diff data_manager/kraken2_build_database.xml @ 5:2f27f3b86827 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"

--- a/data_manager/kraken2_build_database.xml	Mon Nov 23 20:49:52 2020 +0000
+++ b/data_manager/kraken2_build_database.xml	Mon Nov 08 15:40:34 2021 +0000
@@ -23,7 +23,14 @@
           --database-type ${database_type.database_type}
           #if $database_type.database_type == "minikraken"
             --minikraken2-version ${database_type.minikraken2_version}
-          #else if $database_type.database_type == "standard"
+          #else if $database_type.database_type == "standard_prebuilt"
+            --standard-prebuilt-size ${database_type.standard_prebuilt_size}
+            #if $database_type.prebuilt_date_custom != ""
+              --prebuilt-date ${database_type.prebuilt_date_custom}
+            #else
+              --prebuilt-date ${database_type.prebuilt_date}
+            #end if
+          #else if $database_type.database_type == "standard_local_build"
             --threads \${GALAXY_SLOTS:-1}
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
@@ -54,14 +61,27 @@
     <inputs>
         <conditional name="database_type">
             <param name="database_type" type="select" multiple="false" label="Database Type">
-                <option value="standard">Standard</option>
+                <option value="standard_local_build">Standard, Local Build</option>
+                <option value="standard_prebuilt">Standard, Pre-Built</option>      
                 <option value="minikraken">MiniKraken</option>
                 <option value="special">Special</option>
                 <option value="custom">Custom</option>
             </param>
-            <when value="standard">
+            <when value="standard_local_build">
                 <expand macro="common_params" />
             </when>
+            <when value="standard_prebuilt">
+                <param name="standard_prebuilt_size" type="select" multiple="false" label="Select size of prebuilt database to download">
+                    <option value="full">Standard-Full (~50 GB)</option>
+                    <option value="16">Standard-16 (~16 GB)</option>
+                    <option value="8">Standard-8 (~8 GB)</option>
+                </param>
+                <param name="prebuilt_date" type="select" multiple="false" optional="true" label="Select database build date">
+                    <option value="2021-05-17">May 17, 2021</option>
+                    <option value="2020-12-02">December 2, 2020</option>
+                </param>
+                <param name="prebuilt_date_custom" type="text" label="Custom date (YYYY-MM-DD)" help="Any text here will overwrite the selected date above." />
+            </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>