# HG changeset patch
# User iuc
# Date 1721035285 0
# Node ID 1108eae823a8b097170b1e1223e64ba9598f52a8
# Parent  ce75e9475f0fc227352737a9f5f1bbd97db307f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545

diff -r ce75e9475f0f -r 1108eae823a8 data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Sun Apr 16 08:26:45 2023 +0000
+++ b/data_manager/kraken2_build_database.xml	Mon Jul 15 09:21:25 2024 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0"?>
 <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@">2.1.2</token>
-        <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@PROFILE@">21.01</token>
+        <token name="@TOOL_VERSION@">2.1.3</token>
+        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@PROFILE@">22.01</token>
         <xml name="common_params">
             <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
             <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
@@ -12,7 +13,7 @@
             <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
         </xml>
         <xml name="viral">
-            <option value="viral">Viral (viral; ~50 GB)</option>
+            <option value="viral">Viral (viral; ~0.5 GB)</option>
         </xml>
         <xml name="minusb">
             <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
@@ -45,7 +46,6 @@
             <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
         </xml>
     </macros>
-    <description>database builder</description>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
         <requirement type="package" version="3.7">python</requirement>
@@ -103,12 +103,60 @@
             <when value="standard_prebuilt">
                 <conditional name="prebuild">
                     <param name="prebuilt_date" type="select" label="Select index build date">
+                        <option value="2024-06-05">June 5, 2024</option>
+                        <option value="2024-01-12">January 12, 2024</option>
+                        <option value="2023-06-05">June 5, 2023</option>
                         <option value="2022-06-07">June 7, 2022</option>
                         <option value="2021-05-17">May 17, 2021</option>
                         <option value="2021-01-27">January 27, 2021</option>
                         <option value="2020-12-02">December 2, 2020</option>
                         <option value="2020-09-19">September 19, 2020</option>
                     </param>
+                    <when value="2024-06-05">
+                        <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="2024-01-12">
+                        <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="2023-06-05">
+                        <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="2022-06-07">
                         <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
                             <expand macro="viral"/>
@@ -206,7 +254,7 @@
                 <param name="kmer_len" value="35" />
                 <param name="minimizer_spaces" value="6"/>
                 <param name="load_factor" value="0.7" />
-                <param name="clean" truevalue="--clean"/>
+                <param name="clean" value="true"/>
             </conditional>
             <output name="out_file">
                 <assert_contents>
@@ -221,15 +269,55 @@
                 <param name="database_type" value="standard_prebuilt" />
                 <conditional name="prebuild">
                     <param name="prebuilt_date" value="2022-06-07"/>
-                    <param name="prebuilt_db" value="standard_08gb"/>
+                    <param name="prebuilt_db" value="viral"/>
                 </conditional>
             </conditional>
             <output name="out_file">
                 <assert_contents>
                     <has_text text="kraken2_databases"/>
                     <has_text text="path"/>
-                    <has_text text="Standard-8"/>
-                    <has_text text="_standard_prebuilt_standard_08gb_2022-06-07"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2022-06-07"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test with latest version -->
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2024-01-12"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2024-01-12"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test with first 2024 version -->
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2024-06-05"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2024-06-05"/>
                     <has_text text="Version"/>
                     <has_text text="Downloaded"/>
                 </assert_contents>