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changeset 0:234b3e869b16 draft default tip

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"
author galaxy-australia
date Wed, 26 Oct 2022 06:54:04 +0000
parents
children
files blobtools_plot.xml blobtools_view.xml macros.xml test-data/test.blobDB.json test-data/test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.bam0.png test-data/test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.read_cov.bam0.png test-data/test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.stats.txt test-data/test.blobDB.table.txt
diffstat 6 files changed, 288 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blobtools_plot.xml	Wed Oct 26 06:54:04 2022 +0000
@@ -0,0 +1,124 @@
+<tool id="blobtools_plot" name="Blobtools plot" version="1.1" >
+    <description>Generate Blobtools plot</description>
+    <xrefs>
+        <xref type='bio.tools'>blobtools</xref>
+    </xrefs>
+    <macros>
+	  <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" /> 
+    <command><![CDATA[
+	    @SET_TMP_DIR@ &&
+	    cp $input_json input.json &&
+	    blobtools plot
+	    -i input.json 
+	    -o output 
+
+	    ]]></command>
+    <inputs>
+	    <param name="input_json" type="data" format="json" label="json File" help="Input BlobDB json file"/>
+	    <section name="adv_options" title="Advance Options" expanded="False">
+		<param argument="--notitle" type="boolean" truevalue="--notitle" falsevalue="" checked="false" label="Title" help="Do not add filename as title to plot"/>
+		<param argument="--filelabel" type="boolean" truevalue="--filelabel" falsevalue="" checked="false" label="File Label" help="Label axis based on filenames"/>
+                <param argument="--length" type="integer" value="100" label="Minimum Sequence Length" help="Minimum sequence length considered for plotting [default: 100]"/>
+                <param argument="--cindex" type="boolean" truevalue="--cindex" falsevalue="" checked="false" label="Colour" help="Colour blobs by 'c index' [default: False]"/>
+                <param argument="--nohit" type="boolean" truevalue="--nohit" falsevalue="" checked="false" label="Hide sequence" help="Hide sequences without taxonomic annotation [default: False]"/>
+	        <param argument="--noscale" type="boolean" truevalue="--noscale" falsevalue="" checked="false" label="Scale sequence" help="Do no scale sequences by length [default: False]"/>
+                <param argument="--legend" type="boolean" truevalue="--legend" falsevalue="" checked="false" label="Plot legend" help="Plot legend of bobplot in separate figure"/>
+                <param argument="--multiplot" type="boolean" truevalue="--multiplot" falsevalue="" checked="false" label="Multi-plot" help="Print blobplot for each taxonomic separately"/>
+                <param argument="--sort" type="text" value="span" label="Sort order" help="Sort order for plotting [default: span]"/>
+                <param name="taxrule" type="select" display="radio" label="Taxonomy Rule" help="Taxonomy rule for computing taxonomy: default bestsum">
+                      <option selected="true" value="bestsum">best sum</option>
+                      <option value="bestsumorder">best sum order</option>
+                </param>
+                <param name="rank" type="select" display="radio" label="Taxonomic rank">
+                          <option value="species">Species</option>
+                          <option value="genus">Genus</option>
+                          <option value="family">Family</option>
+                          <option value="order">Order</option>
+                          <option value="phylum" selected="true">Phylum</option>
+                          <option value="superkingdom">Superkingdom</option>
+                          <option value="all">All</option>
+                </param>
+                <param argument="--label" type="text" value="" label="Groups label" help="Relabel (taxonomic) groups, can be used several times."/>
+	    </section>
+    </inputs>
+    <outputs>
+
+	    <data name="coverage" format="png" from_work_dir="output*.blobplot.cov0.*" label="${tool.name} on ${on_string} : coverage"/>
+	    <data name="read_coverage" format="png" from_work_dir="output*.read_cov.cov0.*" label="${tool.name} on ${on_string} : read coverage"/>
+	    <data name="statistic" format="txt" from_work_dir="output*.stats.txt" label="${tool.name} on ${on_string} : statistics "/>
+    </outputs>
+
+    <tests>
+	 <test>
+	     <!-- #1 blobtools create -->
+            <param name="input_json" value="test.blobDB.json" ftype="json"/>
+	    <output name="coverage" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.bam0.png" ftype="png"/>
+	    <output name="read_coverage" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.read_cov.bam0.png" ftype="png"/>
+            <output name="statistic" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.stats.txt" ftype="txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+	    
+*To visualize, quality control and taxonomic partitioning of genome datasets. Blobtools plot is used to produce two coverage plot in png format and a statistic file.*
+	    
+**Input**
+	    
+- Blob file - a Blob json file. 
+
+**Parameters**
+
+- infile - BlobDB file (created with "blobtools create")
+- lib - Plot only certain covlib(s). Separated by ","
+- notitle - Do not add filename as title to plot
+- filelabel - Label axis based on filenames
+- plotgroups INT - Number of (taxonomic) groups to plot, remaining groups are placed in 'other' [default: 8]
+- length INT - Minimum sequence length considered for plotting [default: 100]
+- cindex - Colour blobs by 'c index' [default: False]
+- nohit - Hide sequences without taxonomic annotation [default: False] 
+- noscale - Do not scale sequences by length [default: False]
+- legend - Plot legend of blobplot in separate figure
+- multiplot - Multi-plot. Print blobplot for each (taxonomic) group separately
+- cumulative - Print plot after addition of each (taxonomic) group
+- sort <ORDER> - Sort order for plotting [default: span] 1) span  : plot with decreasing span 2) count : plot with decreasing count
+- hist <HIST> - Data for histograms [default: span] 1) span  : span-weighted histograms 2) count : count histograms
+- rank <RANK> - Taxonomic rank used for colouring of blobs [default: phylum] (Supported: species, genus, family, order,phylum, superkingdom)	
+- taxrule <TAXRULE> - Taxrule which has been used for computing taxonomy (Supported: bestsum, bestsumorder) [default: bestsum]
+- format FORMAT -  Figure format for plot (png, pdf, eps, jpeg,ps, svg, svgz, tiff) [default: png]
+- label GROUPS - Relabel (taxonomic) groups, can be used several times. e.g. "A=Actinobacteria,Proteobacteria
+- colours COLOURFILE - File containing colours for (taxonomic) groups. This allows having more than 9 colours.
+- exclude GROUPS - Exclude these (taxonomic) groups (also works for 'other') e.g. "Actinobacteria,Proteobacteria,other"
+- refcov <FILE> - File containing number of "total" and "mapped" reads per coverage file. (e.g.: bam0,900,100). If provided, info will be used in read coverage plot(s).
+-catcolour <FILE> - Colour plot based on categories from FILE (format : "seq category").
+
+
+**Command line Example:**
+
+- blobtools plot -i example_blobDB.json -o output_file_preifix
+
+**Output**
+
+- Coverage PNG file
+- Read Coverage PNG file
+- Statistic file
+ 
+.. class:: infomark
+	    
+**Contributor**
+
+Galaxy Australia wrapped the Blobtools: the original software is available in this `Github repository <https://github.com/DRL/blobtools>`_.
+
+**References**
+ 
+     ]]></help>
+     <citations>
+        <citation type="doi">DOI: 10.12688/f1000research.12232.1</citation>
+     </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blobtools_view.xml	Wed Oct 26 06:54:04 2022 +0000
@@ -0,0 +1,103 @@
+<tool id="blobtools_view" name="Blobtools view" version="1.1" >
+    <description>Transform BlobDB json file into view format</description>
+    <xrefs>
+        <xref type='bio.tools'>blobtools</xref>
+    </xrefs>	
+    <macros>
+	  <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" /> 
+    <command><![CDATA[
+	    cp $input_json input.json &&
+	    blobtools view 
+	    $adv_options.hits
+	    -x $adv_options.taxrule
+	    -r $adv_options.rank
+	    #if $adv_options.cov:
+	        '$cov'
+	    #end if
+	    #if $adv_options.concoct:
+	        '$concoct'
+	    #end if
+	    -i input.json 
+	    -o output 
+	    && mv output.input.table.txt '$blobDB_table'
+	    2>&1
+
+	    ]]></command>
+    <inputs>
+	    <param name="input_json" type="data" format="json" label="json File" help="Input BlobDB json file"/>
+	    <section name="adv_options" title="Advance Options" expanded="False">
+		    <param name="taxrule" type="select" display="radio" label="Taxonomy Rule" help="Taxonomy rule for computing taxonomy: default bestsum">
+		        <option selected="true" value="bestsum">best sum</option>
+		        <option value="bestsumorder">best sum order</option>
+		    </param>
+		    <param name="rank" type="select" display="radio" label="Taxonomic rank">
+			  <option value="species">Species</option>
+			  <option value="genus">Genus</option>
+		          <option value="family">Family</option>
+                          <option value="order">Order</option>
+                          <option value="phylum" selected="true">Phylum</option>
+			  <option value="superkingdom">Superkingdom</option>
+                          <option value="all">All</option>
+		    </param>
+		    <param name="hits" type="boolean" truevalue="--hits" falsevalue="" checked="False" label="Displays taxonomic hits from tax files that contributed to the taxonomy"/>
+		    <param argument="--concoct" type="boolean" truevalue="--concoct" falsevalue="" checked="false" label="Generate concoct files" help="default: False"/>
+		    <param argument="--cov" type="boolean" truevalue="--cov" falsevalue="" checked="false" label="Generate cov files" help="Generate cov files"/>
+	    </section>
+    </inputs>
+    <outputs>
+	    <data name="blobDB_table" format="tabular" label="${tool.name} on ${on_string}"/>
+    </outputs>
+
+    <tests>
+	 <test>
+	     <!-- #1 blobtools view test -->
+	    <param name="input_json" value="test.blobDB.json" ftype="json"/>
+	    <output name="blobDB_table" file="test.blobDB.table.txt" ftype="tabular"/>
+         </test>
+    </tests>
+    <help><![CDATA[
+	    
+.. class:: infomark
+
+*Blobtools view is used to generate a blobDB.table.json before creating a plot using blobtools plot.*
+
+**Input**
+
+- a json file - output file created with Blobtools create.
+
+**Parameters**
+
+- taxrule - Taxrule used for computing taxonomy (supported: "bestsum", "bestsumorder") [ default: bestsum ]
+- rank - Taxonomic rank(s) at which output will be written. (supported: 'species', 'genus', 'family', 'order', 'phylum', 'superkingdom', 'all') [default: phylum]
+- hits - Displays taxonomic hits from tax files that contributed to the taxonomy.
+- concoct - Generate cov files [default: False]
+- calculate_cov - Legacy coverage when getting coverage from BAM file
+
+**Command line example:**
+
+- blobtools view -i prefix.blobDB.json
+
+**Output**
+
+- prefix.blobDB.table.json - a text base output file
+- coverage file - a text base coverage file output file with column # contig_id  read_cov  base_cov #  - if cov is specified 
+- prefix.blobDB.concoct_coverage_info.tsv - a text base coverage output file with base cov column only - if concoct is specified.
+
+
+.. class:: infomark
+
+**Contributor**
+
+Galaxy Australia wrapped the Blobtools: the original software is available in this `Github repository <https://github.com/DRL/blobtools>`_.
+
+**References**
+
+     ]]></help>
+     <citations>
+        <citation type="doi">DOI: 10.12688/f1000research.12232.1</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Oct 26 06:54:04 2022 +0000
@@ -0,0 +1,30 @@
+<macros>
+    <xml name="requirements">
+	   <requirements>
+		   <requirement type="package" version="1.1.1">blobtools</requirement>
+		   <requirement type="package" version="3.2.2">matplotlib</requirement>
+           </requirements>
+   </xml>
+   <xml name="stdio">
+     <stdio>
+        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal" description="Error" />
+     </stdio>
+   </xml>
+  <xml name="version_command">
+      <version_command><![CDATA[
+	      blobtools --version 2>&1 | head -1       
+      ]]></version_command>
+  </xml>
+  <xml name="macro_create_input">
+	  <param name="input_fasta" type="data" format="fasta" label="Sequence file"/>
+	  <param name="input_bam" type="data" format="bam" label="Alignment file"/>
+	  <param name="input_blast" type="data" format="tabular" label="Simplified Blast file"/>
+  </xml>
+  <xml name="macro_view_input">
+	  <param name="input_json" type="data" format="json" label="Json input file"/>
+  </xml>
+  <token name="@SET_TMP_DIR@">
+	export MPLCONFIGDIR="/tmp"
+  </token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.blobDB.json	Wed Oct 26 06:54:04 2022 +0000
@@ -0,0 +1,1 @@
+{"title": "example/test.blobDB.json", "assembly_f": "/home/mthang/tools/blobtools/example/assembly.fna", "lineages": {"979556": {"species": "Microbacterium testaceum", "genus": "Microbacterium", "family": "Microbacteriaceae", "order": "Micrococcales", "phylum": "Actinobacteria", "superkingdom": "Bacteria"}, "6252": {"species": "Ascaris lumbricoides", "genus": "Ascaris", "family": "Ascarididae", "order": "Rhabditida", "phylum": "Nematoda", "superkingdom": "Eukaryota"}, "232323": {"species": "Hypsibius dujardini", "genus": "Hypsibius", "family": "Hypsibiidae", "order": "Parachela", "phylum": "Tardigrada", "superkingdom": "Eukaryota"}}, "order_of_blobs": ["contig_1", "contig_2", "contig_3", "contig_4", "contig_5", "contig_6", "contig_7", "contig_8", "contig_9", "contig_10"], "dict_of_blobs": {"contig_1": {"name": "contig_1", "length": 756, "n_count": 0, "agct_count": 756, "gc": 0.2606, "covs": {"bam0": 120.8277}, "read_cov": {"bam0": 369}, "hits": {"tax0": [{"name": "contig_1", "taxId": "979556", "score": 200.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Microbacterium testaceum", "score": 200.0, "c_index": 0}, "genus": {"tax": "Microbacterium", "score": 200.0, "c_index": 0}, "family": {"tax": "Microbacteriaceae", "score": 200.0, "c_index": 0}, "order": {"tax": "Micrococcales", "score": 200.0, "c_index": 0}, "phylum": {"tax": "Actinobacteria", "score": 200.0, "c_index": 0}, "superkingdom": {"tax": "Bacteria", "score": 200.0, "c_index": 0}}}}, "contig_2": {"name": "contig_2", "length": 1060, "n_count": 0, "agct_count": 1060, "gc": 0.2623, "covs": {"bam0": 197.1055}, "read_cov": {"bam0": 844}, "hits": {"tax0": [{"name": "contig_2", "taxId": "979556", "score": 500.0}, {"name": "contig_2", "taxId": "979556", "score": 1000.0}, {"name": "contig_2", "taxId": "979556", "score": 500.0}, {"name": "contig_2", "taxId": "979556", "score": 300.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Microbacterium testaceum", "score": 2300.0, "c_index": 0}, "genus": {"tax": "Microbacterium", "score": 2300.0, "c_index": 0}, "family": {"tax": "Microbacteriaceae", "score": 2300.0, "c_index": 0}, "order": {"tax": "Micrococcales", "score": 2300.0, "c_index": 0}, "phylum": {"tax": "Actinobacteria", "score": 2300.0, "c_index": 0}, "superkingdom": {"tax": "Bacteria", "score": 2300.0, "c_index": 0}}}}, "contig_3": {"name": "contig_3", "length": 602, "n_count": 0, "agct_count": 602, "gc": 0.2342, "covs": {"bam0": 77.3078}, "read_cov": {"bam0": 188}, "hits": {"tax0": [{"name": "contig_3", "taxId": "979556", "score": 10000.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Microbacterium testaceum", "score": 10000.0, "c_index": 0}, "genus": {"tax": "Microbacterium", "score": 10000.0, "c_index": 0}, "family": {"tax": "Microbacteriaceae", "score": 10000.0, "c_index": 0}, "order": {"tax": "Micrococcales", "score": 10000.0, "c_index": 0}, "phylum": {"tax": "Actinobacteria", "score": 10000.0, "c_index": 0}, "superkingdom": {"tax": "Bacteria", "score": 10000.0, "c_index": 0}}}}, "contig_4": {"name": "contig_4", "length": 951, "n_count": 0, "agct_count": 951, "gc": 0.3155, "covs": {"bam0": 545.5981}, "read_cov": {"bam0": 2096}, "hits": {"tax0": [{"name": "contig_4", "taxId": "979556", "score": 1000.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Microbacterium testaceum", "score": 1000.0, "c_index": 0}, "genus": {"tax": "Microbacterium", "score": 1000.0, "c_index": 0}, "family": {"tax": "Microbacteriaceae", "score": 1000.0, "c_index": 0}, "order": {"tax": "Micrococcales", "score": 1000.0, "c_index": 0}, "phylum": {"tax": "Actinobacteria", "score": 1000.0, "c_index": 0}, "superkingdom": {"tax": "Bacteria", "score": 1000.0, "c_index": 0}}}}, "contig_5": {"name": "contig_5", "length": 614, "n_count": 0, "agct_count": 614, "gc": 0.329, "covs": {"bam0": 183.8478}, "read_cov": {"bam0": 456}, "hits": {"tax0": [{"name": "contig_5", "taxId": "6252", "score": 2000.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Ascaris lumbricoides", "score": 2000.0, "c_index": 0}, "genus": {"tax": "Ascaris", "score": 2000.0, "c_index": 0}, "family": {"tax": "Ascarididae", "score": 2000.0, "c_index": 0}, "order": {"tax": "Rhabditida", "score": 2000.0, "c_index": 0}, "phylum": {"tax": "Nematoda", "score": 2000.0, "c_index": 0}, "superkingdom": {"tax": "Eukaryota", "score": 2000.0, "c_index": 0}}}}, "contig_6": {"name": "contig_6", "length": 216, "n_count": 0, "agct_count": 216, "gc": 0.1944, "covs": {"bam0": 59.5953}, "read_cov": {"bam0": 52}, "hits": {"tax0": [{"name": "contig_6", "taxId": "232323", "score": 2000.0}, {"name": "contig_6", "taxId": "6252", "score": 2000.0}, {"name": "contig_6", "taxId": "979556", "score": 2000.0}, {"name": "contig_6", "taxId": "232323", "score": 2000.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Hypsibius dujardini", "score": 4000.0, "c_index": 2}, "genus": {"tax": "Hypsibius", "score": 4000.0, "c_index": 2}, "family": {"tax": "Hypsibiidae", "score": 4000.0, "c_index": 2}, "order": {"tax": "Parachela", "score": 4000.0, "c_index": 2}, "phylum": {"tax": "Tardigrada", "score": 4000.0, "c_index": 2}, "superkingdom": {"tax": "Eukaryota", "score": 6000.0, "c_index": 1}}}}, "contig_7": {"name": "contig_7", "length": 4060, "n_count": 0, "agct_count": 4060, "gc": 0.2584, "covs": {"bam0": 61.2776}, "read_cov": {"bam0": 1005}, "hits": {"tax0": [{"name": "contig_7", "taxId": "6252", "score": 2000.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Ascaris lumbricoides", "score": 2000.0, "c_index": 0}, "genus": {"tax": "Ascaris", "score": 2000.0, "c_index": 0}, "family": {"tax": "Ascarididae", "score": 2000.0, "c_index": 0}, "order": {"tax": "Rhabditida", "score": 2000.0, "c_index": 0}, "phylum": {"tax": "Nematoda", "score": 2000.0, "c_index": 0}, "superkingdom": {"tax": "Eukaryota", "score": 2000.0, "c_index": 0}}}}, "contig_8": {"name": "contig_8", "length": 2346, "n_count": 0, "agct_count": 2346, "gc": 0.2801, "covs": {"bam0": 106.364}, "read_cov": {"bam0": 1008}, "hits": {"tax0": [{"name": "contig_8", "taxId": "6252", "score": 2000.0}, {"name": "contig_8", "taxId": "979556", "score": 2000.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "unresolved", "score": 2000.0, "c_index": 1}, "genus": {"tax": "unresolved", "score": 2000.0, "c_index": 1}, "family": {"tax": "unresolved", "score": 2000.0, "c_index": 1}, "order": {"tax": "unresolved", "score": 2000.0, "c_index": 1}, "phylum": {"tax": "unresolved", "score": 2000.0, "c_index": 1}, "superkingdom": {"tax": "unresolved", "score": 2000.0, "c_index": 1}}}}, "contig_9": {"name": "contig_9", "length": 1599, "n_count": 0, "agct_count": 1599, "gc": 0.2439, "covs": {"bam0": 85.7676}, "read_cov": {"bam0": 554}, "hits": {"tax0": [{"name": "contig_9", "taxId": "6252", "score": 200.0}]}, "taxonomy": {"bestsum": {"species": {"tax": "Ascaris lumbricoides", "score": 200.0, "c_index": 0}, "genus": {"tax": "Ascaris", "score": 200.0, "c_index": 0}, "family": {"tax": "Ascarididae", "score": 200.0, "c_index": 0}, "order": {"tax": "Rhabditida", "score": 200.0, "c_index": 0}, "phylum": {"tax": "Nematoda", "score": 200.0, "c_index": 0}, "superkingdom": {"tax": "Eukaryota", "score": 200.0, "c_index": 0}}}}, "contig_10": {"name": "contig_10", "length": 6273, "n_count": 0, "agct_count": 6273, "gc": 0.3067, "covs": {"bam0": 336.4195}, "read_cov": {"bam0": 8525}, "hits": {}, "taxonomy": {"bestsum": {"species": {"tax": "no-hit", "score": 0.0, "c_index": 0}, "genus": {"tax": "no-hit", "score": 0.0, "c_index": 0}, "family": {"tax": "no-hit", "score": 0.0, "c_index": 0}, "order": {"tax": "no-hit", "score": 0.0, "c_index": 0}, "phylum": {"tax": "no-hit", "score": 0.0, "c_index": 0}, "superkingdom": {"tax": "no-hit", "score": 0.0, "c_index": 0}}}}}, "length": 18477, "seqs": 10, "n_count": 0, "nodesDB_f": null, "covLibs": {"bam0": {"name": "bam0", "fmt": "bam", "f": "/home/mthang/tools/blobtools/example/mapping_1.sorted.bam", "cov_sum": 1774.110884383095, "reads_total": 15313, "reads_mapped": 15313, "reads_unmapped": 0, "mean_cov": 177.4110884383095}}, "hitLibs": {"tax0": {"name": "tax0", "fmt": "tax", "f": "/home/mthang/tools/blobtools/example/blast.out"}}, "taxrules": ["bestsum"], "version": "1.1.1", "min_score": 0.0, "min_diff": 0.0, "tax_collision_random": false}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.stats.txt	Wed Oct 26 06:54:04 2022 +0000
@@ -0,0 +1,9 @@
+## 1.1.1
+## bam0=/home/mthang/tools/blobtools/example/mapping_1.sorted.bam
+# name	colour	count_visible	count_visible_perc	span_visible	span_visible_perc	n50	gc_mean	gc_std	bam0_mean	bam0_std	bam0_read_map	bam0_read_map_p
+all	None	10	100.0%	18,477	100.0%	4,060	0.27	0.039	177.4	146.7	15,097	98.6%
+Nematoda	#1f77b4	3	100.0%	6,273	100.0%	4,060	0.28	0.037	110.3	53.0	2,015	13.2%
+no-hit	#d3d3d3	1	100.0%	6,273	100.0%	6,273	0.31	0.0	336.4	0.0	8,525	55.7%
+Actinobacteria	#ff7f0e	4	100.0%	3,369	100.0%	951	0.27	0.03	235.2	184.3	3,497	22.8%
+unresolved	#d62728	1	100.0%	2,346	100.0%	2,346	0.28	0.0	106.4	0.0	1,008	6.6%
+Tardigrada	#9467bd	1	100.0%	216	100.0%	216	0.19	0.0	59.6	0.0	52	0.3%
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.blobDB.table.txt	Wed Oct 26 06:54:04 2022 +0000
@@ -0,0 +1,21 @@
+## 1.1.1
+## assembly	: /home/mthang/tools/blobtools/example/assembly.fna
+## coverage	 bam0 - /home/mthang/tools/blobtools/example/mapping_1.sorted.bam
+## taxonomy	 tax0 - /home/mthang/tools/blobtools/example/blast.out
+## nodesDB	: None
+## taxrule	: bestsum
+## min_score	: 0.0
+## min_diff	: 0.0
+## tax_collision_random	: False
+##
+# name	length	GC	N	bam0	phylum.t.6%s	phylum.s.7%s	phylum.c.8
+contig_1	756	0.2606	0	120.8277	Actinobacteria	200.0	0
+contig_2	1060	0.2623	0	197.1055	Actinobacteria	2300.0	0
+contig_3	602	0.2342	0	77.3078	Actinobacteria	10000.0	0
+contig_4	951	0.3155	0	545.5981	Actinobacteria	1000.0	0
+contig_5	614	0.329	0	183.8478	Nematoda	2000.0	0
+contig_6	216	0.1944	0	59.5953	Tardigrada	4000.0	2
+contig_7	4060	0.2584	0	61.2776	Nematoda	2000.0	0
+contig_8	2346	0.2801	0	106.364	unresolved	2000.0	1
+contig_9	1599	0.2439	0	85.7676	Nematoda	200.0	0
+contig_10	6273	0.3067	0	336.4195	no-hit	0.0	0
\ No newline at end of file