diff --git a/tools/taxpasta/taxpasta.xml b/tools/taxpasta/taxpasta.xml
index 0712ca48530..b39d65644eb 100644
--- a/tools/taxpasta/taxpasta.xml
+++ b/tools/taxpasta/taxpasta.xml
@@ -1,34 +1,66 @@
-<tool id="taxpasta" name="taxpasta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+<tool id="taxpasta" name="taxpasta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>standardise taxonomic profiles</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.5.0</token>
+        <token name="@TOOL_VERSION@">0.6.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">22.01</token>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">taxpasta</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">taxpasta</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        ## Getting the NCBI taxonomy database
-        ## In the future could find the one that exists in Galaxy and give the user the option to instead use that cached one
-
-        curl -O -s ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz &&
-        mkdir ./taxdump &&
-        tar -C ./taxdump -xzf taxdump.tar.gz &&
-        taxpasta $action -p $profiler -o ./output.tsv --taxonomy taxdump --add-name
-        #for $file in $infile:
-            '$file'
-        #end for
-        &&
-        mv ./output.tsv $output
-
-    ## Outputs
+taxpasta 
+    $action.action 
+    --profiler $profiler
+    --taxonomy '$taxonomy.fields.path'
+#if $action.action == 'merge'
+    --output-format '$action.format.output_format'
+    #if $action.format.output_format == 'TSV'
+    --output '$tabular_output'
+    $action.format.wide
+    #else if $action.format.output_format == 'BIOM'
+    --output '$biom_output'
+    #end if
+#else
+    --output-format 'TSV'
+    --output '$tabular_output'
+#end if
+    $add_name
+    $add_rank
+    $add_lineage
+    $add_id_lineage
+    $add_rank_lineage
+#for $file in $infile
+    '$file'
+#end for
     ]]></command>
     <inputs>
-        <param name="infile" type="data" format="tabular" multiple="true" label="Choose taxonomic report(s) to standardise" help="Select one or many reports, but only from the same profiling tool" />
-        <param name="profiler" type="select" label="What profiling tool created this report?" help="Select one profiler only">
+        <conditional name="action">
+            <param name="action" type="select" label="Taxpasta action">
+                <option value="standardise">Standardise input(s)</option>
+                <option value="merge">Standardise and combine multiple taxonomic profiles from the same profiler</option>
+            </param>
+            <when value="standardise"/>
+            <when value="merge">
+                <conditional name="format">
+                    <param argument="--output-format" type="select" label="Desired output format">
+                        <option value="TSV">Tabular</option>
+                        <option value="BIOM">BIOM</option>
+                    </param>
+                    <when value="TSV">
+                        <param argument="--wide" type="boolean" truevalue="--wide" falsevalue="--long" checked="true" label="Output merged abundance data in either wide or (tidy) long format"/>
+                    </when>
+                    <when value="BIOM"/>
+                </conditional>
+            </when>
+        </conditional>
+        <param argument="--profiler" type="select" label="What profiling tool created this report?" help="Select one profiler only">
             <option value="bracken">Bracken</option>
             <option value="Centrifuge">Centrifuge</option>
-            <option value="diamond">diamond</option>
+            <option value="diamond">DIAMOND</option>
             <option value="ganon">ganon</option>
             <option value="kaiju">Kaiju</option>
             <option value="kraken2">Kraken2</option>
@@ -37,63 +69,139 @@
             <option value="metaphlan">MetaPhlAn</option>
             <option value="motus">mOTUs</option>
         </param>
-       <param name="action" type="select" label="What should taxpasta do?" help="Only run merge if inputs are from the same profiler">
-           <option value="standardise">Standardise input(s)</option>
-           <option value="merge">Standardise and merge inputs</option>
-       </param>
+        <param name="infile" type="data" format="tabular" multiple="true" label="Taxonomic report(s) to standardise" help="The reports should be from the same profiling tool" />
+        <param argument="--taxonomy" type="select" label="NCBI taxonomy" help="To have actual human-readable taxon names in the standardised output">
+            <options from_data_table="ncbi_taxonomy">
+                <validator message="No NCBI database is available" type="no_options"/>
+            </options>
+        </param>
+        <param argument="--add-name" type="boolean" truevalue="--add-name" falsevalue="" checked="true" label="Add the taxon name to the output"/>
+        <param argument="--add-rank" type="boolean" truevalue="--add-rank" falsevalue="" checked="false" label="Add the taxon rank to the output"/>
+        <param argument="--add-lineage" type="boolean" truevalue="--add-lineage" falsevalue="" checked="false" label="Add the taxon's entire lineage to the output" 
+            help="The taxon names are separated by semi-colons"/>
+        <param argument="--add-id-lineage" type="boolean" truevalue="--add-id-lineage" falsevalue="" checked="false" label="Add the taxon's entire lineage to the output" 
+            help="The taxon identifiers are separated by semi-colons"/>
+        <param argument="--add-rank-lineage" type="boolean" truevalue="--add-rank-lineage" falsevalue="" checked="false" label="Add the taxon's entire rank lineage to the output" 
+            help="These are taxon ranks separated by semi-colons"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="output"/>      
+        <data name="tabular_output" format="tabular" label="${tool.name} on ${on_string}: Tabular">
+            <filter>(action['action'] == 'merge' and action['format']['output_format'] == 'TSV') or action['action'] == 'standardise'</filter>
+        </data>
+        <data name="biom_output" format="biom1" label="${tool.name} on ${on_string}: BIOM">
+            <filter>(action['action'] == 'merge' and action['format']['output_format'] == 'BIOM')</filter>
+        </data>
     </outputs>
     <tests>
         <!-- test data from taxpasta https://github.com/taxprofiler/taxpasta/tree/dev/tests/data-->
         <test expect_num_outputs="1">
-            <param name="infile" value="ERR7569997.txt"/>
+            <conditional name="action">
+                <param name="action" value="standardise"/>
+            </conditional>
             <param name="profiler" value="metaphlan"/>
-            <param name="action" value="standardise"/>
-            <output name="output">
+            <param name="infile" value="ERR7569997.txt"/>
+            <param name="taxonomy" value="test-db-tox"/>
+            <param name="add_name" value="true"/>
+            <param name="add_rank" value="false" />
+            <param name="add_lineage" value="false"/>
+            <param name="add_id_lineage" value="false"/>
+            <param name="add_rank_lineage" value="false"/>
+            <output name="tabular_output" ftype="tabular">
                 <assert_contents>
-                    <has_text text="Pseudomonadota"/>
+                    <has_text text="Proteobacteria"/>
                     <has_n_columns n="3"/>
+                    <has_n_lines n="241"/>
                 </assert_contents>
             </output>
         </test>
-         
         <!-- test multiple inputs and the merge command-->
         <test expect_num_outputs="1">
-            <param name="infile" value="ERR7569997.txt,ERR7569998.txt"/>
+            <conditional name="action">
+                <param name="action" value="merge"/>
+                <conditional name="format">
+                    <param name="output_format" value="TSV"/>
+                    <param name="wide" value="true"/>
+                </conditional>
+            </conditional>
             <param name="profiler" value="metaphlan"/>
-            <param name="action" value="merge"/>
-            <output name="output">
+            <param name="infile" value="ERR7569997.txt,ERR7569998.txt"/>
+            <param name="taxonomy" value="test-db-tox"/>
+            <param name="add_name" value="true"/>
+            <param name="add_rank" value="false" />
+            <param name="add_lineage" value="false"/>
+            <param name="add_id_lineage" value="false"/>
+            <param name="add_rank_lineage" value="false"/>
+            <output name="tabular_output" ftype="tabular">
                 <assert_contents>
-                    <has_text text="Pseudomonadota"/>
+                    <has_text text="Gammaproteobacteria"/>
                     <has_n_columns n="4"/>
+                    <has_n_lines n="252"/>
                 </assert_contents>
             </output>
         </test>
-    
         <!-- testing diamond input-->
         <test expect_num_outputs="1">
-            <param name="infile" value="diamond_valid_1.tsv"/>
-            <param name="profiler" value="diamond"/>
+            <conditional name="action">
+                <param name="action" value="standardise"/>
+            </conditional>
             <param name="action" value="standardise"/>
-            <output name="output">
+            <param name="profiler" value="diamond"/>
+            <param name="infile" value="diamond_valid_1.tsv"/>
+            <param name="taxonomy" value="test-db-tox"/>
+            <param name="add_name" value="true"/>
+            <param name="add_rank" value="false" />
+            <param name="add_lineage" value="false"/>
+            <param name="add_id_lineage" value="false"/>
+            <param name="add_rank_lineage" value="false"/>
+            <output name="tabular_output" ftype="tabular">
                 <assert_contents>
-                    <has_text text="Acinetobacter"/>
+                    <has_text text="1310613"/>
                     <has_n_columns n="3"/>
+                    <has_n_lines n="4"/>
                 </assert_contents>
             </output>
         </test>
-    
-        <!-- testing kraken input-->
+        <!-- testing kraken input and all boolean-->
         <test expect_num_outputs="1">
-            <param name="infile" value="2612_pe-ERR5766176-db1.kraken2.report.txt"/>
+            <conditional name="action">
+                <param name="action" value="standardise"/>
+            </conditional>
             <param name="profiler" value="kraken2"/>
-            <param name="action" value="standardise"/>
-            <output name="output">
+            <param name="infile" value="2612_pe-ERR5766176-db1.kraken2.report.txt"/>
+            <param name="taxonomy" value="test-db-tox"/>
+            <param name="add_name" value="true"/>
+            <param name="add_rank" value="true" />
+            <param name="add_lineage" value="true"/>
+            <param name="add_id_lineage" value="true"/>
+            <param name="add_rank_lineage" value="true"/>
+            <output name="tabular_output" ftype="tabular">
                 <assert_contents>
                     <has_text text="root"/>
-                    <has_n_columns n="3"/>
+                    <has_text text="rank_lineage"/>
+                    <has_n_columns n="7"/>
+                    <has_n_lines n="45"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- testing BIOM output-->
+        <test expect_num_outputs="1">
+            <conditional name="action">
+                <param name="action" value="merge"/>
+                <conditional name="format">
+                    <param name="output_format" value="BIOM"/>
+                </conditional>
+            </conditional>
+            <param name="profiler" value="kraken2"/>
+            <param name="infile" value="2612_pe-ERR5766176-db1.kraken2.report.txt,2611_se-ERR5766174-db1.kraken2.report.txt"/>
+            <param name="taxonomy" value="test-db-tox"/>
+            <param name="add_name" value="true"/>
+            <param name="add_rank" value="false" />
+            <param name="add_lineage" value="false"/>
+            <param name="add_id_lineage" value="false"/>
+            <param name="add_rank_lineage" value="false"/>
+            <output name="biom_output" ftype="biom1">
+                <assert_contents>
+                    <has_text text="314146"/>
                 </assert_contents>
             </output>
         </test>
@@ -104,23 +212,22 @@
 
 **What it does**
 
-* Taxpasta standardises the taxonomic profiles produced from other tools. 
-* It reformats these outputs into a table of NCBI taxonomy identifiers and their integer counts.
-* Then, it converts these identifiers to taxon names.
-* It can also merge outputs across samples, from the same profiling tool. 
+The main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. 
+We call those tools taxonomic profilers. They each come with their own particular tabular output format. 
+Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as 
+any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart 
+and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a 
+minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge 
+them across samples for the same profiler into a single table.
 
 **Input(s)**
 
 * One or many outputs from a particular profiling tool, such as kraken2 or diamond.
-* Check that this report is in the correct format for taxpasta: for detail, see https://taxpasta.readthedocs.io/en/latest/supported_profilers/.
-* For example, for kraken2, taxpasta expects the kraken-report output file with 6 or 8 columns.
-* For example, for diamond, taxpasta expects a tabular file with 3 columns.
-
 
 **Output**
 
-* A reformatted report, either for the single input, or for multiple inputs, as long as they are from the same profiling tool.
-* The report is in tabular format. 
+* A reformatted report in tabular format, either for the single input, or for multiple inputs, as long as they are from the same profiling tool.
+
 
 For more information see: https://taxpasta.readthedocs.io/en/latest/
 
diff --git a/tools/taxpasta/test-data/2611_se-ERR5766174-db1.kraken2.report.txt b/tools/taxpasta/test-data/2611_se-ERR5766174-db1.kraken2.report.txt
new file mode 100644
index 00000000000..078b360fea3
--- /dev/null
+++ b/tools/taxpasta/test-data/2611_se-ERR5766174-db1.kraken2.report.txt
@@ -0,0 +1,44 @@
+ 99.98	787758	787758	U	0	unclassified
+  0.02	119	0	R	1	root
+  0.02	119	0	R1	131567	  cellular organisms
+  0.02	119	0	D	2759	    Eukaryota
+  0.02	119	0	D1	33154	      Opisthokonta
+  0.01	96	0	K	4751	        Fungi
+  0.01	96	0	K1	451864	          Dikarya
+  0.01	96	0	P	4890	            Ascomycota
+  0.01	96	0	P1	716545	              saccharomyceta
+  0.01	96	0	P2	147537	                Saccharomycotina
+  0.01	96	0	C	4891	                  Saccharomycetes
+  0.01	96	0	O	4892	                    Saccharomycetales
+  0.01	96	0	F	4893	                      Saccharomycetaceae
+  0.01	96	0	G	4930	                        Saccharomyces
+  0.01	96	0	S	4932	                          Saccharomyces cerevisiae
+  0.01	96	96	S1	559292	                            Saccharomyces cerevisiae S288C
+  0.00	23	0	K	33208	        Metazoa
+  0.00	23	0	K1	6072	          Eumetazoa
+  0.00	23	0	K2	33213	            Bilateria
+  0.00	23	0	K3	33511	              Deuterostomia
+  0.00	23	0	P	7711	                Chordata
+  0.00	23	0	P1	89593	                  Craniata
+  0.00	23	0	P2	7742	                    Vertebrata
+  0.00	23	0	P3	7776	                      Gnathostomata
+  0.00	23	0	P4	117570	                        Teleostomi
+  0.00	23	0	P5	117571	                          Euteleostomi
+  0.00	23	0	P6	8287	                            Sarcopterygii
+  0.00	23	0	P7	1338369	                              Dipnotetrapodomorpha
+  0.00	23	0	P8	32523	                                Tetrapoda
+  0.00	23	0	P9	32524	                                  Amniota
+  0.00	23	0	C	40674	                                    Mammalia
+  0.00	23	0	C1	32525	                                      Theria
+  0.00	23	0	C2	9347	                                        Eutheria
+  0.00	23	0	C3	1437010	                                          Boreoeutheria
+  0.00	23	0	C4	314146	                                            Euarchontoglires
+  0.00	23	0	O	9443	                                              Primates
+  0.00	23	0	O1	376913	                                                Haplorrhini
+  0.00	23	0	O2	314293	                                                  Simiiformes
+  0.00	23	0	O3	9526	                                                    Catarrhini
+  0.00	23	0	O4	314295	                                                      Hominoidea
+  0.00	23	0	F	9604	                                                        Hominidae
+  0.00	23	0	F1	207598	                                                          Homininae
+  0.00	23	0	G	9605	                                                            Homo
+  0.00	23	23	S	9606	                                                              Homo sapiens
diff --git a/tools/taxpasta/test-data/ncbi_taxonomy.loc b/tools/taxpasta/test-data/ncbi_taxonomy.loc
new file mode 100644
index 00000000000..96b1a97157b
--- /dev/null
+++ b/tools/taxpasta/test-data/ncbi_taxonomy.loc
@@ -0,0 +1 @@
+test-db-tox	Test Database	${__HERE__}/test-db
\ No newline at end of file
diff --git a/tools/taxpasta/test-data/test-db/names.dmp b/tools/taxpasta/test-data/test-db/names.dmp
new file mode 100644
index 00000000000..fa5e7ef33d4
--- /dev/null
+++ b/tools/taxpasta/test-data/test-db/names.dmp
@@ -0,0 +1,74 @@
+83333	|	Escherichia coli K-12	|		|	scientific name	|
+83333	|	Escherichia coli K12	|		|	equivalent name	|
+562	|	"Bacillus coli" Migula 1895	|		|	authority	|
+562	|	"Bacterium coli commune" Escherich 1885	|		|	authority	|
+562	|	"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896	|		|	authority	|
+562	|	ATCC 11775	|		|	type material	|
+562	|	Bacillus coli	|		|	synonym	|
+562	|	Bacterium coli	|		|	synonym	|
+562	|	Bacterium coli commune	|		|	synonym	|
+562	|	CCUG 24	|		|	type material	|
+562	|	CCUG 29300	|		|	type material	|
+562	|	CIP 54.8	|		|	type material	|
+562	|	DSM 30083	|		|	type material	|
+562	|	Enterococcus coli	|		|	synonym	|
+562	|	Escherchia coli	|		|	misspelling	|
+562	|	Escherichia coli	|		|	scientific name	|
+562	|	Escherichia coli (Migula 1895) Castellani and Chalmers 1919	|		|	authority	|
+562	|	Escherichia sp. MAR	|		|	includes	|
+562	|	Escherichia/Shigella coli	|		|	equivalent name	|
+562	|	Eschericia coli	|		|	misspelling	|
+562	|	JCM 1649	|		|	type material	|
+562	|	LMG 2092	|		|	type material	|
+562	|	NBRC 102203	|		|	type material	|
+562	|	NCCB 54008	|		|	type material	|
+562	|	NCTC 9001	|		|	type material	|
+562	|	bacterium 10a	|		|	includes	|
+562	|	bacterium E3	|		|	includes	|
+561	|	Escherchia	|		|	misspelling	|
+561	|	Escherichia	|		|	scientific name	|
+561	|	Escherichia Castellani and Chalmers 1919	|		|	authority	|
+543	|	Enterobacteraceae	|		|	synonym	|
+543	|	Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.	|		|	synonym	|
+543	|	Enterobacteriaceae	|		|	scientific name	|
+543	|	Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.	|		|	synonym	|
+543	|	Enterobacteriaceae Rahn 1937	|		|	synonym	|
+543	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#1>	|	in-part	|
+91347	|	'Enterobacteriales'	|		|	synonym	|
+91347	|	Enterobacteriaceae and related endosymbionts	|		|	synonym	|
+91347	|	Enterobacteriaceae group	|		|	synonym	|
+91347	|	Enterobacteriales	|		|	scientific name	|
+91347	|	enterobacteria	|	enterobacteria<blast91347>	|	blast name	|
+91347	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#5>	|	in-part	|
+1236	|	Gammaproteobacteria	|		|	scientific name	|
+1236	|	Gammaproteobacteria Garrity et al. 2005	|		|	synonym	|
+1236	|	Proteobacteria gamma subdivision	|		|	synonym	|
+1236	|	Purple bacteria, gamma subdivision	|		|	synonym	|
+1236	|	g-proteobacteria	|	gamma proteos<blast1236>	|	blast name	|
+1236	|	gamma proteobacteria	|		|	synonym	|
+1236	|	gamma subdivision	|		|	synonym	|
+1236	|	gamma subgroup	|		|	synonym	|
+1224	|	Proteobacteria	|		|	scientific name	|
+1224	|	Proteobacteria Garrity et al. 2005	|		|	authority	|
+1224	|	Proteobacteria [class] Stackebrandt et al. 1988	|		|	authority	|
+1224	|	not Proteobacteria Cavalier-Smith 2002	|		|	authority	|
+1224	|	proteobacteria	|	proteobacteria<blast1224>	|	blast name	|
+1224	|	purple bacteria	|		|	common name	|
+1224	|	purple bacteria and relatives	|		|	common name	|
+1224	|	purple non-sulfur bacteria	|		|	common name	|
+1224	|	purple photosynthetic bacteria	|		|	common name	|
+1224	|	purple photosynthetic bacteria and relatives	|		|	common name	|
+2	|	Bacteria	|	Bacteria <prokaryote>	|	scientific name	|
+2	|	Monera	|	Monera <Bacteria>	|	in-part	|
+2	|	Procaryotae	|	Procaryotae <Bacteria>	|	in-part	|
+2	|	Prokaryota	|	Prokaryota <Bacteria>	|	in-part	|
+2	|	Prokaryotae	|	Prokaryotae <Bacteria>	|	in-part	|
+2	|	bacteria	|	bacteria <blast2>	|	blast name	|
+2	|	eubacteria	|		|	genbank common name	|
+2	|	not Bacteria Haeckel 1894	|		|	synonym	|
+2	|	prokaryote	|	prokaryote <Bacteria>	|	in-part	|
+2	|	prokaryotes	|	prokaryotes <Bacteria>	|	in-part	|
+1	|	all	|		|	synonym	|
+1	|	root	|		|	scientific name	|
+131567	|	biota	|		|	synonym	|
+131567	|	cellular organisms	|		|	scientific name	|
diff --git a/tools/taxpasta/test-data/test-db/nodes.dmp b/tools/taxpasta/test-data/test-db/nodes.dmp
new file mode 100644
index 00000000000..4e292c27101
--- /dev/null
+++ b/tools/taxpasta/test-data/test-db/nodes.dmp
@@ -0,0 +1,10 @@
+83333	|	562	|	no rank	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+562	|	561	|	species	|	EC	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+561	|	543	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+543	|	91347	|	family	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+91347	|	1236	|	order	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+1236	|	1224	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+1224	|	2	|	phylum	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+2	|	131567	|	superkingdom	|		|	0	|	0	|	11	|	0	|	0	|	0	|	0	|	0	|		|
+131567	|	1	|	no rank	|		|	8	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
+1	|	1	|	no rank	|		|	8	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
diff --git a/tools/taxpasta/tool-data/ncbi_taxonomy.loc.sample b/tools/taxpasta/tool-data/ncbi_taxonomy.loc.sample
new file mode 100644
index 00000000000..d8aa67d3958
--- /dev/null
+++ b/tools/taxpasta/tool-data/ncbi_taxonomy.loc.sample
@@ -0,0 +1 @@
+#value	name	path
\ No newline at end of file
diff --git a/tools/taxpasta/tool_data_table_conf.xml.sample b/tools/taxpasta/tool_data_table_conf.xml.sample
new file mode 100644
index 00000000000..a17ce28eece
--- /dev/null
+++ b/tools/taxpasta/tool_data_table_conf.xml.sample
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+        <!-- Locations of taxonomy data downloaded from NCBI -->
+    <table name="ncbi_taxonomy" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" />
+    </table>
+</tables>
diff --git a/tools/taxpasta/tool_data_table_conf.xml.test b/tools/taxpasta/tool_data_table_conf.xml.test
new file mode 100644
index 00000000000..a17ce28eece
--- /dev/null
+++ b/tools/taxpasta/tool_data_table_conf.xml.test
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+        <!-- Locations of taxonomy data downloaded from NCBI -->
+    <table name="ncbi_taxonomy" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" />
+    </table>
+</tables>