diff --git a/tool_collections/kraken2/kraken2/kraken2.xml b/tool_collections/kraken2/kraken2/kraken2.xml
index dc5ce74797c..c18d8eb0eca 100644
--- a/tool_collections/kraken2/kraken2/kraken2.xml
+++ b/tool_collections/kraken2/kraken2/kraken2.xml
@@ -14,10 +14,34 @@
     <version_command>kraken2 --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
+        #if $kraken2_database.database_source == "history":
+            ## this is a hack to get the actual path to the directory until https://github.com/galaxyproject/galaxy/pull/20857 is merged and deployed
+            #import os
+            #set files_in_path = os.listdir($kraken2_database.custom_database.extra_files_path)
+            #if 'hash.k2d' in files_in_path:
+                #set db_dir_name = $kraken2_database.custom_database.extra_files_path
+            #else:
+                #set found_dir = False
+                #for filename in files_in_path:
+                    #if filename.startswith('dataset_'):
+                        #set db_dir_name = $kraken2_database.custom_database.extra_files_path + '/' + $filename
+                        #set found_dir = True
+                    #end if
+                    #break
+                #end for
+                #if not found_dir:
+                    #raise Exception("Could not find the extracted directory for the custom database. Please make sure the uploaded zip file contains the files hash.k2d, opts.k2d and taxo.k2d at its root. " + str(files_in_path))
+                #end if
+            #end if
+        #end if 
         kraken2
             --threads \${GALAXY_SLOTS:-1}
-            --db '${kraken2_database.fields.path}'
-
+            #if $kraken2_database.database_source == "builtin"
+                --db '${kraken2_database.builtin_database.fields.path}'
+            #elif $kraken2_database.database_source == "history"
+                --db '${db_dir_name}'
+            #end if
+            
             $quick
 
             #if $single_paired.single_paired_selector == "collection":
@@ -37,9 +61,9 @@
                 #end if
             #end if
 
-            --confidence '${confidence}'
-            --minimum-base-quality '${min_base_quality}'
-            --minimum-hit-groups '${minimum_hit_groups}'
+            --confidence ${confidence}
+            --minimum-base-quality ${min_base_quality}
+            --minimum-hit-groups ${minimum_hit_groups}
 
             $use_names
 
@@ -129,6 +153,7 @@
         <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
     </outputs>
     <tests>
+        <!-- test1 -->
         <test expect_num_outputs="1">
             <conditional name="single_paired">
                 <param name="single_paired_selector" value="no"/>
@@ -137,10 +162,14 @@
             <param name="split_reads" value="false"/>
             <param name="quick" value="no"/>
             <param name="confidence" value=".2"/>
-            <param name="kraken2_database" value="test_entry"/>
+            <conditional name="kraken2_database">
+                <param name="database_source" value="builtin" />
+                <param name="builtin_database" value="test_entry"/>
+            </conditional>
             <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
         </test>
 
+        <!-- test2 -->
         <test expect_num_outputs="3">
             <conditional name="single_paired">
                 <param name="single_paired_selector" value="no"/>
@@ -149,12 +178,16 @@
             <param name="split_reads" value="true"/>
             <param name="quick" value="no"/>
             <param name="confidence" value=".2"/>
-            <param name="kraken2_database" value="test_entry"/>
+            <conditional name="kraken2_database">
+                <param name="database_source" value="builtin" />
+                <param name="builtin_database" value="test_entry"/>
+            </conditional>
             <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
             <output name="classified_out_s" file="kraken_test1_cl.fas" ftype="fasta"/>
             <output name="unclassified_out_s" file="kraken_test1_un.fas" ftype="fasta"/>
         </test>
 
+        <!-- test3 -->
         <test expect_num_outputs="7">
             <conditional name="single_paired">
                 <param name="single_paired_selector" value="collection"/>
@@ -169,7 +202,10 @@
             <param name="split_reads" value="true"/>
             <param name="quick" value="no"/>
             <param name="confidence" value="0"/>
-            <param name="kraken2_database" value="test_entry"/>
+            <conditional name="kraken2_database">
+                <param name="database_source" value="builtin" />
+                <param name="builtin_database" value="test_entry"/>
+            </conditional>
             <output_collection name="out_unclassified_paired" type="paired">
                 <element name="forward" file="un_test2_output_1.fastq" ftype="fastqsanger.gz" decompress="true"/>
                 <element name="reverse" file="un_test2_output_2.fastq" ftype="fastqsanger.gz" decompress="true"/>
@@ -184,6 +220,7 @@
             </assert_command>
         </test>
 
+        <!-- test4 -->
         <test expect_num_outputs="2">
             <conditional name="single_paired">
                 <param name="single_paired_selector" value="collection"/>
@@ -199,9 +236,44 @@
                 <param name="create_report" value="true"/>
                 <param name="report_minimizer_data" value="true"/>
             </section>
-            <param name="kraken2_database" value="test_entry"/>
+            <conditional name="kraken2_database">
+                <param name="database_source" value="builtin" />
+                <param name="builtin_database" value="test_entry"/>
+            </conditional>
             <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/>
         </test>
+
+        <!-- test6 -->
+        <test expect_num_outputs="1">
+            <conditional name="single_paired">
+                <param name="single_paired_selector" value="no"/>
+                <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
+            </conditional>
+            <param name="split_reads" value="false"/>
+            <param name="quick" value="no"/>
+            <param name="confidence" value=".2"/>
+            <conditional name="kraken2_database">
+                <param name="database_source" value="history" />
+                <param name="custom_database" ftype="zip" value="test_db.zip" />
+            </conditional>
+            <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
+        </test>
+
+        <!-- test6 -->
+        <test expect_num_outputs="1">
+            <conditional name="single_paired">
+                <param name="single_paired_selector" value="no"/>
+                <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
+            </conditional>
+            <param name="split_reads" value="false"/>
+            <param name="quick" value="no"/>
+            <param name="confidence" value=".2"/>
+            <conditional name="kraken2_database">
+                <param name="database_source" value="history" />
+                <param name="custom_database" class="Directory" value="test_db" />
+            </conditional>
+            <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
+        </test>
     </tests>
     <help>
         <![CDATA[
@@ -225,6 +297,23 @@ Each sequence classified by Kraken results in a single line of output. Output li
             c) the next 31 k-mers contained an ambiguous nucleotide
             d) the next k-mer was not in the database
             e) the last 3 k-mers mapped to taxonomy ID #562
+
+
+-----
+
+**Custom databases**
+
+The database can either be provided from a built-in selection of databases on the Galaxy server, in which case they are installed by the Galaxy administrator, typically using a tool manager, or can be provided by the user.
+
+The kraken2 tool can use custom databases provided, as directories, from the user's history. These directory datasets must contain the files `hash.k2d`, `opts.k2d` and `taxo.k2d`. Since Galaxy does not support uploading directory datatypes directly, users can upload a zip file containing these three files and then extract it using the "Extract compressed file" tool in Galaxy. The resulting directory can then be used as a custom database for Kraken2. A compressed zip archive can also be used as input to the tool, in which case Galaxy will automatically extract it before running the tool.
+
+To further clarify, the structure of the uploaded zip file should be as follows::
+
+    hash.k2d
+    opts.k2d
+    taxo.k2d
+
+For more information on building custom databases for Kraken2, please refer to the `Kraken2 documentation <https://github.com/DerrickWood/kraken2/wiki/Manual#custom-databases>`_.
         ]]>
     </help>
     <expand macro="citations" />
diff --git a/tool_collections/kraken2/kraken2/test-data/kraken_test1_un.fas b/tool_collections/kraken2/kraken2/test-data/kraken_test1_un.fas
index 0a5218f87b3..19025e816c1 100644
--- a/tool_collections/kraken2/kraken2/test-data/kraken_test1_un.fas
+++ b/tool_collections/kraken2/kraken2/test-data/kraken_test1_un.fas
@@ -1,8 +1,8 @@
->gi|145231|gb|M33724.1|ECOALPHOA Escherichia coli K-12 truncated PhoA (phoA) gene, partial cds; and transposon Mu dI, partial sequence
+>gi|145231|gb|M33724.1|ECOALPHOA
 CAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAACTCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCAATGAAGCGGCGCACGAAAAACGCGAAAGCGT
->gi|145232|gb|M33725.1|ECOALPHOB Escherichia coli K12 phoA pseudogene and transposon Mu dl-R, partial sequence
+>gi|145232|gb|M33725.1|ECOALPHOB
 CTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAAGCCCGGACACCAGTGAAGCGGCGCACGAAAAACGCGAAAGCGT
->gi|145234|gb|M33727.1|ECOALPHOE Escherichia coli K12 upstream sequence of psiA5::Mu dI. is identical to psiA30 upstream sequence; putative (phoA) pseudogene and transposon Mu dl-R, partial sequence
+>gi|145234|gb|M33727.1|ECOALPHOE
 TTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGTGAAGCGGCGCACGAAAAACGCGAAAGCGT
->gi|146195|gb|J01619.1|ECOGLTA Eschericia coli gltA gene, sdhCDAB operon and sucABCD operons, complete sequence
+>gi|146195|gb|J01619.1|ECOGLTA
 GAATTCGACCGCCATTGCGCAAGGCATCGCCATGACCAGGCAGGATACAAAAGAGAGTCGATAAATATTCACGGTGTCCATACCTGATAAATATTTTATGAAAGGCGGCGATGATGCCGCAAAATAATACTTATTTATAATCCAGCACGTAGGTTGCGTTAGCGGTTACTTCACCTGCCGTGACATCGACTGCATTATCAATTTGTTCCATCCAGGCGAAAAAGTTCAGCGTCTGTTCTGATGAGCTTGCATCCAGGTCAAGATCTGGCGCGGCTGAACCTAATACGATGTTACCGTCATTTTTGTCCATCAGTCGTACACCGACCCCAGTTGCTTCGCCTGCACTGGTGTTGCTCAACAAAGGCGTAGCACCAGTTGTCTTAGCCGTGCTATCGAAGGTTACGCCAAACTTTGGATACCGGCATTCCGCTACCGTTGTCAGAAGCAGGCAGATCACAGTTGATCAAGCGAATGTCGACGGCCACTTTATTGCTATGATGCTCCCGGTTTATATGGGTTGTCGTGACTTGTCCAAGATCTATGTTTTTATCAATATCTTCTGGATGAATTTCACAAGGTGCTTCAATAACCTCCCCCTTAAAGTGAATTTCGCCAGAACCTTCATCAGCAGCATAAACAGGTGCAGTGAACAGCAGAGATACGGCCAGTGCGGCCAATGTTTTTTGTCCTTTAAACATAACAGAGTCCTTTAAGGATATAGAATAGGGGTATAGCTACGCCAGAATATCGTATTTGATTATTGCTAGTTTTTAGTTTTGCTTAAAAAATATTGTTAGTTTTATTAAATTGGAAAACTAAATTATTGGTATCATGAATTGTTGTATGATGATAAATATAGGGGGGATATGATAGACGTCATTTTCATAGGGTTATAAAATGCGACTACCATGAAGTTTTTAATTCAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAAGTTTTTTGTGTTTAGGCATATAAAAATCAAGCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCGAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTCAGCACTTCATGGCAGGTTTCACGCATTACGGTGGCGCGCGGGTCGTAATTTTTGTACACGCGGTGACCGAAGCCCATCAGGCGGAAAGAATCATTTTTGTCTTTCGCACGACGAAAAAATTCCGGAATGTGTTTAACGGAGCTGATTTCTTCCAGCATTTTCAGCGCCGCTTCGTTAGCACCGCCGTGCGCAGGTCCCCACAGTGAAGCAATACCTGCTGCGATACAGGCAAACGGGTTCGCACCCGAAGAGCCAGCGGTACGCACGGTGGAGGTAGAGGCGTTCTGTTCATGGTCAGCGTGCAGGATCAGAATACGGTCCATAGCACGTTCCAGAATCGGATTAACTTCATACGGTTCGCACGGCGTGGAGAACATCATATTCAGGAAGTTACCGGCGTAGGAGAGATCGTTGCGCGGGTAAACAAATGGCTGACCAATGGAATACTTGTAACACATCGCGGCCATGGTCGGCATTTTCGACAGCAGGCGGAACGCGGCAATTTCACGGTGACGAGGATTGTTAACATCCAGCGAGTCGTGATAGAACGCCGCCAGCGCGCCGGTAATACCACACATGACTGCCATTGGATGCGAGTCGCGACGGAAAGCATGGAACAGACGGGTAATCTGCTCGTGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTCACCATTCAGCAGGATGTAACAAACTTCCAGGTAGTTAGAATCGGTCGCCAGCTGATCGATCGGGAAACCGCGGTGCAGCAAAATACCTTCATCACCATCAATAAAAGTAATTTTAGATTCGCAGGATGCGGTTGAAGTGAAGCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCTTGCAGGTAAAGGATCCATTGATGACGAATAAATGGCGAATCAAGTACTTAGCAATCCGAATTATTAAACTTGTCTACCACTAATAACTGTCCCGAATGAATTGGTCAATACTCCACACTGTTACATAAGTTAATCTTAGGTGAAATACCGACTTCATAACTTTTACGCATTATATGCTTTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGATTGTCAAATTAGATGATTAAAAATTAAATAAATGTTGTTATCGTGACCTGGATCACTGTTCAGGATAAAACCCGACAAACTATATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATACTGCCGCCAGTCTCCGGAACACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATGACGCGCAGTTATAGAAAGGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCAGGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTCATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGGCGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCTTCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTCAAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGATGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTACTGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAAGCAACGCCTCCGCATTAGGACGCAATGGCGTACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTTTTTCGCTACCAGTGGCGAGCTGACATATGAAGTCTGGATCGGTTTCTTCGCCTCTGCGTTCACCAAAGTGTTCACCCTGCTGGCGCTGTTTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACTACGTTAAACCGCTGGCTTTGCGCCTGATGCTGCAACTGGTGATTGTCGTTGCACTGGTGGTTTACGTGATTTATGGATTCGTTGTGGTGTGGGGTGTGTGATGAAATTGCCAGTCAGAGAATTTGATGCAGTTGTGATTG
diff --git a/tool_collections/kraken2/kraken2/test-data/test_db.zip b/tool_collections/kraken2/kraken2/test-data/test_db.zip
new file mode 100644
index 00000000000..ad64f8020a5
Binary files /dev/null and b/tool_collections/kraken2/kraken2/test-data/test_db.zip differ
diff --git a/tool_collections/kraken2/macros.xml b/tool_collections/kraken2/macros.xml
index 0bcddbd22a0..202b6d19b65 100644
--- a/tool_collections/kraken2/macros.xml
+++ b/tool_collections/kraken2/macros.xml
@@ -1,15 +1,26 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.1.3</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">2.1.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">24.0</token>
     <token name="@INTYPES@">fasta,fasta.gz,fasta.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
     <xml name="input_database">
-        <param label="Select a Kraken2 database" name="kraken2_database" type="select">
-            <options from_data_table="kraken2_databases">
-                <validator message="No Kraken2 database is available" type="no_options" />
-            </options>
-        </param>
+        <conditional name="kraken2_database">
+            <param type="select" name="database_source" label="Kraken2 database source">
+                <option value="builtin" selected="true">Use a database from the Galaxy server</option>
+                <option value="history">Use a database from the history</option>
+            </param>
+            <when value="builtin">
+                <param label="Select a Kraken2 database" name="builtin_database" type="select">
+                    <options from_data_table="kraken2_databases">
+                        <validator message="No Kraken2 database is available" type="no_options" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" name="custom_database" label="Kraken2 database" format="directory" help="A kraken2 is a directory containing the files hash.k2d, opts.k2d and taxo.k2d"/>
+            </when>
+        </conditional>
     </xml>
     <xml name="citations">
         <citations>