| Next changeset 1:498d57610fcd (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_plotComplexity.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 ab2030f217a9 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Nov 08 18:51:48 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 ab2030f217a9 dada2_plotComplexity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dada2_plotComplexity.xml Fri Nov 08 18:51:48 2019 -0500 |
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| b'@@ -0,0 +1,194 @@\n+<tool id="dada2_plotComplexity" name="dada2: plotComplexity" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">\n+ <description>Plot sequence complexity profile</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+##name files by linking\n+#import re\n+mkdir forward &&\n+#if $batch_cond.paired_cond.paired_select != "single"\n+ mkdir reverse &&\n+#end if\n+\n+#if $batch_cond.batch_select == "batch":\n+ #set elid = re.sub(\'[^\\w\\-\\.]\', \'_\', str($batch_cond.paired_cond.reads.element_identifier))\n+ #if $batch_cond.paired_cond.paired_select != "paired"\n+ ln -s \'$batch_cond.paired_cond.reads\' forward/\'$elid\' &&\n+ #else\n+ ln -s \'$batch_cond.paired_cond.reads.forward\' forward/\'$elid\' &&\n+ ln -s \'$batch_cond.paired_cond.reads.reverse\' reverse/\'$elid\' &&\n+ #end if\n+ #if $batch_cond.paired_cond.paired_select == "separate"\n+ ln -s \'$batch_cond.paired_cond.sdaer\' reverse/\'$elid\' &&\n+ #end if\n+#else\n+ #for $read in $batch_cond.paired_cond.reads:\n+ #set elid = re.sub(\'[^\\w\\-\\.]\', \'_\', str($read.element_identifier))\n+ #if $batch_cond.paired_cond.paired_select != "paired"\n+ ln -s \'$read\' forward/\'$elid\' &&\n+ #else\n+ ln -s \'$read.forward\' forward/\'$elid\' &&\n+ ln -s \'$read.reverse\' reverse/\'$elid\' &&\n+ #end if\n+ #end for\n+ #if $batch_cond.paired_cond.paired_select == "separate"\n+ #for $read in $batch_cond.paired_cond.sdaer:\n+ #set elid = re.sub(\'[^\\w\\-\\.]\', \'_\', str($read.element_identifier))\n+ ln -s \'$read\' reverse/\'$elid\' &&\n+ #end for\n+ #end if\n+#end if\n+\n+ Rscript --slave \'$dada2_script\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="dada2_script"><![CDATA[\n+#import re\n+library(ggplot2, quietly=T)\n+library(dada2, quietly=T)\n+\n+#if $batch_cond.batch_select != "batch"\n+agg <- $batch_cond.aggregate\n+#else\n+agg <- FALSE\n+#end if\n+\n+#if str($window) == ""\n+ wndw <- NULL\n+#else\n+ wndw <- $window\n+#end if\n+\n+fwd_files <- list.files("forward", full.names=T)\n+qp <- plotComplexity(fwd_files, kmerSize=$kmerSize, window=wndw, by=$by, n=$n, bins=$bins, aggregate = agg)\n+ggsave(\'output.pdf\', qp, width = 20,height = 15,units = c("cm"))\n+\n+#if $batch_cond.paired_cond.paired_select != "single"\n+rev_files <- list.files("reverse", full.names=T)\n+qp <- plotComplexity(rev_files, kmerSize=$kmerSize, window=wndw, by=$by, n=$n, bins=$bins, aggregate = agg)\n+ggsave(\'output_rev.pdf\', qp, width = 20,height = 15,units = c("cm"))\n+#end if\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="batch_cond">\n+ <param name="batch_select" type="select" label="Processing mode" help="Joint processing processes all reads at once in a single job creating a single output (two in the case of paired data). Batch processes the samples in separate jobs and creates separate output for each">\n+ <option value="joint">Joint</option>\n+ <option value="batch">Batch</option>\n+ </param>\n+ <when value="joint">\n+ <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/>\n+ <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/>\n+ </when>\n+ <when value="batch">\n+ <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fl" argument_rev="fl"/>\n+ </when>\n+ </conditional>\n+ <param argument="kmerSize" type="integer" value="2" label="kmer size" help="kmer: also known as oligonucleotides words"/>\n+ '..b'red_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="batch_cond|aggregate" value="FALSE"/>\n+ <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ </test>\n+ <!-- single, non-batch, aggregate, small sample -->\n+ <test expect_num_outputs="1">\n+ <param name="batch_cond|batch_select" value="joint"/>\n+ <param name="batch_cond|paired_cond|paired_select" value="single"/>\n+ <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="n" value="10000"/>\n+ <param name="batch_cond|aggregate" value="TRUE"/>\n+ <output name="output" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ </test>\n+\n+ <!-- paired, batch -->\n+ <test expect_num_outputs="2">\n+ <param name="batch_cond|batch_select" value="batch"/>\n+ <param name="batch_cond|paired_cond|paired_select" value="paired"/>\n+ <param name="batch_cond|paired_cond|reads">\n+ <collection type="paired">\n+ <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ </collection>\n+ </param>\n+ <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ </test>\n+ <!-- paired-separate batch (sim_size because element ids differ)-->\n+ <test expect_num_outputs="2">\n+ <param name="batch_cond|batch_select" value="batch"/>\n+ <param name="batch_cond|paired_cond|paired_select" value="separate"/>\n+ <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ </test>\n+ <!-- single, batch -->\n+ <test expect_num_outputs="1">\n+ <param name="batch_cond|batch_select" value="batch"/>\n+ <param name="batch_cond|paired_cond|paired_select" value="single"/>\n+ <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="n" value="10000"/>\n+ <output name="output" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Summary\n+.......\n+\n+This function plots a histogram of the distribution of sequence complexities in the form of effective numbers of kmers as determined by seqComplexity. By default, kmers of size 2 are used, in which case a perfectly random sequences will approach an effective kmer number of 16 = 4 (nucleotides)^ 2 (kmer size).\n+\n+Details\n+.......\n+\n+This function calculates the kmer complexity of input sequences. Complexity is quantified as the Shannon richness of kmers, which can be thought of as the effective number of kmers if they were all at equal frequencies. If a window size is provided, the minimum Shannon richness observed over sliding window along the sequence is returned.\n+\n+\n+@HELP_OVERVIEW@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r ab2030f217a9 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Nov 08 18:51:48 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 ab2030f217a9 static/images/pairpipe.png |
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| diff -r 000000000000 -r ab2030f217a9 static/images/pairpipe.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/pairpipe.svg Fri Nov 08 18:51:48 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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| @@ -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 ab2030f217a9 test-data/learnErrors_F3D0_R2.pdf |
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| Binary file test-data/learnErrors_F3D0_R2.pdf has changed |
| b |
| diff -r 000000000000 -r ab2030f217a9 test-data/makeSequenceTable_F3D0.pdf |
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| Binary file test-data/makeSequenceTable_F3D0.pdf has changed |
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| diff -r 000000000000 -r ab2030f217a9 test-data/makeSequenceTable_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/makeSequenceTable_F3D0.tab Fri Nov 08 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ + V1 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 22 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 18 +TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 11 +TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 5 +TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 5 +TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 3 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 2 |
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| diff -r 000000000000 -r ab2030f217a9 test-data/mergePairs_F3D0.Rdata |
| b |
| Binary file test-data/mergePairs_F3D0.Rdata has changed |
| b |
| diff -r 000000000000 -r ab2030f217a9 test-data/mergePairs_F3D0_nondefault.Rdata |
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| Binary file test-data/mergePairs_F3D0_nondefault.Rdata has changed |
| b |
| diff -r 000000000000 -r ab2030f217a9 test-data/qualityProfile.pdf |
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| Binary file test-data/qualityProfile.pdf has changed |
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| diff -r 000000000000 -r ab2030f217a9 test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Fri Nov 08 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>A;B;C;D;E; +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>A;B;C;F;G; +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r ab2030f217a9 test-data/reference_species.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_species.fa Fri Nov 08 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>IDA GenusA speciesA +ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC +>IDB GenusB speciesB +CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC |
| b |
| diff -r 000000000000 -r ab2030f217a9 test-data/removeBimeraDenovo_F3D0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/removeBimeraDenovo_F3D0.tab Fri Nov 08 18:51:48 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 ab2030f217a9 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 18:51:48 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 ab2030f217a9 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 18:51:48 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 ab2030f217a9 test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata |
| b |
| Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed |
| b |
| diff -r 000000000000 -r ab2030f217a9 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 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples dadaF +dada_F3D0_R1.Rdata 189 |
| b |
| diff -r 000000000000 -r ab2030f217a9 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 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples filter reads.in filter reads.out +filterAndTrim_F3D0.tab 250 249 |
| b |
| diff -r 000000000000 -r ab2030f217a9 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 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples merge +mergePairs_F3D0.Rdata 66 |
| b |
| diff -r 000000000000 -r ab2030f217a9 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 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples nochim +V1 66 |
| b |
| diff -r 000000000000 -r ab2030f217a9 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 18:51:48 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +samples seqtab +V1 66 |
| b |
| diff -r 000000000000 -r ab2030f217a9 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 18:51:48 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 ab2030f217a9 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 18:51:48 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 ab2030f217a9 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 18:51:48 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 ab2030f217a9 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 18:51:48 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> |
