changeset 0:0ab4501d805b draft

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
author qfabrepo
date Mon, 14 Sep 2020 07:38:57 +0000
parents
children e0225f3e8ef6
files phyloseq_richness.r phyloseq_richness.xml test-data/GP.biom test-data/biom_out.html test-data/count.txt test-data/metadata.txt test-data/observation.txt test-data/test.biom
diffstat 8 files changed, 6910 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_richness.r	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,83 @@
+library('getopt')
+suppressPackageStartupMessages(library('phyloseq'))
+Sys.setenv("DISPLAY"=":1")
+
+options(warn=-1)
+option_specification = matrix(c(
+   'biomfile','b',2,'character',
+   'metafile','m',2,'character',
+     'xcolumn','x',2,'numeric',
+     'lcolumn','l',2,'numeric',
+     'outdir','o',2,'character',
+   'htmlfile','h',2,'character'
+),byrow=TRUE,ncol=4);
+
+
+options <- getopt(option_specification);
+options(bitmapType="cairo")
+ 
+
+if (!is.null(options$outdir)) {
+  # Create the directory
+  dir.create(options$outdir,FALSE)
+}
+
+
+galaxy_biom <- import_biom(options$biomfile)
+galaxy_map <- import_qiime_sample_data(options$metafile)
+tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
+tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
+
+number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
+
+if( number.of.tax.rank == 7){
+colnames(tax_table(galaxy_biom)) <- tax_col_norm
+}else{
+colnames(tax_table(galaxy_biom)) <- tax_col_extra
+}
+
+
+AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
+
+
+x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
+l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
+
+
+
+
+pdffile <- gsub("[ ]+", "", paste(options$outdir,"/pdffile.pdf"))
+pngfile_richness <- gsub("[ ]+", "", paste(options$outdir,"/richness.png"))
+htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
+
+
+# Produce PDF file
+pdf(pdffile);
+plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn)
+garbage<-dev.off();
+
+#png('richness.png')
+bitmap(pngfile_richness,"png16m")
+plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn)
+garbage<-dev.off()
+
+# Produce the HTML file
+htmlfile_handle <- file(htmlfile)
+html_output = c('<html><body>',
+	            '<table align="center">',
+		        '<tr>',
+		        '<td valign="middle" style="vertical-align:middle;">',
+                '<a href="pdffile.pdf"><img src="richness.png"/></a>',
+		        '</td>',
+		        '</tr>',
+		        '</table>',
+	        '<table align="center>',
+		'<tr>',
+		'<td valign="middle" style="vertical-align:middle;">',
+                '<a href="pdffile.pdf"><img src="richness.png"/></a>',
+		'</td>',
+		'</tr>',
+		'</table>',
+                '</html></body>');
+writeLines(html_output, htmlfile_handle);
+close(htmlfile_handle);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_richness.xml	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,79 @@
+<tool id="phyloseq_richness" name="Phyloseq Richness" version="1.22.3.2" hidden="false">
+  <description>Phyloseq Richness Plot</description>
+     <requirements>
+	         <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
+			 <requirement type="package" version="1.20.0">r-getopt</requirement>
+			 <requirement type="package" version="9.18">ghostscript</requirement>
+	</requirements>
+	<version_command><![CDATA[
+		echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+	]]></version_command>
+  <command detect_errors="exit_code"><![CDATA[
+        Rscript '${__tool_directory__}/phyloseq_richness.r' 
+			--biomfile='$biom_input' 
+			--metafile='$metadata_input' 
+			--xcolumn="${xaxis_column}" 
+			--lcolumn="${legend_column}" 
+			--outdir="$htmlfile.files_path" 
+			--htmlfile='$htmlfile'
+  ]]></command>
+ 
+  <inputs>
+    <param format="biom1" name="biom_input" type="data" label="BIOM file"/>
+    <param format="tabular" name="metadata_input" type="data" label="Metadata file"/>
+    <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/>
+    <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/>
+  </inputs>
+ 
+  <outputs>
+        <data format="html" name="htmlfile" label="${tool.name}.html"/>
+  </outputs>
+
+ <tests>
+ 	<test>
+		<param name="biom_input" value="test.biom" ftype="biom1" />
+		<param name="metadata_input" value="metadata.txt"  />
+		<param name="xaxis_column" value="5" />
+		<param name="legend_column" value="4" />
+		<output name="htmlfile" ftype="html" file="biom_out.html" />
+	</test>
+ </tests>
+
+
+  <help>
+**What it does**
+Creates an alpha biodivesrsity abundance plot using an R package called phyloseq_.
+
+.. _phyloseq: https://joey711.github.io/phyloseq/plot_richness-examples.html
+
+-----
+
+**Input**
+
+
+- **BIOM file** - this is a BIOM_ file format
+- **Metadata file** - this is a metadata file of the experiment design
+- **Column used for X-axis** - The horizontal x-axis display on the barplot.
+- **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to.
+
+.. _BIOM: http://biom-format.org/
+
+-----
+
+=========
+Resources
+=========
+
+**Wrapper Authors**
+
+QFAB Bioinformatics (support@qfab.org)
+ 
+  </help>
+    <citations>
+	    <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
+		<citation type="doi">doi:10.1186/2047-217X-1-7</citation>
+	</citations>
+ -----
+ 
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GP.biom	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,1 @@
+{"id":{},"format":["Biological Observation Matrix 1.0.0-dev"],"format_url":["http://biom-format.org/documentation/format_versions/biom-1.0.html"],"type":["OTU table"],"generated_by":["metagenomeSeq 1.20.1"],"date":["2018-06-01 01:30:56"],"matrix_type":["dense"],"matrix_element_type":["int"],"shape":[19216,26],"rows":[{"id":["549322"],"metadata":{"taxonomy":["549322","Archaea","Crenarchaeota","Thermoprotei"]}},{"id":["522457"],"metadata":{"taxonomy":["522457","Archaea","Crenarchaeota","Thermoprotei"]}},{"id":["951"],"metadata":{"taxonomy":["951","Archaea","Crenarchaeota","Thermoprotei","Sulfolobales","Sulfolobaceae","Sulfolobus","Sulfolobusacidocaldarius"]}},{"id":["244423"],"metadata":{"taxonomy":["244423","Archaea","Crenarchaeota"]}},{"id":["586076"],"metadata":{"taxonomy":["586076","Archaea","Crenarchaeota"]}},{"id":["246140"],"metadata":{"taxonomy":["246140","Archaea","Crenarchaeota"]}},{"id":["143239"],"metadata":{"taxonomy":["143239","Archaea","Crenarchaeota"]}},{"id":["244960"],"metadata":{"taxonomy":["244960","Archaea","Crenarchaeota"]}},{"id":["255340"],"metadata":{"taxonomy":["255340","Archaea","Crenarchaeota"]}},{"id":["144887"],"metadata":{"taxonomy":["144887","Archaea","Crenarchaeota"]}},{"id":["141782"],"metadata":{"taxonomy":["141782","Archaea","Crenarchaeota"]}},{"id":["215972"],"metadata":{"taxonomy":["215972","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","SAGMA-X"]}},{"id":["31759"],"metadata":{"taxonomy":["31759","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","SAGMA-X"]}},{"id":["30678"],"metadata":{"taxonomy":["30678","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","SAGMA-X"]}},{"id":["138353"],"metadata":{"taxonomy":["138353","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["406058"],"metadata":{"taxonomy":["406058","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["30405"],"metadata":{"taxonomy":["30405","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["1126"],"metadata":{"taxonomy":["1126","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["46043"],"metadata":{"taxonomy":["46043","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["512519"],"metadata":{"taxonomy":["512519","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["554594"],"metadata":{"taxonomy":["554594","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["210741"],"metadata":{"taxonomy":["210741","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["550229"],"metadata":{"taxonomy":["550229","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["105798"],"metadata":{"taxonomy":["105798","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["183473"],"metadata":{"taxonomy":["183473","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["541313"],"metadata":{"taxonomy":["541313","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["540305"],"metadata":{"taxonomy":["540305","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["511243"],"metadata":{"taxonomy":["511243","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["568829"],"metadata":{"taxonomy":["568829","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["185612"],"metadata":{"taxonomy":["185612","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["321018"],"metadata":{"taxonomy":["321018","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["549041"],"metadata":{"taxonomy":["549041","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Cenarchaeum"]}},{"id":["153762"],"metadata":{"taxonomy":["153762","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Cenarchaeum"]}},{"id":["155789"],"metadata":{"taxonomy":["155789","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Cenarchaeum"]}},{"id":["155495"],"metadata":{"taxonomy":["155495","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Cenarchaeum","Cenarchaeumsymbiosum"]}},{"id":["1029"],"metadata":{"taxonomy":["1029","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Cenarchaeum","Cenarchaeumsymbiosum"]}},{"id":["155526"],"metadata":{"taxonomy":["155526","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Nitrosopumilus"]}},{"id":["197473"],"metadata":{"taxonomy":["197473","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Nitrosopumilus"]}},{"id":["315545"],"metadata":{"taxonomy":["315545","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Nitrosopumilus"]}},{"id":["348549"],"metadata":{"taxonomy":["348549","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Nitrosopumilus"]}},{"id":["559394"],"metadata":{"taxonomy":[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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biom_out.html	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,9 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count.txt	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,3359 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata.txt	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,19 @@
+#SampleID	dpw	time	Food	Replicate_Group
+F3D0	0	Early	None	Group1
+F3D1	1	Early	None	Group1
+F3D2	2	Early	None	Group1
+F3D3	3	Early	Cheddar	Group2
+F3D5	5	Early	Cheddar	Group2
+F3D6	6	Early	Cheddar	Group2
+F3D7	7	Early	Swiss	Group3
+F3D8	8	Early	Swiss	Group3
+F3D9	9	Early	Swiss	Group3
+F3D141	141	Late	Cheddar	Group4
+F3D142	142	Late	Cheddar	Group4
+F3D143	143	Late	Cheddar	Group4
+F3D144	144	Late	None	Group5
+F3D145	145	Late	None	Group5
+F3D146	146	Late	None	Group5
+F3D147	147	Late	Swiss	Group6
+F3D148	148	Late	Swiss	Group6
+F3D149	149	Late	Swiss	Group6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/observation.txt	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,3359 @@
+OTUID	taxonomy
+775126	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+228502	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+314713	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+314425	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+316122	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+432015	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+4374047	k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__
+344726	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+1078157	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__
+974097	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__
+323154	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+266555	k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__
+4316029	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__; s__
+317867	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+190425	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+323592	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+258628	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+277152	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+271499	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+338644	k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__
+338640	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+313804	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+344723	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+188785	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
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+338004	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+646532	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+131618	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+351343	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus
+309703	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+339092	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus
+468933	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__
+277588	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+4372373	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+4432700	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+4429481	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+4323499	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+140239	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+38755	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+104315	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+832727	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+694039	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
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+249167	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
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+194673	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+323775	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__
+270215	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+270219	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+348088	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+216429	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
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+312515	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+258340	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
+191387	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+193723	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+271784	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__
+266556	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
+162485	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+330452	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
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+315669	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+761977	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+197989	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+689204	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Enterococcaceae; g__Enterococcus; s__
+272328	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+332132	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
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+767392	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
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+133686	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+637525	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+802273	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+785748	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+792826	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+153978	k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__
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+188345	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
+307548	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+334347	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+195475	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+188495	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+785736	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+697920	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+606054	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+606678	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+798357	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+676185	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+666572	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+679698	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+655467	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+715765	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+796526	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+690948	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+256998	k__Bacteria; p__Tenericutes; c__Mollicutes; o__Anaeroplasmatales; f__Anaeroplasmataceae; g__Anaeroplasma; s__
+255940	k__Bacteria; p__Tenericutes; c__Mollicutes; o__Anaeroplasmatales; f__Anaeroplasmataceae; g__Anaeroplasma; s__
+228953	k__Bacteria; p__Tenericutes; c__Mollicutes; o__Anaeroplasmatales; f__Anaeroplasmataceae; g__Anaeroplasma; s__
+231986	k__Bacteria; p__Tenericutes; c__Mollicutes; o__Anaeroplasmatales; f__Anaeroplasmataceae; g__Anaeroplasma; s__
+132772	k__Bacteria; p__Tenericutes; c__Mollicutes; o__Anaeroplasmatales; f__Anaeroplasmataceae; g__Anaeroplasma; s__
+4390755	k__Bacteria; p__Tenericutes; c__Mollicutes; o__Anaeroplasmatales; f__Anaeroplasmataceae; g__Anaeroplasma; s__
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+794524	k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__
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+307193	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__
+183927	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
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+288344	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+212201	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+1961361	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+665761	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+131558	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+247570	k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.biom	Mon Sep 14 07:38:57 2020 +0000
@@ -0,0 +1,1 @@
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