| Previous changeset 2:b8ecbc50af78 (2023-12-18) Next changeset 4:ac9564dcdb99 (2024-03-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6 |
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modified:
frequency.xml macros.xml test-data/AalborgWWTPs-boxplot-group.pdf test-data/AalborgWWTPs-boxplot-point.pdf test-data/AalborgWWTPs-boxplot.pdf test-data/AalborgWWTPs-complete.rds test-data/AalborgWWTPs-core-multiple.pdf test-data/AalborgWWTPs-core.pdf test-data/AalborgWWTPs-frequency.pdf test-data/AalborgWWTPs-heatmap-group-facet.pdf test-data/AalborgWWTPs-heatmap-normalise.pdf test-data/AalborgWWTPs-heatmap-plot_foo_file.pdf test-data/AalborgWWTPs-heatmap-plot_foo_midas.pdf test-data/AalborgWWTPs-heatmap-sort_by_group.pdf test-data/AalborgWWTPs-heatmap-sort_by_sample.pdf test-data/AalborgWWTPs-heatmap-tax.pdf test-data/AalborgWWTPs-heatmap.pdf test-data/AalborgWWTPs-mergereplicates.rds test-data/AalborgWWTPs-octave.pdf test-data/AalborgWWTPs-octave.png test-data/AalborgWWTPs-octave.svg test-data/AalborgWWTPs-ordinate-color-shape-frame.pdf test-data/AalborgWWTPs-ordinate-envfit-factor.pdf test-data/AalborgWWTPs-ordinate-envfit-num.pdf test-data/AalborgWWTPs-ordinate-label-traj-group.pdf test-data/AalborgWWTPs-ordinate-label-traj.pdf test-data/AalborgWWTPs-ordinate-nmds.pdf test-data/AalborgWWTPs-ordinate-rda.pdf test-data/AalborgWWTPs-ordinate-screeplot.pdf test-data/AalborgWWTPs-ordinate-species.pdf test-data/AalborgWWTPs-ordinate.pdf test-data/AalborgWWTPs-otu_network-color_by.pdf test-data/AalborgWWTPs-otu_network.pdf test-data/AalborgWWTPs-rankabundance-nondefault.pdf test-data/AalborgWWTPs-rankabundance.pdf test-data/AalborgWWTPs-rarecurve-color.pdf test-data/AalborgWWTPs-rarecurve-facet.pdf test-data/AalborgWWTPs-rarecurve.pdf test-data/AalborgWWTPs-subset_samples.rds test-data/AalborgWWTPs-subset_taxa.rds test-data/AalborgWWTPs-taxonomy.list test-data/AalborgWWTPs-timeseries-group.pdf test-data/AalborgWWTPs-timeseries-tax.pdf test-data/AalborgWWTPs-timeseries.pdf test-data/AalborgWWTPs-venn-group.pdf test-data/AalborgWWTPs-venn.pdf test-data/AalborgWWTPs.rds test-data/AalborgWWTPs.tsv |
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added:
test-data/AalborgWWTPs-heatmap-normalise_by_sample.pdf test-data/dada2-assignTaxonomy.tabular test-data/dada2-metadata.tsv test-data/dada2-removeBimeraDenovo.tab test-data/output.phyloseq |
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| diff -r b8ecbc50af78 -r cdba4eab5a54 frequency.xml --- a/frequency.xml Mon Dec 18 09:38:02 2023 +0000 +++ b/frequency.xml Mon Feb 26 07:54:14 2024 +0000 |
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| @@ -13,9 +13,10 @@ data <- readRDS("$data") plot <- amp_frequency( data, - #if $group_by - group_by = "$group_by", - #end if + ## https://github.com/KasperSkytte/ampvis2/issues/167 + ## #if $group_by + ## group_by = "$group_by", + ## #end if ## tax_class = NULL, tax_empty = "$tax_empty", tax_aggregate = "$tax_aggregate", @@ -29,7 +30,8 @@ </configfiles> <inputs> <expand macro="rds_metadata_input_macro"/> - <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/> + <!-- https://github.com/KasperSkytte/ampvis2/issues/167 + <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/> --> <expand macro="tax_empty_macro"/> <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs"> <option value="OTU" selected="true">OTU/ASV</option> @@ -48,12 +50,13 @@ <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf"/> </test> <!-- group_by --> + <!-- https://github.com/KasperSkytte/ampvis2/issues/167 <test expect_num_outputs="1"> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> <param name="group_by" value="Plant"/> <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf"/> - </test> + </test> --> </tests> <help><![CDATA[ What it does |
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| diff -r b8ecbc50af78 -r cdba4eab5a54 macros.xml --- a/macros.xml Mon Dec 18 09:38:02 2023 +0000 +++ b/macros.xml Mon Feb 26 07:54:14 2024 +0000 |
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| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.7.22</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.8.6</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.01</token> <xml name="header"> <xrefs> @@ -8,7 +8,8 @@ </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement> - <requirement type="package" version="2.1.1">r-readr</requirement> + <requirement type="package" version="2.1.5">r-readr</requirement> + <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement> </requirements> <version_command><![CDATA[ echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ") @@ -36,7 +37,7 @@ <token name="@SAVE_TAX_LIST@"><![CDATA[ for(level in colnames(data\$tax)){ for(u in unique(data\$tax[level])){ - write(u, file="$taxonomy_list_out", append=T) + write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T) } } ]]></token> @@ -152,7 +153,20 @@ </expand> </xml> + <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by + sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168 + leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) --> <xml name="metadata_sample_select" token_argument=""> + <param argument="@ARGUMENT@" type="select" optional="true"> + <options from_dataset="metadata_list"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples --> + <filter type="unique_value" column="1"/> + </options> + </param> + </xml> + <xml name="metadata_sample_or_variable_select" token_argument=""> <conditional name="@ARGUMENT@_cond"> <param name="@ARGUMENT@_sel" type="select"> <option value="no">No</option> @@ -164,14 +178,7 @@ <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/> </when> <when value="sample"> - <param argument="@ARGUMENT@" type="select" optional="true"> - <options from_dataset="metadata_list"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples --> - <filter type="unique_value" column="1"/> - </options> - </param> + <expand macro="metadata_sample_select"/> </when> </conditional> </xml> |
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| diff -r b8ecbc50af78 -r cdba4eab5a54 test-data/AalborgWWTPs-taxonomy.list --- a/test-data/AalborgWWTPs-taxonomy.list Mon Dec 18 09:38:02 2023 +0000 +++ b/test-data/AalborgWWTPs-taxonomy.list Mon Feb 26 07:54:14 2024 +0000 |
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| b'@@ -1,495 +1,495 @@\n-k__Bacteria\n-p__Firmicutes\n-p__Bacteroidetes\n-p__Proteobacteria\n-p__Actinobacteria\n-p__Hydrogenedentes\n-p__Parcubacteria\n-p__Planctomycetes\n-p__Acidobacteria\n-p__Chloroflexi\n-\n-p__Saccharibacteria\n-p__Candidate division SR1\n-p__Cyanobacteria\n-p__Synergistetes\n-p__Deinococcus-Thermus\n-p__Chlorobi\n-p__Verrucomicrobia\n-p__GOUTA4\n-p__Nitrospirae\n-p__WCHB1-60\n-p__Elusimicrobia\n-p__SM2F11\n-p__TM6\n-p__Armatimonadetes\n-p__Fusobacteria\n-p__Tenericutes\n-p__Lentisphaerae\n-p__Microgenomates\n-c__Clostridia\n-c__Cytophagia\n-c__Betaproteobacteria\n-c__Actinobacteria\n-c__Gammaproteobacteria\n-c__Deltaproteobacteria\n-c__Bacilli\n-c__\n-c__Sphingobacteriia\n-c__Planctomycetacia\n-c__Holophagae\n-c__Chloroflexia\n-c__Caldilineae\n-\n-c__Anaerolineae\n-c__Flavobacteriia\n-c__Negativicutes\n-c__Alphaproteobacteria\n-c__Unknown 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1\n-g__uncultured\n-g__Brooklawnia\n-g__Sulfuritalea\n'..b'onas\tGenus\n+g__Pirellula\tGenus\n+g__Clostridium sensu stricto 1\tGenus\n+g__Acetoanaerobium\tGenus\n+g__Nitrospira\tGenus\n+g__Propioniciclava\tGenus\n+g__Parabacteroides\tGenus\n+g__Actinomyces\tGenus\n+g__Aeromicrobium\tGenus\n+g__Clostridium sensu stricto 6\tGenus\n+g__Reyranella\tGenus\n+g__Proteiniclasticum\tGenus\n+g__B1-K1A-105\tGenus\n+g__Prevotellaceae UCG-004\tGenus\n+g__Haliangium\tGenus\n+g__Ureibacillus\tGenus\n+g__Ruminococcus 2\tGenus\n+g__CYCU-0281\tGenus\n+g__Parafilimonas\tGenus\n+g__Aestuariimicrobium\tGenus\n+g__Diaminobutyricimonas\tGenus\n+g__K2-78\tGenus\n+g__Erysipelatoclostridium\tGenus\n+g__CL500-29 marine group\tGenus\n+g__Bacteroides\tGenus\n+g__Tessaracoccus\tGenus\n+g__Gordonia\tGenus\n+g__Senegalimassilia\tGenus\n+g__Atopobium\tGenus\n+g__Proteiniphilum\tGenus\n+g__Uliginosibacterium\tGenus\n+g__WCHB1-50\tGenus\n+g__Christensenellaceae R-7 group\tGenus\n+g__Fodinibacter\tGenus\n+g__Defluviicoccus\tGenus\n+g__Acidovorax\tGenus\n+g__Salana\tGenus\n+g__Propionimicrobium\tGenus\n+g__Litorilinea\tGenus\n+g__Faecalitalea\tGenus\n+g__Ruminiclostridium 5\tGenus\n+g__Rivicola\tGenus\n+g__[Eubacterium] coprostanoligenes group\tGenus\n+g__Lewinella\tGenus\n+s__\tSpecies\n+\tSpecies\n+s__sublineage I\tSpecies\n+s__cluster 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| @@ -1,4 +1,4 @@ -SampleID Plant Date Year Period + Plant Date Year Period 16SAMP-747 16SAMP-747 Aalborg East 2010-02-04 2010 Winter 16S-AMP-1168 16S-AMP-1168 Aalborg West 2013-05-06 2013 Spring 16SAMP-4603 16SAMP-4603 Aalborg East 2014-08-19 2014 Summer |
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| b |
| b'@@ -0,0 +1,233 @@\n+\tKingdom\tPhylum\tClass\tOrder\tFamily\tGenus\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tRikenellaceae\tAlistipes\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGATCGTTAAGTCAGTGGTCAAATTGAGGGGCTCAACCCCTTCCCGCCATTGAAACTGGCGATCTTGAGTGGAAGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATGCCGGCTTCCTACTGACGCTGAAGCACGAAAGCGTGGGGATCGAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATG'..b'CATTTGAAACTGTTTTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tOscillospirales\tOscillospiraceae\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGTGGCAGGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTTGAAACTGTCCAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tLachnospirales\tLachnospiraceae\tAnaerostipes\n+GACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTCCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCGTAGAGATCGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCGAATGGG\tBacteria\tCyanobacteria\tCyanobacteriia\tChloroplast\tNA\tNA\n+TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGTCAGGCTAGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tLachnospirales\tLachnospiraceae\tNA\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCTGTGCAAGTCTGAAGTGAAAGGCCGGGGCCCAACCCCGGGAGTGCTTTGGAAACTGTGCGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGTCTTGCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tLachnospirales\tLachnospiraceae\tLachnospiraceae_UCG-006\n+TACGTAGGGGGCGAGCGTTGTCCGGAATGACTGGGCGTAAAGGGAGTGTAGGCGGCCTTTTAAGTTATGTGTGAAAGCCCACGGCTCAACTGTGGAATTGCACATAAAACTGGGAGGCTGGAGTGCAGGAGAGGTAAGCGGAATTTCCAGTGTAGCGGTGGAATGCGTAGATATTGGGAAGAACACCGGAGGCGAAGGCGGCTTACTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tNA\tNA\tNA\n+TACGTAGGGAGCGAGCGTTATCCGGATTTATTGGGTGTAAAGGGTGCGTAGACGGGGAATTAAGTTAGTTGTGAAATCCCAAGGCTCAACTTTGGAACTGCAACTAAAACTAATTTTCTTGAGTACTGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACAGAAACTGACGTTGAGGCACGAAAGTGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridia_UCG-014\tNA\tNA\n+TACGTAGGTGGCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGTGCGCAGGCGGTTTGTTAAGTCTAAAATCAAAGCCCGAAGCTTAACTTCGGTTCGTTTTAGAAACTGGCAGGCTTGAGTATGGTAGAGGCAAACGGAATTTCTAGTGTAGCGGTAAAATGCGTAGATATTAGAAGGAACACCAGTGGCGAAGGCGGTTTGCTGGGCCATTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAATAGG\tBacteria\tFirmicutes\tBacilli\tRF39\tNA\tNA\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGGCAAGTTAGTAGCGTAATTCCGGGGCTCAACTTCGGAACTACTACTAAAACTGCTGGGCTTGAGTGCAGGAGGGGCATATGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGATATGCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridia_vadinBB60_group\tNA\tNA\n+TACGTAGGGAGCGAGCGTTATCCGGATTTATTGGGTGTAAAGGGTGCGTAGACGGGAAATTAAGTTAGTTGTGAAATCCCTCGGCTCAACCGAGGAACTGCAACTAAAACTGATATTCTTGAGTACTGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACAGAAACTGACGTTGAGGCACGAAAGTGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridia_UCG-014\tNA\tNA\n+TACGGAGGATGCGAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGACAAGTTGGTAGCGTAACTCCGGGGCTCAACCTCGGCACTACTACCAAAACTGTTGGACTTGAGTGCAGGAGGGGCAAATGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGATTTGCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridia_vadinBB60_group\tNA\tNA\n+TACGGAGGGGGCGAGCGTTATCCGGATTCATTGGGCGTAAAGCGCGCGTAGGCGGCCTGTTAGGTCGGGGGTCAAATACCGGGGCTCAACCCCGGTCCGCCCCCGATACCGGCAGGCTTGAGTCTGGTAGGGGAAGGCGGAATTCCCAGTGTAGCGGTGGAATGCGCAGATATTGGGAAGAACACCGGCGGCGAAGGCGGCCTTCTGGGCCACGACTGACGCTGAGGCGCGAAAGCTAGGGGAGCGAACAGG\tBacteria\tActinobacteriota\tCoriobacteriia\tCoriobacteriales\tAtopobiaceae\tOlsenella\n+TACGTAGGGGGCGAGCGTTATCCGGATTTATTGGGCGTAAAGGGTGCGTAGGCGGTATGTTAAGTCTAAAATCAAAGCCCGAGGCTTAACCTCGGTTCGTTTTAGAAACTGGCAAACTAGAGTGCAGTAGAGGCAAGTGGAATTTCTAGTGTAGCGGTTAAATGCGTAGATATTAGAAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAATAGG\tBacteria\tFirmicutes\tBacilli\tRF39\tNA\tNA\n' |
| b |
| diff -r b8ecbc50af78 -r cdba4eab5a54 test-data/dada2-metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dada2-metadata.tsv Mon Feb 26 07:54:14 2024 +0000 |
| b |
| @@ -0,0 +1,21 @@ +Sample time +F3D0 early +F3D1 early +F3D2 early +F3D3 early +F3D5 early +F3D6 early +F3D7 early +F3D8 early +F3D9 early +F3D141 late +F3D142 late +F3D143 late +F3D144 late +F3D145 late +F3D146 late +F3D147 late +F3D148 late +F3D149 late +F3D150 late +Mock mock |
| b |
| diff -r b8ecbc50af78 -r cdba4eab5a54 test-data/dada2-removeBimeraDenovo.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dada2-removeBimeraDenovo.tab Mon Feb 26 07:54:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,233 @@\n+\tF3D0\tF3D1\tF3D141\tF3D142\tF3D143\tF3D144\tF3D145\tF3D146\tF3D147\tF3D148\tF3D149\tF3D150\tF3D2\tF3D3\tF3D5\tF3D6\tF3D7\tF3D8\tF3D9\tMock\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAGG\t579\t405\t444\t289\t228\t421\t645\t325\t1495\t863\t883\t317\t3488\t988\t327\t1014\t648\t272\t511\t0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\t345\t353\t362\t304\t176\t277\t489\t230\t1215\t729\t779\t229\t1587\t602\t268\t674\t504\t352\t423\t0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\t449\t231\t345\t158\t204\t302\t522\t254\t913\t581\t723\t399\t1175\t465\t284\t588\t438\t349\t482\t0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\t430\t69\t502\t164\t231\t357\t583\t388\t1089\t853\t897\t471\t472\t200\t158\t404\t314\t147\t206\t0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG\t154\t140\t189\t180\t130\t104\t307\t179\t453\t443\t417\t169\t338\t402\t151\t476\t470\t582\t596\t0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\t470\t41\t331\t181\t244\t353\t476\t275\t1182\t872\t637\t216\t115\t25\t23\t17\t11\t0\t0\t0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\t282\t96\t243\t163\t152\t240\t396\t214\t861\t579\t560\t238\t325\t167\t123\t282\t195\t130\t210\t0\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t184\t190\t321\t89\t83\t41\t125\t71\t75\t507\t515\t120\t1211\t381\t207\t261\t213\t286\t438\t0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGATCGTTAAGTCAGTGGTCAAATTGAGGGGCTCAACCCCTTCCCGCCATTGAAACTGGCGATCTTGAGTGGAAGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATGCCGGCTTCCTACTGACGCTGAAGCACGAAAGCGTGGGGATCGAACAGG\t45\t69\t167\t89\t109\t158\t202\t113\t769\t409\t426\t241\t434\t307\t178\t205\t176\t113\t146\t0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG\t158\t106\t130\t78\t67\t155\t229\t88\t269\t198\t288\t149\t609\t298\t207\t242\t276\t197\t225\t0\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\t17\t102\t168\t42\t78\t269\t317\t178\t448\t411\t478\t61\t55\t171\t61\t45\t16\t19\t27\t103\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTG'..b'GAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGG\t0\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGTGTAAAGGGCGTGTAGGCGGGAAAGCAAGTCAGATGTGAAAACTCAGGGCTCAACCCTGAGCCTGCATTTGAAACTGTTTTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t0\t0\t0\t0\t0\t0\t0\t0\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGTGGCAGGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTTGAAACTGTCCAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+GACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTCCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCGTAGAGATCGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCGAATGGG\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\n+TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGTCAGGCTAGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCTGTGCAAGTCTGAAGTGAAAGGCCGGGGCCCAACCCCGGGAGTGCTTTGGAAACTGTGCGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGTCTTGCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGGGGCGAGCGTTGTCCGGAATGACTGGGCGTAAAGGGAGTGTAGGCGGCCTTTTAAGTTATGTGTGAAAGCCCACGGCTCAACTGTGGAATTGCACATAAAACTGGGAGGCTGGAGTGCAGGAGAGGTAAGCGGAATTTCCAGTGTAGCGGTGGAATGCGTAGATATTGGGAAGAACACCGGAGGCGAAGGCGGCTTACTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGGAGCGAGCGTTATCCGGATTTATTGGGTGTAAAGGGTGCGTAGACGGGGAATTAAGTTAGTTGTGAAATCCCAAGGCTCAACTTTGGAACTGCAACTAAAACTAATTTTCTTGAGTACTGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACAGAAACTGACGTTGAGGCACGAAAGTGTGGGGAGCAAACAGG\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGTGGCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGTGCGCAGGCGGTTTGTTAAGTCTAAAATCAAAGCCCGAAGCTTAACTTCGGTTCGTTTTAGAAACTGGCAGGCTTGAGTATGGTAGAGGCAAACGGAATTTCTAGTGTAGCGGTAAAATGCGTAGATATTAGAAGGAACACCAGTGGCGAAGGCGGTTTGCTGGGCCATTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAATAGG\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGAGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGGCAAGTTAGTAGCGTAATTCCGGGGCTCAACTTCGGAACTACTACTAAAACTGCTGGGCTTGAGTGCAGGAGGGGCATATGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGATATGCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGGAGCGAGCGTTATCCGGATTTATTGGGTGTAAAGGGTGCGTAGACGGGAAATTAAGTTAGTTGTGAAATCCCTCGGCTCAACCGAGGAACTGCAACTAAAACTGATATTCTTGAGTACTGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACAGAAACTGACGTTGAGGCACGAAAGTGTGGGGAGCAAACAGG\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\n+TACGGAGGATGCGAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGACAAGTTGGTAGCGTAACTCCGGGGCTCAACCTCGGCACTACTACCAAAACTGTTGGACTTGAGTGCAGGAGGGGCAAATGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGATTTGCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGGAGGGGGCGAGCGTTATCCGGATTCATTGGGCGTAAAGCGCGCGTAGGCGGCCTGTTAGGTCGGGGGTCAAATACCGGGGCTCAACCCCGGTCCGCCCCCGATACCGGCAGGCTTGAGTCTGGTAGGGGAAGGCGGAATTCCCAGTGTAGCGGTGGAATGCGCAGATATTGGGAAGAACACCGGCGGCGAAGGCGGCCTTCTGGGCCACGACTGACGCTGAGGCGCGAAAGCTAGGGGAGCGAACAGG\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+TACGTAGGGGGCGAGCGTTATCCGGATTTATTGGGCGTAAAGGGTGCGTAGGCGGTATGTTAAGTCTAAAATCAAAGCCCGAGGCTTAACCTCGGTTCGTTTTAGAAACTGGCAAACTAGAGTGCAGTAGAGGCAAGTGGAATTTCTAGTGTAGCGGTTAAATGCGTAGATATTAGAAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAATAGG\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r b8ecbc50af78 -r cdba4eab5a54 test-data/output.phyloseq |
| b |
| Binary file test-data/output.phyloseq has changed |
