# HG changeset patch
# User iuc
# Date 1771503214 0
# Node ID 1663e897c832e43238d5e6c2d073e7c8562f1b48
# Parent  150ea60a4ebc9afa9b826b49f3bc9e1dc0b73c0a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit 797b5fc5c1b1eb7903c2ab681f399777b77501e3

diff -r 150ea60a4ebc -r 1663e897c832 data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Wed Nov 05 13:31:52 2025 +0000
+++ b/data_manager/kraken2_build_database.xml	Thu Feb 19 12:13:34 2026 +0000
@@ -1,7 +1,7 @@
 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>database builder</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.1.6</token>
+        <token name="@TOOL_VERSION@">2.17.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <token name="@PROFILE@">24.0</token>
         <xml name="common_params">
@@ -56,7 +56,7 @@
 #import datetime
 #import re
 
-#set now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+#set now = datetime.datetime.now(datetime.UTC).strftime("%Y-%m-%dT%H%M%SZ")
 #set commands = []
 mkdir '$out_file.extra_files_path' &&
 
@@ -75,6 +75,7 @@
         'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)",
     }
     #set special_name = {
+        "core_nt_20251015": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (October, 2025)",
         "core_nt_20250609": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (July, 2025)",
         "core_nt_20241228": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (December, 2024)",
         "core_nt_20240904": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (September, 2024)",
@@ -144,24 +145,21 @@
     #end if
 
     #if $database_type.database_type == "custom"
-        #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
-            "--download-taxonomy",
+        #silent command = ["k2", "download-taxonomy",
             "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'",
             str($database_type.skip_maps)]
         #silent commands.append(" ".join(command))
-        #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
-            "--add-to-library", "'" + str($database_type.custom_fasta) + "'",
+        #silent command = ["k2", "add-to-library", "--threads", '"${GALAXY_SLOTS:-1}"',
+            "--file", "'" + str($database_type.custom_fasta) + "'",
             "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
         #silent commands.append(" ".join(command))
     #end if
 
-    #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"']
+    #silent command = ["k2", "build", "--threads", '"${GALAXY_SLOTS:-1}"']
     #if $database_type.database_type == "standard_local_build"
         #silent command.append("--standard")
     #else if $database_type.database_type == "special"
         #silent command.extend(["--special", str($database_type.special_database_type)])
-    #else if $database_type.database_type == "custom"
-        #silent command.append("--build")
     #end if
     #silent command.extend([
         "--kmer-len", str($database_type.kmer_len),
@@ -172,8 +170,7 @@
     #silent commands.append(" ".join(command))
 
     #if $database_type.clean
-        #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
-            "--clean",
+        #silent command = ["k2", "clean",
             "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
         #silent commands.append(" ".join(command))
     #end if
@@ -208,6 +205,7 @@
             <when value="standard_prebuilt">
                 <conditional name="prebuilt">
                     <param name="prebuilt_date" type="select" label="Select index build date">
+                        <option value="2025-10-15">October 15, 2025</option>
                         <option value="2025-07-14">July 14, 2025</option>
                         <option value="2024-12-28">December 28, 2024</option>
                         <option value="2024-09-04">September 4, 2024</option>
@@ -220,6 +218,21 @@
                         <option value="2020-12-02">December 2, 2020</option>
                         <option value="2020-09-19">September 19, 2020</option>
                     </param>
+                    <when value="2025-10-15">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
                     <when value="2025-07-14">
                         <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
                             <expand macro="viral"/>
@@ -374,6 +387,7 @@
             <when value="special_prebuilt">
                 <conditional name="prebuilt">
                     <param name="xyz" type="select" multiple="false" label="Select pre-built database to download">
+                        <option value="core_nt_20251015">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (October, 2025)</option>
                         <option value="core_nt_20250609">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (July, 2025)</option>
                         <option value="core_nt_20241228">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (December, 2024)</option>
                         <option value="core_nt_20240904">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (September, 2024)</option>
@@ -382,6 +396,10 @@
                         <option value="eupathdb48_20230407">EuPathDB-46 (April 18, 2023)</option>
                         <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
                     </param>
+                    <when value="core_nt_20251015">
+                        <param name="prebuilt_db" type="hidden" value="core_nt"/>
+                        <param name="prebuilt_date" type="hidden" value="20251015"/>
+                    </when>
                     <when value="core_nt_20250609">
                         <param name="prebuilt_db" type="hidden" value="core_nt"/>
                         <param name="prebuilt_date" type="hidden" value="20250609"/>
@@ -460,13 +478,13 @@
                 <expand macro="common_params" />
             </when>
         </conditional>
-        <param name="run_test_command" type="hidden"/>
+        <param name="run_test_command" type="hidden" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />
     </outputs>
     <tests>
-        <!-- standard_local_build -->
+        <!-- standard_local_build - test 1 -->
 
         <test expect_num_outputs="1">
             <conditional name="database_type">
@@ -487,7 +505,7 @@
             </output>
         </test>
 
-        <!-- standard_prebuilt -->
+        <!-- standard_prebuilt - test 2 -->
         <test>
             <conditional name="database_type">
                 <param name="database_type" value="standard_prebuilt" />
@@ -508,7 +526,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- test with latest version -->
+        <!-- test with latest version - test 3 -->
         <test>
             <conditional name="database_type">
                 <param name="database_type" value="standard_prebuilt" />
@@ -529,7 +547,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- test with first 2024 version -->
+        <!-- test with first 2024 version - test 4 -->
         <test>
             <conditional name="database_type">
                 <param name="database_type" value="standard_prebuilt" />
@@ -551,7 +569,7 @@
             </output>
         </test>
 
-        <!-- minikraken -->
+        <!-- minikraken - test 5 -->
 
         <test>
             <conditional name="database_type">
@@ -570,7 +588,7 @@
             </output>
         </test> 
 
-        <!-- special_prebuilt -->
+        <!-- special_prebuilt - test 6 -->
 
        <test>
             <conditional name="database_type">
@@ -594,7 +612,7 @@
             </output>
         </test> 
 
-        <!-- amplicon_prebuilt -->
+        <!-- amplicon_prebuilt - test 7 -->
 
        <test>
             <conditional name="database_type">
@@ -615,7 +633,7 @@
             </output>
         </test> 
 
-        <!-- special -->
+        <!-- special - test 8 -->
 
         <test expect_num_outputs="1">
             <conditional name="database_type">
@@ -636,6 +654,8 @@
                 </assert_contents>
             </output>
         </test>
+
+        <!-- special - test 9 -->
         <test expect_num_outputs="1">
             <conditional name="database_type">
                 <param name="database_type" value="special" />
@@ -656,7 +676,7 @@
             </output>
         </test>
 
-        <!-- custom -->
+        <!-- custom - test 10 -->
 
         <test expect_num_outputs="1">
             <conditional name="database_type">