diff data_manager/kraken2_build_database.xml @ 10:4726ecf3b61b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a

--- a/data_manager/kraken2_build_database.xml	Fri Oct 18 17:08:05 2024 +0000
+++ b/data_manager/kraken2_build_database.xml	Fri Nov 15 22:31:20 2024 +0000
@@ -1,9 +1,8 @@
-<?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@">2.1.3</token>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@VERSION_SUFFIX@">4</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" />
@@ -70,6 +69,9 @@
     --prebuilt-date '$database_type.prebuild.prebuilt_date'
 #else if $database_type.database_type == "minikraken"
     --minikraken2-version '$database_type.minikraken2_version'
+#else if $database_type.database_type == "special_prebuilt"
+    --prebuilt-db '$database_type.special_prebuild.prebuilt_db'
+    --prebuilt-date '$database_type.special_prebuild.prebuilt_date'
 #else if $database_type.database_type == "special"
     --threads \${GALAXY_SLOTS:-1}
     --special-database-type '$database_type.special_database_type'
@@ -98,6 +100,7 @@
                 <option value="standard_local_build">Standard, Local Build</option>
                 <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
                 <option value="minikraken">MiniKraken</option>
+                <option value="special_prebuilt">Special Pre-Built indexes</option>
                 <option value="special">Special</option>
                 <option value="custom">Custom</option>
             </param>
@@ -223,6 +226,22 @@
                     </when>
                 </conditional>
             </when>
+            <when value="special_prebuilt">
+                <conditional name="special_prebuild">
+                    <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
+                        <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option>
+                        <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
+                    </param>
+                    <when value="eupathdb48_20230407">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
+                    </when>
+                    <when value="eupathdb48_20201113">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
+                    </when>
+                </conditional>
+            </when>
             <when value="minikraken">
                 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
                     <option value="v2">Version 2</option>