| Next changeset 1:39638e0aff59 (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_learnErrors.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 fd892c845981 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Nov 08 18:49:30 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 fd892c845981 dada2_learnErrors.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dada2_learnErrors.xml Fri Nov 08 18:49:30 2019 -0500 |
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| b'@@ -0,0 +1,118 @@\n+<tool id="dada2_learnErrors" name="dada2: learnErrors" 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+library(ggplot2, quietly=T)\n+library(dada2, quietly=T)\n+\n+args <- commandArgs(trailingOnly = TRUE)\n+nthreads <- as.integer(args[1])\n+\n+files <- c()\n+#for $read in $fls:\n+files <- c(files, \'$read\')\n+#end for\n+\n+err <- learnErrors(files, nbases = 10**$nbases,\n+ errorEstimationFunction = $advanced.errfoo, multithread = nthreads,\n+ randomize = $advanced.randomize, MAX_CONSIST = $advanced.maxconsist, OMEGA_C = $advanced.omegac)\n+\n+saveRDS(err, file=\'$errors\')\n+\n+## generate error plots\n+plot <- plotErrors(err, obs = $plotopt.obs, err_out = $plotopt.err_out, err_in = $plotopt.err_in, nominalQ = $plotopt.nominalQ)\n+ggsave(\'plot.pdf\', plot, width = 20,height = 15,units = c("cm"))\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param argument="fls" type="data" multiple="true" format="fastq,fastq.gz" label="Short read data" help="forward or reverse reads should be processed separately"/>\n+ <param argument="nbases" type="integer" value="8" min="0" label="Magnitide of number of bases to use for learning"/>\n+ <section name="advanced" title="Advanced Option">\n+ <expand macro="errorEstimationFunction"/>\n+ <param argument="randomize" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Randomize samples" help="Pick samples at random, otherwise samples are read in the provided order until enough reads are obtained (default)."/>\n+ <param name="maxconsist" argument="MAX_CONSIST" type="integer" value="10" min="0" label="Maximum number of times to step through the selfconsistency loop" help="If convergence was not reached in MAX_CONSIST steps, the estimated error rates in the last step are returned."/>\n+ <param name="omegac" argument="OMEGA_C" type="float" value="0" min="0" label="Threshold at which unique sequences inferred to contain errors are corrected" help="For reasons of convergence, and because it is\n+more conservative, it is recommended to set this value to 0, which means that\n+all reads are counted and contribute to estimating the error rates."/>\n+ </section>\n+ <section name="plotopt" title="Plotting Option">\n+ <param argument="obs" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Plot observed error rates"/>\n+ <param argument="err_out" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Plot output error rates"/>\n+ <param argument="err_in" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Plot input error rates"/>\n+ <param argument="nominalQ" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Plot expected error rates"/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="errors" format="dada2_errorrates" label="${tool.name} on ${on_string}"/>\n+ <data name="plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}: error rates plot"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz"/>\n+ <output name="errors" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates"/>\n+ <output name="plot" value="learnErrors_F3D0_R1.pdf" ftype="pdf" compare="sim_size" />\n+ </test>\n+ <!-- test w non-default parameters -->\n+ <test>\n+ <param name="fls" value="filterAndTr'..b'e="FALSE" />\n+ <param name="plotopt|err_out" value="FALSE" />\n+ <param name="plotopt|err_in" value="TRUE" />\n+ <param name="plotopt|nominalQ" value="FALSE"/>\n+ <output name="errors" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" compare="sim_size" delta="14000"/>\n+ <output name="plot" value="learnErrors_F3D0_R1.pdf" ftype="pdf" compare="sim_size" />\n+ </test>\n+ <!-- TODO test w multiple inputs -->\n+ </tests>\n+ <help><![CDATA[\n+Description\n+...........\n+\n+Error rates are learned by alternating between sample inference and error rate estimation until convergence. Additionally a plot is generated that shows the observed frequency of each transition (eg. A->C) as a function of the associated quality score, the final estimated error rates (if they exist), the initial input rates, and the expected error rates under the nominal definition of quality scores.\n+\n+In addition a plot is generated (with plotErrors) that shows the observed frequency of each transition (eg. A->C) as a function of the associated quality score. Also the final estimated error rates (if they exist) are shown. Optionally also the initial input rates and the expected error rates under the nominal definition of quality scores can be added to the plot.\n+\n+Usage\n+.....\n+\n+**Input** are the FASTQ dataset containing the filtered and trimmed reads of the samples.\n+\n+**Output** a dataset with type *dada2_errorrates* (which is a RData file containing the output of dada2\'s learnErrors function) and a **plot** showing the error rates for each possible transition (A\xe2\x86\x92C, A\xe2\x86\x92G,...)\n+\n+- Points are the observed error rates for each consensus quality score.\n+- The black line shows the estimated error rates after convergence of the machine-learning algorithm.\n+- The red line shows the error rates expected under the nominal definition of the Q-score.\n+\n+The learned error rates are input the the *dada2: dada* tool.\n+\n+Details\n+.......\n+\n+The learnErrors method learns a parametric error model from the data, by alternating estimation of the error rates and inference of sample composition until they converge on a jointly consistent solution. As in many machine-learning problems, the algorithm must begin with an initial guess, for which the maximum possible error rates in this data are used (the error rates if only the most abundant sequence is correct and all the rest are errors).\n+\n+It is expected that the estimated error rates (black lines in the plot) are in a good fit to the observed rates (points in the plot), and that the error rates drop with increased quality. Try to increase the **number of bases to use for learning** if this is not the case.\n+\n+Error functions:\n+\n+- loessErrfun: accepts a matrix of observed transitions, with each transition corresponding to a row (eg. row 2 = A->C) and each column to a quality score (eg. col 31 = Q30). It returns a matrix of estimated error rates of the same shape. Error rates are estimates by a loess fit of the observed rates of each transition as a function of the quality score. Self-transitions (i.e. A->A) are taken to be the left-over probability.\n+- noqualErrfun: accepts a matrix of observed transitions, groups together all observed transitions regardless of quality scores, and estimates the error rate for that transition as the observed fraction of those transitions. The effect is that quality scores will be effectively ignored.\n+- PacBioErrfun: This function accepts a matrix of observed transitions from PacBio CCS amplicon sequencing data, with each transition corresponding to a row (eg. row 2 = A->C) and each column to a quality score (eg. col 31 = Q30). It returns a matrix of estimated error rates of the same shape. Error rates are estimates by loessErrfun for quality scores 0-92, and individually by the maximum likelihood estimate for the maximum quality score of 93.\n+\n+@HELP_OVERVIEW@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r fd892c845981 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Nov 08 18:49:30 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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| diff -r 000000000000 -r fd892c845981 static/images/pairpipe.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/pairpipe.svg Fri Nov 08 18:49:30 2019 -0500 |
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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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| diff -r 000000000000 -r fd892c845981 test-data/assignTaxonomyAddspecies_F3D0_boot.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assignTaxonomyAddspecies_F3D0_boot.tab Fri Nov 08 18:49:30 2019 -0500 |
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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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| diff -r 000000000000 -r fd892c845981 test-data/makeSequenceTable_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/makeSequenceTable_F3D0.tab Fri Nov 08 18:49:30 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 fd892c845981 test-data/mergePairs_F3D0.Rdata |
| b |
| Binary file test-data/mergePairs_F3D0.Rdata has changed |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/mergePairs_F3D0_nondefault.Rdata |
| b |
| Binary file test-data/mergePairs_F3D0_nondefault.Rdata has changed |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/qualityProfile.pdf |
| b |
| Binary file test-data/qualityProfile.pdf has changed |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Fri Nov 08 18:49:30 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>A;B;C;D;E; +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>A;B;C;F;G; +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/reference_species.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_species.fa Fri Nov 08 18:49:30 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>IDA GenusA speciesA +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>IDB GenusB speciesB +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/removeBimeraDenovo_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0.tab Fri Nov 08 18:49:30 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 fd892c845981 test-data/removeBimeraDenovo_F3D0_dada_uniques.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0_dada_uniques.tab Fri Nov 08 18:49:30 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 fd892c845981 test-data/removeBimeraDenovo_F3D0_derep_uniques.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0_derep_uniques.tab Fri Nov 08 18:49:30 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 fd892c845981 test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata |
| b |
| Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/seqCounts_F3D0_dadaF.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_dadaF.tab Fri Nov 08 18:49:30 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples dadaF +dada_F3D0_R1.Rdata 189 |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/seqCounts_F3D0_filter.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_filter.tab Fri Nov 08 18:49:30 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples filter reads.in filter reads.out +filterAndTrim_F3D0.tab 250 249 |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/seqCounts_F3D0_merge.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_merge.tab Fri Nov 08 18:49:30 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples merge +mergePairs_F3D0.Rdata 66 |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/seqCounts_F3D0_nochim.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_nochim.tab Fri Nov 08 18:49:30 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples nochim +V1 66 |
| b |
| diff -r 000000000000 -r fd892c845981 test-data/seqCounts_F3D0_seqtab.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqCounts_F3D0_seqtab.tab Fri Nov 08 18:49:30 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples seqtab +V1 66 |
| b |
| diff -r 000000000000 -r fd892c845981 tool-data/dada2_species.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dada2_species.loc.sample Fri Nov 08 18:49:30 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 fd892c845981 tool-data/dada2_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dada2_taxonomy.loc.sample Fri Nov 08 18:49:30 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 fd892c845981 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 08 18:49:30 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 fd892c845981 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Nov 08 18:49:30 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> |
