.paired_select == "paired"\n+ fwd <- c(fwd, \'$paired_cond.reads.forward\')\n+ rev <- c(rev, \'$paired_cond.reads.reverse\')\n+ filt.fwd <- c(filt.fwd, \'$paired_output.forward\')\n+ filt.rev <- c(filt.rev, \'$paired_output.reverse\')\n+#else if $paired_cond.paired_select == "separate"\n+ fwd <- c(fwd, \'$paired_cond.reads\')\n+ rev <- c(rev, \'$paired_cond.sdaer\')\n+ filt.fwd <- c(filt.fwd, \'$output_fwd\')\n+ filt.rev <- c(filt.rev, \'$output_rev\')\n+#else\n+ fwd <- c(fwd, \'$paired_cond.reads\')\n+ filt.fwd <- c(filt.fwd, \'$output_single\')\n+#end if\n+\n+#if str($orientFwd) == ""\n+ orientFwd <- NULL\n+#else\n+ orientFwd <- "$orientFwd"\n+#end if\n+\n+library(dada2, quietly=T)\n+\n+ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev, compress = TRUE,\n+ truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen,\n+ minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.lowcomplex = $rmlowcomplex,\n+ rm.phix = $rmPhiX, orient.fwd = orientFwd)\n+\n+rownames(ftout) <- c( \'$paired_cond.reads.element_identifier\' )\n+write.table(ftout, "$outtab", quote=F, sep="\\t", col.names=NA)\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fwd" argument_rev="rev"/>\n+ <expand macro="trimmers"/>\n+ <expand macro="filters"/>\n+ <conditional name="seprev_cond">\n+ <param name="seprev_select" type="select" label="Separate filters and trimmers for reverse reads" help="only applies to paired end data">\n+ <option value="no">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no"/>\n+ <when value="yes">\n+ <expand macro="trimmers"/>\n+ <expand macro="filters"/>\n+ </when>\n+ </conditional>\n+ <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" />\n+ <param name="rmlowcomplex" argument="rm.lowcomplex" type="integer" value="0" min="0" label="Low complexity filter kmer threshold" help="see below'..b'\n+ <param name="seprev_cond|trim|truncQ" value="30" />\n+ <param name="seprev_cond|trim|trimLeft" value="150" />\n+ <param name="seprev_cond|trim|trimRight" value="2" />\n+ <param name="seprev_cond|trim|truncLen" value="2" />\n+ <param name="seprev_cond|filter|maxLen" value="255" />\n+ <param name="seprev_cond|filter|minLen" value="60" />\n+ <param name="seprev_cond|filter|maxN" value="100" />\n+ <param name="seprev_cond|filter|minQ" value="13" />\n+ <param name="seprev_cond|filter|maxEE" value="1" />\n+ <param name="output_statistics" value="FALSE" />\n+ <output_collection name="paired_output" type="paired" count="2"/>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+Description\n+...........\n+\n+Filters and trims a FASTQ dataset (can be compressed) based on several user-definable criteria, and outputs a compressed FASTQ data set containing those trimmed reads which passed the filters. For paired end data forward and reverse FASTQ datasets can be provided as pair of FASTQ datasets (or two separate data sets), in which case filtering is performed on the forward and reverse reads independently, and both reads must pass for the read pair to be in the output.\n+\n+Usage\n+.....\n+\n+**Input** is a FASTQ dataset (or a pair in case of paired end data) containing all reads of a sample. It is suggested to organize them in a (paired) collection (in particular if you have multiple samples).\n+\n+**Output** is a (paired) collection of filtered and trimmed paired FASTQ datasets (again one data set or pair per sample).\n+\n+Upstream dada2 tools are *dada2: learnErrorRates* and *dada2: dada*. Note that these tools do not work on paired end data. So, if you have paired end data you need to split the generated paired collection into one containing the forward reads and one containing the reverse reads. This can be done by the *unzip collection* tool.\n+\n+An additional tabular output gives the number of reads before and after trimming. This can data set can be used as input for *dada2: sequence counts* to track the sequence counts for each sample through all dada2 pipeline step.\n+\n+Details\n+.......\n+\n+*Trimming and filtering*:\n+\n+- Truncation of the read length is enforced after trimming of the right end.\n+- The long read filter is applied before trimming and the short read filter after trimming.\n+- For details on the calculation of the number of expected errors see also https://doi.org/10.1093/bioinformatics/btv401\n+\n+\n+*String present at the start of valid reads* (orient.fwd):\n+\n+This string is compared to the start of each read, and the reverse complement of each read. If it exactly matches the start of the read, the read is kept. If it exactly matches the start of the reverse complement read, the read is reverse-complemented and kept. Otherwise the read if filtered out. For paired reads, the string is compared to the start of the forward and reverse reads, and if it matches the start of the reverse read the reads are swapped and kept. The primary use of this parameter is to unify the orientation of amplicon sequencing libraries that are a mixture of forward and reverse orientations, and that include the forward primer on the reads.\n+\n+*Low complexity filter kmer threshold"*\n+\n+If greater than 0, reads with an effective number of kmers less than this value will be removed. The effective number of kmers is determined as a Shannon information approximation. The default kmer-size is 2, and therefore perfectly random sequences will approachan effective kmer number of 16 = 4 (nucleotides) ^ 2 (kmer size).\n+\n+Notes\n+.....\n+\n+This step may be replaced by alternative tools to filter and trim short read data if the following is ensured:\n+\n+- For paired end data unpaired reads must be removed.\n+- There must not be a read containing a non-canonical nucleotide (N).\n+\n+@HELP_OVERVIEW@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r cc41546adf56 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Nov 08 18:48:06 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 cc41546adf56 test-data/makeSequenceTable_F3D0.pdf |
| b |
| Binary file test-data/makeSequenceTable_F3D0.pdf has changed |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/makeSequenceTable_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/makeSequenceTable_F3D0.tab Fri Nov 08 18:48:06 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 cc41546adf56 test-data/mergePairs_F3D0.Rdata |
| b |
| Binary file test-data/mergePairs_F3D0.Rdata has changed |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/mergePairs_F3D0_nondefault.Rdata |
| b |
| Binary file test-data/mergePairs_F3D0_nondefault.Rdata has changed |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/qualityProfile.pdf |
| b |
| Binary file test-data/qualityProfile.pdf has changed |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Fri Nov 08 18:48:06 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>A;B;C;D;E; +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>A;B;C;F;G; +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/reference_species.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_species.fa Fri Nov 08 18:48:06 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>IDA GenusA speciesA +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>IDB GenusB speciesB +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/removeBimeraDenovo_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0.tab Fri Nov 08 18:48:06 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 cc41546adf56 test-data/removeBimeraDenovo_F3D0_dada_uniques.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0_dada_uniques.tab Fri Nov 08 18:48:06 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 cc41546adf56 test-data/removeBimeraDenovo_F3D0_derep_uniques.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0_derep_uniques.tab Fri Nov 08 18:48:06 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 cc41546adf56 test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata |
| b |
| Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/seqCounts_F3D0_dadaF.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_dadaF.tab Fri Nov 08 18:48:06 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples dadaF +dada_F3D0_R1.Rdata 189 |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/seqCounts_F3D0_filter.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_filter.tab Fri Nov 08 18:48:06 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples filter reads.in filter reads.out +filterAndTrim_F3D0.tab 250 249 |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/seqCounts_F3D0_merge.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_merge.tab Fri Nov 08 18:48:06 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples merge +mergePairs_F3D0.Rdata 66 |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/seqCounts_F3D0_nochim.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_nochim.tab Fri Nov 08 18:48:06 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples nochim +V1 66 |
| b |
| diff -r 000000000000 -r cc41546adf56 test-data/seqCounts_F3D0_seqtab.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_seqtab.tab Fri Nov 08 18:48:06 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples seqtab +V1 66 |
| b |
| diff -r 000000000000 -r cc41546adf56 tool-data/dada2_species.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dada2_species.loc.sample Fri Nov 08 18:48:06 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 cc41546adf56 tool-data/dada2_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dada2_taxonomy.loc.sample Fri Nov 08 18:48:06 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 cc41546adf56 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 08 18:48:06 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 cc41546adf56 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Nov 08 18:48:06 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> |
