diff data_manager/data_manager_build_amrfinderplus.xml @ 2:a5921c09b7b7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709

--- a/data_manager/data_manager_build_amrfinderplus.xml	Sun Apr 16 08:29:18 2023 +0000
+++ b/data_manager/data_manager_build_amrfinderplus.xml	Thu May 30 13:06:37 2024 +0000
@@ -1,62 +1,28 @@
 <tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>AMRfinderplus database builder</description>
+    <description>AMRFinderPlus database builder</description>
     <macros>
         <import>macro.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
       <![CDATA[
-        python '$__tool_directory__/data_manager_build_amrfinderplus.py'
-        '$output_file'
-        --db_version '$database_list.database_version_select'
-        #if $database_list.database_version_select != 'latest':
-            --db_date '$database_list.database_date_select'
-        #end if
-        $test_data_manager
+python '$__tool_directory__/data_manager_build_amrfinderplus.py'
+    '$output_file'
+    --db_version '$database_list.database_version_select'
+    #if $database_list.database_version_select != 'latest':
+    --db_date '$database_list.database_date_select'
+    #end if
+    $test_data_manager
       ]]></command>
     <inputs>
         <conditional name="database_list">
             <param name="database_version_select" type="select" label="Database version">
-                <option value="latest" selected="true">Latest available version</option>
-                <option value="3.10">V3.10</option>
-                <option value="3.9">V3.9</option>
-                <option value="3.8">V3.8</option>
-                <option value="3.6">V3.6</option>
+                <option value="3.12">V3.12</option>
             </param>
-            <when value="latest">
-            </when>
-            <when value="3.10">
+            <when value="3.12">
                 <param name="database_date_select" type="select" label="Date version">
-                <option value="2022-10-11.2" selected="true">2022-10-11.2</option>
-                <option value="2022-08-09.1">2022-08-09.1</option>
-                <option value="2022-05-26.1">2022-05-26.1</option>
-                <option value="2022-04-04.1">2022-04-04.1</option>
-                <option value="2021-12-21.1">2021-12-21.1</option>
-                <option value="2021-09-30.1">2021-09-30.1</option>
-                <option value="2021-09-30.1">2021-08-11.1</option>
-                <option value="2021-09-30.1">2021-06-01.1</option>
-                <option value="2021-09-30.1">2021-03-01.1</option>
-                </param>
-            </when>
-            <when value="3.9">
-                <param name="database_date_select" type="select" label="Date version">
-                <option value="2020-11-09.1" selected="true">2020-11-09.1</option>
-                <option value="2020-12-17.1">2020-12-17.1</option>
-                </param>
-            </when>
-             <when value="3.8">
-                <param name="database_date_select" type="select" label="Date version">
-                <option value="2020-09-30.1" selected="true">2020-09-30.1</option>
-                <option value="2020-09-22.2">2020-09-22.2</option>
-                <option value="2020-07-16.2">2020-07-16.2</option>
-                <option value="2020-06-11.1">2020-06-11.1</option>
-                <option value="2020-05-04.1">2020-05-04.1</option>
-                </param>
-            </when>
-            <when value="3.6">
-                <param name="database_date_select" type="select" label="Date version">
-                <option value="2020-01-22.1" selected="true">2020-01-22.1</option>
-                <option value="2020-03-20.1">2020-03-20.1</option>
+                    <option value="2024-05-02.2">2024-05-02.2</option>
+                    <option value="2024-01-31.1">2024-01-31.1</option>
                 </param>
             </when>
         </conditional>
@@ -73,24 +39,31 @@
                 <assert_contents>
                     <has_n_lines n="1"/>
                     <has_text text="{&quot;data_tables&quot;"/>
-                    <has_text text="amrfinderplus_database"/>
+                    <has_text text="amrfinderplus_versioned_database"/>
+                    <has_text text='"db_version": "3.12"'/>
                 </assert_contents>
             </output>
         </test>
-        <!-- Test_2 DB 3.2 -->
+        <!-- Test_2 DB 3.12 2024-01-31.1 -->
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
             <conditional name="database_list">
-                <param name="database_version_select" value="3.6"/>
-                <param name="database_date_select" value="2020-03-20.1"/>
+                <param name="database_version_select" value="3.12"/>
+                <param name="database_date_select" value="2024-01-31.1"/>
             </conditional>
-            <output name="output_file" value="amrfinderplus_test_data_manager_2.json"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_text text="{&quot;data_tables&quot;"/>
+                    <has_text text="amrfinderplus_versioned_database"/>
+                    <has_text text='"name": "V3.12-2024-01-31.1"'/>
+                    <has_text text='"db_version": "3.12"'/>
+                </assert_contents>
+            </output>
         </test>
-
-
     </tests>
     <help><![CDATA[
-        Download amrfinderplus database from the NCBI server
+Download AMRFinderPlus database from the NCBI server
     ]]></help>
     <citations>
         <citation type="doi">10.1038/s41598-021-91456-0</citation>