| Next changeset 1:0feab98f9577 (2022-04-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3" |
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added:
TODO 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-group_by.pdf test-data/AalborgWWTPs-frequency.pdf test-data/AalborgWWTPs-functions.tsv test-data/AalborgWWTPs-heatmap-group-facet.pdf test-data/AalborgWWTPs-heatmap-group-facet.tsv 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-metadata.list 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.fa test-data/AalborgWWTPs.nwk test-data/AalborgWWTPs.otu.csv test-data/AalborgWWTPs.otu.csv-wtax test-data/AalborgWWTPs.rds test-data/AalborgWWTPs.tax test-data/AalborgWWTPs.tsv test-data/generate.R test-data/generate.sh test-data/min_sparse_otu_table_hdf5.biom test-data/min_sparse_otu_table_hdf5.rds test-data/rich-dense.biom test-data/rich-dense.rds test-data/rich-sparse.biom test-data/rich-sparse.rds test-data/rich_sparse_otu_table_hdf5.biom test-data/rich_sparse_otu_table_hdf5.rds |
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| @@ -0,0 +1,6 @@ +use duplicated options instead of tokens to define defaults + + +detailed data for boxplot (see heatmap) + + |
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| diff -r 000000000000 -r f77f7c426d6f frequency.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency.xml Mon Apr 04 10:18:21 2022 +0000 |
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| @@ -0,0 +1,81 @@ +<tool id="ampvis2_frequency" name="ampvis2 frequency plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="header"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$rscript' + ]]></command> + <configfiles> + <configfile name="rscript"><![CDATA[ + library(ampvis2, quietly = TRUE) + data <- readRDS("$data") + plot <- amp_frequency( + data, + #if $group_by + group_by = "$group_by", + #end if + ## tax_class = NULL, + tax_empty = "$tax_empty", + tax_aggregate = "$tax_aggregate", + weight = $weight, + normalise = $normalise, + ## TODO + detailed_output = FALSE + ) + @OUTPUT_TOKEN@ + ]]></configfile> + </configfiles> + <inputs> + <expand macro="rds_metadata_input_macro"/> + <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> + </expand> + <param argument="weight" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Weight the frequency by abundance"/> + <expand macro="normalise_macro" checked="true"/> + <expand macro="out_format_macro"/> + </inputs> + <outputs> + <expand macro="out_macro"/> + </outputs> + <tests> + <!-- defaults --> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf"/> + </test> + <!-- group_by --> + <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> + </tests> + <help><![CDATA[ +What it does +============ + +Generates a barplot with frequency vs read abundance. + +The Galaxy tool calls the `amp_frequency +<https://madsalbertsen.github.io/ampvis2/reference/amp_frequency.html>`_ function +of the ampvis2 package. + +Input +===== + +@HELP_RDS_INPUT@ + +@HELP_METADATA_LIST_INPUT@ + +Output +====== + +A frequency plot in the chosen output format. + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r f77f7c426d6f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Apr 04 10:18:21 2022 +0000 |
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| b'@@ -0,0 +1,271 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">2.7.17</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">22.01</token>\n+ <xml name="header">\n+ <xrefs>\n+ <xref type="bio.tools">ampvis</xref>\n+ </xrefs>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement>\n+ <requirement type="package" version="2.1.1">r-readr</requirement>\n+ </requirements>\n+ <version_command><![CDATA[\n+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: ")\n+ ]]></version_command>\n+\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1101/299537</citation>\n+ <yield/>\n+ </citations>\n+ </xml>\n+\n+ <xml name="rds_input_macro">\n+ <param argument="data" type="data" format="ampvis2" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/>\n+ </xml>\n+ \n+ <xml name="rds_metadata_input_macro" token_metadata_optional="true">\n+ <expand macro="rds_input_macro"/>\n+ <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list">\n+ <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator>\n+ </param>\n+ </xml>\n+\n+ <token name="@SAVE_TAX_LIST@"><![CDATA[\n+ for(level in colnames(data\\$tax)){\n+ for(u in unique(data\\$tax[level])){\n+ write(u, file="$taxonomy_list_out", append=T)\n+ }\n+ }\n+ ]]></token>\n+\n+ <token name="@SAVE_METADATA_LIST@"><![CDATA[\n+ classes <- sapply(data\\$metadata, class)\n+ for(name in names(data\\$metadata)){\n+ ## check if it is the column containing the sample names\n+ ## the additional column in the ist file can the be used\n+ ## to filter SampleIDs from select inputs\n+ ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails)\n+ if(classes[[name]] == "character" && all(data\\$metadata[[name]] == rownames(data\\$metadata))){\n+ sample_names <- TRUE;\n+ }else{\n+ sample_names <- FALSE;\n+ }\n+ for(m in unique(data\\$metadata[[name]])){\n+ write(paste(name, m, sample_names, classes[[name]], sep="\\t"), file="$metadata_list_out", append=T);\n+ }\n+ }\n+ ]]></token>\n+\n+ <!-- defaults can be set by redefining an on option with selected="true" -->\n+ <xml name="taxlevel_macro" token_argument="" token_multiple="false" token_optional="false" token_label="" token_help="">\n+ <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">\n+ <option value="OTU">OTU/ASV</option>\n+ <option value="Species">Species</option>\n+ <option value="Genus">Genus</option>\n+ <option value="Family">Family</option>\n+ <option value="Order">Order</option>\n+ <option value="Class">Class</option>\n+ <option value="Phylum">Phylum</option>\n+ <option value="Kingdom">Kingdom</option>\n+ <yield/>\n+ </param>\n+ </xml>\n+\n+ <xml name="tax_empty_macro">\n+ <param argument="tax_empty" type="select" label="How to show OTUs without taxonomic information">\n+ <option value="remove">Remove OTUs without taxonomic information</option>\n+ <option value="best" selected="true">Use the best classification possible</option>\n+ '..b'of the facets" token_help="">\n+ <param argument="@ARGUMENT@" type="select" optional="true" label="@LABEL@" help="@HELP@">\n+ <option value="fixed">Same scale</option>\n+ <option value="free">Free scale</option>\n+ <option value="free_x">Free x-scale</option>\n+ <option value="free_y">Free y-scale</option>\n+ </param>\n+ </xml>\n+\n+ <token name="@OUTPUT_TOKEN@">\n+ ggsave("$plot", \n+ print(plot),\n+ device="$output_options.out_format"\n+ #if str($output_options.plot_width) != \'\'\n+ , width = $output_options.plot_width\n+ #end if\n+ #if str($output_options.plot_height) != \'\'\n+ , height = $output_options.plot_height\n+ #end if\n+ )\n+ </token>\n+ <xml name="out_macro" token_name="plot" token_label="">\n+ <data name="@NAME@" format="pdf" label="${tool.name} on ${on_string}@LABEL@">\n+ <yield/>\n+ <change_format>\n+ <when input="output_options.out_format" value="png" format="png" />\n+ <when input="output_options.out_format" value="svg" format="svg" />\n+ </change_format>\n+ </data>\n+ </xml>\n+ <xml name="out_format_macro">\n+ <section name="output_options" title="Output options" expanded="false">\n+ <param name="out_format" type="select" label="Output format">\n+ <option value="pdf" selected="true">PDF</option>\n+ <option value="png">PNG</option>\n+ <option value="svg">SVG</option>\n+ <yield/>\n+ </param>\n+ <param name="plot_width" type="float" value="" min="1" optional="true" label="Plot width in cm"/>\n+ <param name="plot_height" type="float" value="" min="1" optional="true" label="Plot height in cm"/>\n+ </section>\n+ </xml>\n+\n+ <token name="@RAREFY_TOKEN@">\n+ #if str($rarefy) != ""\n+ , rarefy = $rarefy\n+ #end if\n+ </token>\n+ <xml name="rarefy_macro" token_help="">\n+ <param argument="rarefy" type="integer" optional="true" value="" min="0" label="Rarefy species richness to this value" help="@HELP@"/>\n+ </xml>\n+\n+ <xml name="normalise_macro" token_checked="false">\n+ <param argument="normalise" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="@CHECKED@" label="Normalise read counts" help="Transform the OTU read counts to be in percent per sample."/>\n+ </xml>\n+\n+ <token name="@HELP_RDS_INPUT@">\n+ An ampvis2 RDS dataset obtained by the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or one of the\n+ ``ampvis2: subset ...`` tools).\n+ </token>\n+ <token name="@HELP_METADATA_LIST_INPUT@">\n+ The metadata list output of the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or the\n+ ``ampvis2: subset sample`` tool). This input is only used for providing\n+ values to the parameters alowing to select metadata variables or values.\n+ </token>\n+\n+ <token name="@HELP_RELATIVE_ABUNDANCES@">\n+Preserving relative abundances in a subset of larger data\n+=========================================================\n+\n+By default the raw read counts in the abundance matrix are normalised\n+(transformed to percentages) by some ampvis2 plotting tools (for\n+example ``ampvis2: heatmap``, ``ampvis2: timeseries``, and more). \n+If this is applied to data generated by one of the ``ampvis2: subset ...`` tools\n+this means that the relative\n+abundances shown will be calculated based on the remaining taxa after the\n+subset, not including the removed taxa, if any. To circumvent this, enable\n+``normalise`` when subsetting with the ``ampvis2: subset ...``` tools,\n+and then disable ``normalise`` in the plotting tool. This will\n+transform the OTU counts to relative abundances BEFORE the subset.\n+ </token>\n+</macros>\n\\ No newline at end of file\n' |
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| @@ -0,0 +1,80 @@ +Genus Foo Bar +g__Acetitomaculum A Z +g__Ruminococcaceae UCG-005 A Z +g__Dyadobacter A Z +g__Nitrosomonas A Z +g__Tetrasphaera A Z +g__Desulforegula A Z +g__Rummeliibacillus A Z +g__ A Z +g__Fusicatenibacter A Z +g__Ruminiclostridium 1 A Z +g__uncultured A Z +g__Brooklawnia A Z +g__Sulfuritalea A Z +g__Lactobacillus A Z +g__Flavobacterium A Z +g__Acidicaldus A Z +g__Candidatus Defluviifilum A Z +g__Ruminococcaceae UCG-010 A Z +g__SBR2113 A Z +g__Subdoligranulum A Z +g__Ramlibacter B Z +g__Bosea B Z +g__Desulfobulbus B Z +g__Nocardioides B Z +g__Fusibacter B Z +g__SM1F10 B Z +g__Hyphomicrobium B Z +g__Meiothermus B Z +g__Trichococcus B Y +g__oca15 B Y +g__Simplicispira B Y +g__Sandaracinus B Y +g__OM27 clade B Y +g__Collinsella B Y +g__MNG7 B Y +g__Roseomonas B Y +g__Pirellula B Y +g__Clostridium sensu stricto 1 B Y +g__Acetoanaerobium B Y +g__Nitrospira B Y +g__Propioniciclava B Y +g__Parabacteroides C Y +g__Actinomyces C Y +g__Aeromicrobium C Y +g__Clostridium sensu stricto 6 C Y +g__Reyranella C Y +g__Proteiniclasticum C Y +g__B1-K1A-105 C Y +g__Prevotellaceae UCG-004 C Y +g__Haliangium C Y +g__Ureibacillus C Y +g__Ruminococcus 2 C Y +g__CYCU-0281 C Y +g__Parafilimonas C Y +g__Aestuariimicrobium C Y +g__Diaminobutyricimonas C Y +g__K2-78 C Y +g__Erysipelatoclostridium C Y +g__CL500-29 marine group C Y +g__Bacteroides C Y +g__Tessaracoccus C Y +g__Gordonia C Y +g__Senegalimassilia C Y +g__Atopobium C Y +g__Proteiniphilum C Y +g__Uliginosibacterium C Y +g__WCHB1-50 C Y +g__Christensenellaceae R-7 group C X +g__Fodinibacter C X +g__Defluviicoccus C X +g__Acidovorax C X +g__Salana C X +g__Propionimicrobium C X +g__Litorilinea C X +g__Faecalitalea C X +g__Ruminiclostridium 5 C X +g__Rivicola C X +g__[Eubacterium] coprostanoligenes group C X +g__Lewinella C X |
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| @@ -0,0 +1,11 @@ +"Aalborg East 2006" "Aalborg East 2007" "Aalborg East 2008" "Aalborg East 2009" "Aalborg East 2010" "Aalborg East 2011" "Aalborg East 2012" "Aalborg East 2013" "Aalborg East 2014" "Aalborg East 2015" "Aalborg West 2006" "Aalborg West 2007" "Aalborg West 2008" "Aalborg West 2009" "Aalborg West 2010" "Aalborg West 2011" "Aalborg West 2012" "Aalborg West 2013" "Aalborg West 2014" "Aalborg West 2015" +"Proteobacteria" 38.1319941850736 35.9175566196596 35.3239223028173 34.9909501829368 36.3283102328281 38.9915608421962 53.8529383953324 51.3460117968074 72.8722023985104 57.4344068148402 54.2087542087542 36.4326282804544 38.4757369086407 38.3005233882427 37.9516676472635 40.6258026017424 38.6472843550883 44.6513837857578 60.526398421492 45.2994925859604 +"Actinobacteria" 16.1262929321795 18.8003924243249 19.7958105485988 12.3985441180767 11.9508628506455 11.9822773321894 12.658277703168 9.86692802463733 4.41749530915451 5.99609488982366 17.8451178451178 30.1393785089437 27.2165206926683 27.0923034080929 28.0991209423852 18.3670127700203 20.8878481743068 14.4816058069532 5.78450375894784 6.93249190968154 +"Chloroflexi" 18.3131199353417 13.271226587611 18.1723687926502 29.7622211645584 27.2162188095204 27.4083281864652 13.3425292037346 12.0421436922346 2.84378751176108 1.05381359276388 5.72390572390572 9.29625277451364 13.2781161639047 9.09181786374769 8.90144026478223 13.2039431913116 11.6630983081279 10.2302102712301 9.44167249733746 12.9289629664804 +"Bacteroidetes" 15.238944647955 17.0944898458844 4.80841552255416 6.79789110506974 7.21184338673076 12.2970476460921 12.0216954506151 19.8089694348484 15.1180034568227 26.7842680520852 10.4377104377104 7.90899595247421 4.19318035043356 6.73335761055059 5.58986985476623 11.2276978159685 11.4612545797781 15.2032565168297 14.8111317970807 21.1241394277011 +"Firmicutes" 6.65926307960792 8.08826902584616 13.5323428478027 11.135420901698 12.2381391019829 5.3065353223222 4.15566119372564 5.39379512409247 2.50275820445282 2.65696422748934 6.73400673400673 7.45201723462593 6.59801488988521 10.8497740076687 7.68965190921149 4.23883518319609 4.98282022116985 5.50491710923881 2.78564846131452 2.80406275115902 +"Acidobacteria" 1.84522886779123 3.19309844412278 0.579562724509533 1.22263018757176 1.22019363164889 1.8556042232708 2.61733996209427 0.818911905713214 1.77946201792775 4.74365552197578 3.03030303030303 3.46814205509858 2.58723846405261 4.34169469257189 7.1137753294489 6.57976369495166 6.87742567426134 6.0700195803001 4.28737081122707 9.42431811091215 +"Planctomycetes" 0.746563781302169 0.25464448503398 0.987168692856751 0.411589894060679 0.492479742080341 0.564736695897598 0.0730994152046784 0.152535023867842 0.0235849056603774 0.0250752256770311 1.34680134680135 3.09766288027158 4.52112645443821 1.78687459389214 2.47741727664007 2.23035684449218 1.84033791082559 1.3257701894156 1.01973806934665 0.584070896715898 +"Deinococcus-Thermus" 1.45963179413928 1.00870720718181 5.11548610677814 1.03259577383117 0.684345869495339 0.424454945159917 0.0955583622050142 0 0.0474171268233897 0.685625086716673 0 0 0 0 0 0 0 0 0 0 +"Hydrogenedentes" 0.134770889487871 0.244052637669659 0.152267354395014 0.155400155400155 0.199004975124378 0.308893572463899 0.402906470230555 0.0861326442721792 0.0747487181080226 0.185094894105122 0 0.120772946859903 0.4920049200492 0.562660211783019 0.404258953481751 0.500747105859888 1.36061070732636 0.873921616081284 0.298532298518384 0.373761440277151 +"WCHB1-60" 0.789762842230565 0.41040519763924 0.129960317460317 0.0556483027267668 0.136612021857924 0 0.0730994152046784 0 0 0 0 0.233385559472516 0.879805929046964 0.21706688373355 0.836894586894587 1.25864184270199 1.14445526079798 0.629254175715777 0.0949491695303551 0.148135364082208 |
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| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs-timeseries-group.pdf |
| b |
| Binary file test-data/AalborgWWTPs-timeseries-group.pdf has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs-timeseries-tax.pdf |
| b |
| Binary file test-data/AalborgWWTPs-timeseries-tax.pdf has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs-timeseries.pdf |
| b |
| Binary file test-data/AalborgWWTPs-timeseries.pdf has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs-venn-group.pdf |
| b |
| Binary file test-data/AalborgWWTPs-venn-group.pdf has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs-venn.pdf |
| b |
| Binary file test-data/AalborgWWTPs-venn.pdf has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.fa Mon Apr 04 10:18:21 2022 +0000 |
| b |
| b'@@ -0,0 +1,1879 @@\n+>OTU_8735\n+gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc gatggcgtac taatggaaga\n+agcttcggca gaaaaccggt gtacgccaga gcggcggatg ggtgagtaac gcgtggacaa\n+cctgccctgc actgggggat aacagctgga aacggctgtt aataccgcat atgcgcacga\n+tgccgcatgg cagagggcgg aaagatttat cggtgcagga tgggtccgcg tcggattagc\n+cagttggcgg ggtaacggcc caccaaagcg atgatccgta gccggcctga gagggcgatc\n+ggccacattg ggactgagac acggcccaaa ctcctacggg aggcagcagt gggggatatt\n+gcacaatggg ggaaaccctg atgcagcgac gccgcgtgag cgatgaagtg cttcggcatg\n+taaagctcta tcagcgggga agaagatgac ggtacccgac taagaagccc cggctaacta\n+cgtg\n+>OTU_13382\n+gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac ggacgaggcc ccttcgggga\n+ccgagttagt ggcgaacggg tgagtaacgc gtgagcaacc tgcctttcag tgggggacaa\n+cagttggaaa cgactgctaa taccgcataa aactctaaga ggacatcctc agtgagtcaa\n+agatttattg ctgaaagatg ggctcgcgtc tgattagcta gttggcgggg taacggccca\n+ccaaggcgac gatcagtagc cggactgaga ggttgaacgg ccacattggg actgagatac\n+ggcccagact cctacgggag gcagcagtgg ggaatattgg gcaatggggg aaaccctgac\n+ccagcaacgc cgcgtgaagg aagaaggctt tcgggttgta aacttctttt accagggacg\n+aaggacgtga cggtacctgg agaaaaagcc acggctaact acgtg\n+>OTU_5516\n+gatgaacgct agcggcaggc ttaatacatg caaggcgagg gggcatttcg gtgtcaccgt\n+cgtacgggtg cgtaacgcgt atgcaaccta cctttaactg ggggatagcc cggggaaacc\n+cggattaata ccgcatgaca ctgtgatttc acctgagatt ataagttaaa gatttatcgg\n+ttaaagatgg gcatgcgttc gattagctag ttggcggggt aatggcccac caaggcgacg\n+atcgataggg gagctgagag gttgatcccc cacacgggca ctgagatacg ggcccgactc\n+ctacgggagg cagcagtagg gaatattggg caatggatgc aagtctgacc cagccatgcc\n+gcgtgccgga cgaaggccct cagggttgta aacggctttt attcgggaag aagagcaggg\n+atgcgtcctt gtgtgacggt accgaatgaa taagcaccgg ctaactccgt g\n+>OTU_8315\n+attgaacgct ggcggcatgc tttacacatg caagtcgaac ggcagcacga gtgcttgcac\n+ttggtggcga gtggcggacg ggtgagtaat acatcggaac gtatcctaaa gtgggggata\n+acgcatcgaa agatgtgcta ataccgcata tactctgagg aggaaagtag gggatcgaaa\n+gaccttatgc ttttggagcg gccgatgtct gattagctag ttggtaaggt aatggcttac\n+caaggcaacg atcagtagtt ggtctgagag gacgaccagc cacactggga ctgagacacg\n+gcccagactc ctacgggagg cagcagtggg gaattttgga caatgggcgc aagcctgatc\n+cagcaatgcc gcgtgagtga agaaggcctt cgggttgtaa agctctttca gttgagaaga\n+aaagattgta actaataatt gcgatccann acngnatcaa canannannc accnnctaac\n+tacgtg\n+>OTU_10522\n+gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtgacgagg agcttgctcc\n+tctgatcagt ggcgaacggg tgagtaacac gtgagtaacc tgccccagac tctgggataa\n+cagttggaaa cagctgctaa taccggatac gagacggaga ggcatctcta ccgtctggaa\n+agtttttcgg tctgggatgg actcgcggcc tatcagcttg ttggtgaggt aatggctcac\n+caaggcgacg acgggtagcc ggcctgagag ggcgaccggc cacactggga ctgagacacg\n+gcccagactc ctacgggagg cagcagtggg gaatattgca caatgggcgc aagcctgatg\n+cagcgacgcc gcgtgaggga tgacggcctt cgggttgtaa accgctttcg acagggaaga\n+aaatgacggt acctgtagaa gaagccccgg ccaactacgt g\n+>OTU_11040\n+attgaacgct ggcggcatgc ctaacacatg caagtcgaac ggcagcgcgg gtagcaatac\n+ctggcggcga gtggcggacg ggtgagtaat gcatcgggat ctacccagac gtgggggata\n+acgtagggaa acttacgcta ataccgcata cgtcctacgg gagaaagcgg gggctcgcaa\n+gacctcgcgc ggttggacga accgatgtgc gattagctag ttggtggggt aatggcccac\n+caaggcgacg atcgctagct ggtctgagag gatgatcagc cacactggga ctgagacacg\n+gcccagactc ctacgggagg cagcagtggg gaatattgga caatgggcgc aagcctgatc\n+cagcaatgcc gcgtgtgtga agaaggcctt cgggttgtaa agcactttta tcaggagcga\n+aatgccattg gttaataccc ggtggagctg acggtacctg aggaataagc accggctaac\n+ttcgtg\n+>OTU_7263\n+aatgaacgct ggcggcgtgc ttaacacatg caagtcgtac gcgaaaggcg ctttcgggtg\n+ctgagtagag tggcgcacgg gtgagtaacg cgtgggtaat ctacccttgg atcttggata\n+acacatcgaa aggtgtgcta atacgggatg aagtctgcgg agatgcgttt ttgcagatga\n+aaggccgcgc aagcggttgt ccgaggatga gcctgcgtcc cattagctag ttggcggggt\n+aaaggcccac caaggctgag atgggtagct ggtctgagag gatgatcagc cacactggaa\n+ctggaacacg gtccagactc ctacgggagg cagcagtgag gaattttgcg caatggggga\n+aaccctgacg cagcaacgcc gcgtgagtga tgaaggcctt cgggtcgtaa agctctgtcg\n+agtgggaaga aaccgttcag attaataacc tgaaccttga cggtaccact aaaggaagca\n+ccggctaact ccgtg\n+>OTU_13379\n+gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc gcatgacgag gagcttgctc\n+ctctgattga gcggcggacg ggtgagtaac acgtgggcaa cctgccctgt agacggggat\n+aacttc'..b'agata gttggcgggg taacggccca\n+ccaagtctgc gatcggtagc cggactgaga ggtcgaacgg ccacattggg actgagatac\n+ggcccagact cctacgggag gcagcagtgg ggaatattgg gcaatgggcg aaagcctgac\n+ccagcaacgc cgcgtgaagg atgaaggttt tcggattgta aacttctttg accaaggacg\n+ataatgacgg tacttggaaa acaagccacg gctaactacg tg\n+>OTU_14173\n+gatgaacgct agctacaggc ttaacacatg caagtcgcgg ggcagcatag ggtttcagca\n+atgaaattcg gatggcgacc ggcgcacggg tgagtaacac gtatccaacc tgccctttac\n+tcggggatag ccttgcgaaa gtaagattaa tacccgatgg cattggattt ccgcatgggg\n+attcaattaa aggtgaaaat tggtaaagga tggggatgcg ttccattagg cagtaggcgg\n+ggtaacggcc cacctaaccg acgatggata ggggttctga gaggaaggtc ccccacattg\n+gaactgagac acggtccaaa ctcctacggg aggcagcagt gaggaatatt ggtcaatggg\n+cgcgagcctg aaccagccaa gtagcgtgaa ggatgactgc cctatgggtt gtaaacttct\n+tttatacggg aataaagtca cttacgtgta agtgtttgta tgtaccttat gaataagcat\n+cggctaactc cgtg\n+>OTU_10746\n+gatgaacgct ggcggcgtgc ctaacacatg caagtcgtac gaaaaagaaa tttttagtgg\n+caaacgggtg agtaacgcgt gagaatttac tcttatggta gaggataact tttagaaata\n+ttagctaaaa ctctatatgc ttttaataag tgaaaaaaga aatttgccta agaaaaagct\n+cgcgtctgat tagctagttg gtagggtaaa ggcctaccaa ggcgatgatc agtagctggt\n+ctgagaggat gatcagccac actggaactg agacacggtc cagactccta cgggaggcag\n+cagtgaggaa ttttctgcaa tgggcgaaag cctgacagag caacgccgcg tgagggaaga\n+aggccttcgg gttgtaaacc tcttttctca aggaggaaga tctgacgtta cttgaggaat\n+aagcatcggc taaccctgtg\n+>OTU_284\n+gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac gtgagggtgc agcgatgtgc\n+ctgaaagtgg cgaacgggtg agtaacacgt aggtgacctg ccctgaagtg ggggataacc\n+actggaaacg gtggctaata ccgcatgagc cttgctgggt gggaatttag caagggaaag\n+ctttagtgct tcaggagggg cctgcgtccg attagctagt tggtggggta aaggcctacc\n+aaggcgatga tcggtagctg gtctgagagg atgatcagcc acacgggaac tgagaaacgg\n+tcccgactcc tacggggggc agcagtgagg aatattgctc aatgggcgaa agcctgaagc\n+agcaacgccg cgtggaggaa gaaggtcttc ggattgtaaa ctccttttct tagggacgag\n+gaaggacggt acctgaggaa taagtcacgg ctaactacgt g\n+>OTU_5049\n+gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtaacgggt ccttcgggat\n+gccgacgagt ggcggacggc tgagtaacgc gtgggaacgt gccccaaagt gagggataac\n+tactcgaaag agtagctaat accgcatatg atcttcggat taaagtattt atacgctttg\n+ggagcggcct gcgtcggatt agatagttgg tgaggtaacg gctcaccaag tcgacgatcc\n+gtagctggtc tgagaggatg accagccaga ctggaactga gacacggtcc agactcctac\n+gggaggcagc agtgaggaat cttccacaat gggcgaaagc ctgatggagc aacgccgcgt\n+gcaggatgaa ggccttcggg ttgtaaactg cttttattag tgaggaatat gacggtaact\n+aatgaataag ggtcggctaa ctacgtg\n+>OTU_2397\n+gatgaacgct ggcggcgtgc ctaatacatg caagtcgaac gcgaagcctg gtttcgactg\n+ggtggagagt ggcggacggg tgagtaacac atggctgacc tgcccttcag agggggacaa\n+ctgctggaaa cggcagctaa taccccatac gctcgtggtg gttaggggac cacgaggaaa\n+ggctgaggtg ctgagggagg gggctgtggc ccatcagcta gttggtaggg taatggccta\n+ccaaggcgag gacgggtagg gggcctgaga gggtgacccc ccacactgga actgagagac\n+ggtccagact cctacgggag gcagcagtaa gggatattgc gacaatgggc gagagcctga\n+cgcagcaacg ccgcgtgcgg gaggaaggcc ttcgggttgt aaaccgcttt tgagggggaa\n+gaggaaggac ggtacccttc gaataagtct cggctaacta cgtg\n+>OTU_2913\n+aacgaacgtt ggcggcgtgg attaggcatg caagtcgcac gaatcccatt tgggtaactg\n+agtgggggaa gtggcgaaag gggcagtaag gcatgggtaa cttgccctgg agtccggaat\n+agccatccta acggatgggt aataccggat gtcgtacctg gagggcctcc ttcgggtacg\n+aaagttcagg cgctccggga ggggcccatg tagtattagc tagttggtga ggtaacggct\n+caccaaggcc aagatgctta gcaggtgtga gagcacgacc tgcgccactg gcactgggac\n+actggccaga ctcctacggg aggctgcagt cgaggatctt cggcaatggg cgcaagcctg\n+accgagcgac gccgcgtgtg cgatgaaggc cttcgggttg taaagcactg tcggggggga\n+gaaaagccgc aaggcttgat cgacccccgg aggaagcacg ggctaagttc gtg\n+>OTU_9512\n+gatgaacgct agcggcaggc ttaacacatg caagttgcgg ggcagcagta cttcggtagc\n+tggcgaccgg cgcacgggtg cgtaacgcgt atgcaaccta ccctttacag ggggatagcc\n+cgaggaaact cggattaata ccccatagtt tggatttttc gcatggaaga tttaataaag\n+ttctggcggt aaaggatggg catgcgtgac attagctagt tggagaggta acggctcacc\n+aaggctacga tgtctagggg tcctgagagg gaaaaccccc acactggtac tgagacacgg\n+accagactcc tacgggaggc agcagtgagg aatattggtc aatgggcgca agcctgaacc\n+agccatgccg cgtgcaggaa gacggcccta tgggttgtaa actgctttta tataggaaga\n+attatattac gtgtaataag ttgacagtac tatatgaata agcaccggct aactccgtg\n' |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.nwk Mon Apr 04 10:18:21 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ 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|
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs.otu.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.otu.csv Mon Apr 04 10:18:21 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs.otu.csv-wtax --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.otu.csv-wtax Mon Apr 04 10:18:21 2022 +0000 |
| b |
| b'@@ -0,0 +1,201 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I\n+OTU_6237\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Verrucomicrobia\tc__OPB35 soil group\to__\tf__\tg__\ts__\n+OTU_8887\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\tk__Bacteria\tp__Tenericutes\tc__Mollicutes\to__Mollicutes 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| [ |
| b'@@ -0,0 +1,201 @@\n+Kingdom\tPhylum\tClass\tOrder\tFamily\tGenus\tSpecies\tOTU\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnospiraceae\tg__Acetitomaculum\ts__\tOTU_8735\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminococcaceae UCG-005\ts__\tOTU_13382\n+k__Bacteria\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Cytophagaceae\tg__Dyadobacter\ts__\tOTU_5516\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Nitrosomonadales\tf__Nitrosomonadaceae\tg__Nitrosomonas\ts__\tOTU_8315\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Intrasporangiaceae\tg__Tetrasphaera\ts__\tOTU_10522\n+k__Bacteria\tp__Proteobacteria\tc__Gammaproteobacteria\to__Xanthomonadales\tf__Xanthomonadaceae\t\t\tOTU_11040\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Desulfobacterales\tf__Desulfobacteraceae\tg__Desulforegula\ts__\tOTU_7263\n+k__Bacteria\tp__Firmicutes\tc__Bacilli\to__Bacillales\tf__Planococcaceae\tg__Rummeliibacillus\ts__\tOTU_13379\n+k__Bacteria\tp__Hydrogenedentes\tc__\to__\tf__\tg__\ts__\tOTU_1418\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnospiraceae\tg__Fusicatenibacter\ts__\tOTU_556\n+k__Bacteria\tp__Parcubacteria\tc__\to__\tf__\tg__\ts__\tOTU_6869\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminiclostridium 1\ts__\tOTU_10171\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Dermatophilaceae\tg__uncultured\ts__\tOTU_2830\n+k__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__AKYH767\tg__\ts__\tOTU_4232\n+k__Bacteria\tp__Planctomycetes\tc__Planctomycetacia\to__Planctomycetales\tf__Planctomycetaceae\t\t\tOTU_12831\n+k__Bacteria\tp__Acidobacteria\tc__Holophagae\to__Holophagales\tf__Holophagaceae\t\t\tOTU_613\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Propionibacteriales\tf__Propionibacteriaceae\tg__Brooklawnia\ts__\tOTU_3625\n+k__Bacteria\tp__Chloroflexi\tc__Chloroflexia\to__Chloroflexales\tf__Roseiflexaceae\tg__\ts__\tOTU_3605\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__PeM15\tf__PeM15\tg__\ts__\tOTU_11148\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\tOTU_656\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Rhodocyclales\tf__Rhodocyclaceae\tg__Sulfuritalea\ts__\tOTU_4382\n+k__Bacteria\t\t\t\t\t\t\tOTU_3834\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\t\t\t\tOTU_13127\n+k__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\t\t\t\tOTU_4528\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Myxococcales\tf__Blfdi19\tg__\ts__\tOTU_4485\n+k__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Lactobacillaceae\tg__Lactobacillus\ts__\tOTU_12265\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\tOTU_11820\n+k__Bacteria\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\tOTU_4093\n+k__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Flavobacteriaceae\tg__Flavobacterium\ts__\tOTU_8360\n+k__Bacteria\tp__Firmicutes\tc__Negativicutes\to__Selenomonadales\tf__Veillonellaceae\t\t\tOTU_15123\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Desulfobacterales\tf__Desulfobacteraceae\t\t\tOTU_11928\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Acetobacteraceae\tg__Acidicaldus\ts__\tOTU_11334\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Myxococcales\tf__mle1-27\tg__\ts__\tOTU_4511\n+k__Bacteria\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\tOTU_3265\n+k__Bacteria\tp__Actinobacteria\t\t\t\t\t\tOTU_2991\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__Candidatus Defluviifilum\ts__\tOTU_522\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Nitrosomonadales\tf__Nitrosomonadaceae\tg__Nitrosomonas\ts__\tOTU_11832\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminococcaceae UCG-010\ts__\tOTU_6358\n+k__Bacteria\tp__Saccharibacteria\tc__Unknown Class\to__Unknown Order\tf__SBR2060\tg__SBR2113\ts__\tOTU_3611\n+k'..b'\to__Clostridiales\tf__Christensenellaceae\tg__Christensenellaceae R-7 group\ts__\tOTU_8245\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\tOTU_10847\n+k__Bacteria\tp__Acidobacteria\tc__Holophagae\to__Holophagales\tf__Holophagaceae\t\t\tOTU_1151\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Intrasporangiaceae\tg__Fodinibacter\ts__\tOTU_1998\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Rhodospirillaceae\tg__Defluviicoccus\ts__cluster I\tOTU_10321\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Burkholderiales\tf__Comamonadaceae\tg__Acidovorax\ts__\tOTU_4721\n+k__Bacteria\tp__Verrucomicrobia\tc__OPB35 soil group\to__\tf__\tg__\ts__\tOTU_6237\n+k__Bacteria\tp__Saccharibacteria\tc__Unknown Class\to__FW73\t\t\t\tOTU_1972\n+k__Bacteria\tp__Elusimicrobia\tc__Elusimicrobia\to__Lineage IIb\tf__\tg__\ts__\tOTU_11364\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Beutenbergiaceae\tg__Salana\ts__\tOTU_1816\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Propionibacteriales\tf__Propionibacteriaceae\tg__Propionimicrobium\ts__\tOTU_14842\n+k__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Leptotrichiaceae\tg__uncultured\ts__\tOTU_6533\n+k__Bacteria\tp__Tenericutes\tc__Mollicutes\to__Mollicutes RF9\tf__\tg__\ts__\tOTU_8887\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__Litorilinea\ts__\tOTU_12690\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Clostridiaceae 1\tg__Proteiniclasticum\ts__\tOTU_3097\n+k__Bacteria\tp__Firmicutes\tc__Erysipelotrichia\to__Erysipelotrichales\tf__Erysipelotrichaceae\tg__Faecalitalea\ts__\tOTU_3257\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Acetobacteraceae\tg__uncultured\ts__\tOTU_3161\n+k__Bacteria\tp__Actinobacteria\tc__Thermoleophilia\to__Solirubrobacterales\tf__480-2\tg__\ts__\tOTU_11903\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminiclostridium 5\ts__\tOTU_7508\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Oligoflexales\tf__\tg__\ts__\tOTU_10969\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Oligoflexales\tf__Oligoflexaceae\tg__\ts__\tOTU_1801\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Neisseriales\tf__Neisseriaceae\tg__Rivicola\ts__\tOTU_3488\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__GR-WP33-30\tf__\tg__\ts__\tOTU_933\n+k__Bacteria\tp__Lentisphaerae\tc__PBS-III-20\to__\tf__\tg__\ts__\tOTU_3824\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rickettsiales\tf__AKIW1012\tg__\ts__\tOTU_777\n+k__Bacteria\tp__TM6\tc__\to__\tf__\tg__\ts__\tOTU_3169\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__[Eubacterium] coprostanoligenes group\ts__\tOTU_12385\n+k__Bacteria\tp__Armatimonadetes\tc__\to__\tf__\tg__\ts__\tOTU_1496\n+k__Bacteria\tp__Actinobacteria\tc__Acidimicrobiia\to__Acidimicrobiales\tf__Microthricaceae\tg__\ts__\tOTU_11294\n+k__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Saprospiraceae\tg__Lewinella\ts__\tOTU_1968\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rickettsiales\t\t\t\tOTU_8832\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\t\t\t\t\tOTU_8652\n+k__Bacteria\tp__Chlorobi\tc__Chlorobia\to__Chlorobiales\tf__OPB56\tg__\ts__\tOTU_13621\n+k__Bacteria\tp__Microgenomates\tc__\to__\tf__\tg__\ts__\tOTU_3043\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\tOTU_10760\n+k__Bacteria\tp__Bacteroidetes\tc__Bacteroidia\to__Bacteroidales\tf__Bacteroidaceae\tg__Bacteroides\ts__\tOTU_14173\n+k__Bacteria\tp__Cyanobacteria\tc__Chloroplast\to__\tf__\tg__\ts__\tOTU_10746\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\tOTU_284\n+k__Bacteria\tp__Saccharibacteria\tc__\to__\tf__\tg__\ts__\tOTU_5049\n+k__Bacteria\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\tOTU_2397\n+k__Bacteria\tp__Planctomycetes\tc__Planctomycetacia\to__Planctomycetales\tf__Planctomycetaceae\tg__uncultured\ts__\tOTU_2913\n+k__Bacteria\tp__Bacteroidetes\t\t\t\t\t\tOTU_9512\n' |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/AalborgWWTPs.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.tsv Mon Apr 04 10:18:21 2022 +0000 |
| b |
| @@ -0,0 +1,68 @@ +SampleID 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 +16S-AMP-1149 16S-AMP-1149 Aalborg East 2013-10-28 2013 Fall +16SAMP-537 16SAMP-537 Aalborg West 2010-08-19 2010 Summer +16S-AMP-1114 16S-AMP-1114 Aalborg West 2013-02-04 2013 Winter +16SAMP-3893 16SAMP-3893 Aalborg East 2014-02-06 2014 Winter +16SAMP-703 16SAMP-703 Aalborg East 2006-02-04 2006 Winter +16SAMP-638 16SAMP-638 Aalborg East 2012-10-28 2012 Fall +16SAMP-2611 16SAMP-2611 Aalborg East 2011-02-04 2011 Winter +16S-AMP-1100 16S-AMP-1100 Aalborg West 2012-08-19 2012 Summer +16SAMP-608 16SAMP-608 Aalborg East 2011-10-28 2011 Fall +16SAMP-636 16SAMP-636 Aalborg East 2012-05-06 2012 Spring +16SAMP-13288 16SAMP-13288 Aalborg West 2015-02-09 2015 Winter +16SAMP-719 16SAMP-719 Aalborg East 2007-08-19 2007 Summer +16S-AMP-1098 16S-AMP-1098 Aalborg West 2012-02-04 2012 Winter +16SAMP-536 16SAMP-536 Aalborg West 2010-05-06 2010 Spring +16S-AMP-1169 16S-AMP-1169 Aalborg West 2013-08-19 2013 Summer +16SAMP-635 16SAMP-635 Aalborg East 2012-02-04 2012 Winter +16SAMP-637 16SAMP-637 Aalborg East 2012-08-19 2012 Summer +16SAMP-717 16SAMP-717 Aalborg East 2007-02-04 2007 Winter +16S-AMP-1148 16S-AMP-1148 Aalborg East 2013-08-19 2013 Summer +16SAMP-735 16SAMP-735 Aalborg West 2008-05-06 2008 Spring +16SAMP-729 16SAMP-729 Aalborg East 2008-08-19 2008 Summer +16SAMP-738 16SAMP-738 Aalborg East 2009-02-04 2009 Winter +16SAMP-2613 16SAMP-2613 Aalborg West 2011-08-19 2011 Summer +16SAMP-10925 16SAMP-10925 Aalborg East 2015-10-27 2015 Fall +16SAMP-3913 16SAMP-3913 Aalborg East 2014-07-03 2014 Summer +16SAMP-716 16SAMP-716 Aalborg West 2006-02-04 2006 Winter +16SAMP-726 16SAMP-726 Aalborg West 2007-08-19 2007 Summer +16SAMP-728 16SAMP-728 Aalborg East 2008-05-06 2008 Spring +16SAMP-625 16SAMP-625 Aalborg West 2011-02-04 2011 Winter +16SAMP-736 16SAMP-736 Aalborg West 2008-08-19 2008 Summer +16SAMP-13281 16SAMP-13281 Aalborg East 2015-02-10 2015 Winter +16SAMP-626 16SAMP-626 Aalborg West 2011-10-28 2011 Fall +16SAMP-704 16SAMP-704 Aalborg East 2006-05-06 2006 Spring +16SAMP-2612 16SAMP-2612 Aalborg East 2011-08-19 2011 Summer +16SAMP-746 16SAMP-746 Aalborg West 2009-05-06 2009 Spring +16SAMP-522 16SAMP-522 Aalborg East 2010-10-28 2010 Fall +16SAMP-516 16SAMP-516 Aalborg West 2009-10-28 2009 Fall +16S-AMP-1170 16S-AMP-1170 Aalborg West 2013-10-28 2013 Fall +16S-AMP-1099 16S-AMP-1099 Aalborg West 2012-05-06 2012 Spring +16SAMP-10932 16SAMP-10932 Aalborg West 2015-10-27 2015 Fall +16SAMP-740 16SAMP-740 Aalborg East 2009-10-28 2009 Fall +16SAMP-739 16SAMP-739 Aalborg East 2009-05-06 2009 Spring +16SAMP-4597 16SAMP-4597 Aalborg West 2014-05-05 2014 Spring +16SAMP-535 16SAMP-535 Aalborg West 2010-02-04 2010 Winter +16SAMP-3941 16SAMP-3941 Aalborg West 2014-08-18 2014 Summer +16SAMP-3953 16SAMP-3953 Aalborg West 2014-11-12 2014 Fall +16SAMP-720 16SAMP-720 Aalborg East 2007-10-28 2007 Fall +16SAMP-705 16SAMP-705 Aalborg East 2006-08-19 2006 Summer +16SAMP-10907 16SAMP-10907 Aalborg East 2015-08-24 2015 Summer +16SAMP-538 16SAMP-538 Aalborg West 2010-10-28 2010 Fall +16SAMP-10911 16SAMP-10911 Aalborg West 2015-08-24 2015 Summer +16SAMP-737 16SAMP-737 Aalborg West 2008-10-28 2008 Fall +16SAMP-4591 16SAMP-4591 Aalborg West 2014-02-04 2014 Winter +16SAMP-745 16SAMP-745 Aalborg West 2009-02-04 2009 Winter +16SAMP-706 16SAMP-706 Aalborg East 2006-10-28 2006 Fall +16SAMP-3946 16SAMP-3946 Aalborg East 2014-11-13 2014 Fall +16S-AMP-1101 16S-AMP-1101 Aalborg West 2012-10-28 2012 Fall +16SAMP-10896 16SAMP-10896 Aalborg West 2015-05-04 2015 Spring +16SAMP-10891 16SAMP-10891 Aalborg East 2015-05-04 2015 Spring +16SAMP-748 16SAMP-748 Aalborg East 2010-05-06 2010 Spring +16SAMP-725 16SAMP-725 Aalborg West 2007-02-04 2007 Winter +16SAMP-730 16SAMP-730 Aalborg East 2008-10-28 2008 Fall +16S-AMP-1107 16S-AMP-1107 Aalborg East 2013-05-06 2013 Spring +16SAMP-727 16SAMP-727 Aalborg East 2008-02-04 2008 Winter |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/generate.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generate.R Mon Apr 04 10:18:21 2022 +0000 |
| b |
| @@ -0,0 +1,10 @@ +library(ampvis2) + +# subset taxa using 200 random OTUs +aalborgwwtps <- amp_subset_taxa(AalborgWWTPs, tax_vector = sample(AalborgWWTPs$tax$OTU, 200)) + +ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk") +amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F) +amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu") +write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F) +write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t") |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/generate.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generate.sh Mon Apr 04 10:18:21 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ + +Rscript generate.R + +sed -i -e 's/"//g' AalborgWWTPs.tax + |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/min_sparse_otu_table_hdf5.biom |
| b |
| Binary file test-data/min_sparse_otu_table_hdf5.biom has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/min_sparse_otu_table_hdf5.rds |
| b |
| Binary file test-data/min_sparse_otu_table_hdf5.rds has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/rich-dense.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rich-dense.biom Mon Apr 04 10:18:21 2022 +0000 |
| [ |
| @@ -0,0 +1,55 @@ +{ + "id":null, + "format": "Biological Observation Matrix 0.9.1-dev", + "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "type": "OTU table", + "generated_by": "QIIME revision 1.4.0-dev", + "date": "2011-12-19T19:00:00", + "rows":[ + {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, + {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, + {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}}, + {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}}, + {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}} + ], + "columns":[ + {"id":"Sample1", "metadata":{ + "BarcodeSequence":"CGCTTATCGAGA", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample2", "metadata":{ + "BarcodeSequence":"CATACCAGTAGC", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample3", "metadata":{ + "BarcodeSequence":"CTCTCTACCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample4", "metadata":{ + "BarcodeSequence":"CTCTCGGCCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample5", "metadata":{ + "BarcodeSequence":"CTCTCTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample6", "metadata":{ + "BarcodeSequence":"CTAACTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}} + ], + "matrix_type": "dense", + "matrix_element_type": "int", + "shape": [5,6], + "data": [[0,0,1,0,0,0], + [5,1,0,2,3,1], + [0,0,1,4,2,0], + [2,1,1,0,0,1], + [0,1,1,0,0,0]] +} |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/rich-dense.rds |
| b |
| Binary file test-data/rich-dense.rds has changed |
| b |
| diff -r 000000000000 -r f77f7c426d6f test-data/rich-sparse.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rich-sparse.biom Mon Apr 04 10:18:21 2022 +0000 |
| [ |
| @@ -0,0 +1,66 @@ +{ + "id":"w00asdt", + "format": "1.0.0", + "format_url": "http://biom-format.org", + "type": "OTU table", + "generated_by": "QIIME revision XYZ", + "date": "2011-12-19T19:00:00", + "rows":[ + {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, + {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, + {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}}, + {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}}, + {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}} + ], + "columns":[ + {"id":"Sample1", "metadata":{ + "BarcodeSequence":"CGCTTATCGAGA", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample2", "metadata":{ + "BarcodeSequence":"CATACCAGTAGC", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample3", "metadata":{ + "BarcodeSequence":"CTCTCTACCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample4", "metadata":{ + "BarcodeSequence":"CTCTCGGCCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample5", "metadata":{ + "BarcodeSequence":"CTCTCTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample6", "metadata":{ + "BarcodeSequence":"CTAACTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}} + ], + "matrix_type": "sparse", + "matrix_element_type": "int", + "shape": [5, 6], + "data":[[0,2,1], + [1,0,5], + [1,1,1], + [1,3,2], + [1,4,3], + [1,5,1], + [2,2,1], + [2,3,4], + [2,5,2], + [3,0,2], + [3,1,1], + [3,2,1], + [3,5,1], + [4,1,1], + [4,2,1] + ] + } |
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