Mercurial > repos > iuc > data_manager_bakta

diff data_manager/bakta_build_database.xml @ 5:baceff842902 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
author iuc
date Wed, 05 Jun 2024 14:20:59 +0000
parents 3e73c97f025d
children 97b1b5ad1cda
line wrap: on
line diff
--- a/data_manager/bakta_build_database.xml	Fri Aug 25 23:34:04 2023 +0000
+++ b/data_manager/bakta_build_database.xml	Wed Jun 05 14:20:59 2024 +0000
@@ -4,24 +4,24 @@
         <import>macro.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="exit_code">
-      <![CDATA[
-        python '$__tool_directory__/bakta_build_database.py'
-        '$output_file'
-        --database_version '$database_select'
-        $test_data_manager
-      ]]></command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/bakta_build_database.py'
+    '$output_file'
+    --database_version '$database_select'
+    $test_data_manager
+]]></command>
     <inputs>
         <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
-            <option value="latest" selected="true">Latest available version</option>
-            <option value="1.0">V1.0_2020-11-20</option>
-            <option value="1.1">V1.1_2020-12-18</option>
-            <option value="2.0">V2.0_2021-04-05</option>
-            <option value="3.0">V3.0_2021-08-05</option>
-            <option value="3.1">V3.1_2022-02-03</option>
-            <option value="4.0">V4.0_2022-08-29</option>
-            <option value="5.0">V5.0_2023-02-20</option>
-            <option value="5.0_light">V5.0_light_2023-02-20</option>
+            <option value="5.1" selected="true">V5.1 (2024-01-19)</option>
+            <option value="5.1_light">V5.1 light (2024-01-19)</option>
+            <option value="5.0">V5.0 (2023-02-20)</option>
+            <option value="5.0_light">V5.0 light (2023-02-20)</option>
+            <option value="4.0">V4.0 (2022-08-29)</option>
+            <option value="3.1">V3.1 (2022-02-03)</option>
+            <option value="3.0">V3.0 (2021-08-05)</option>
+            <option value="2.0">V2.0 (2021-04-05)</option>
+            <option value="1.1">V1.1 (2020-12-18)</option>
+            <option value="1.0">V1.0 (2020-11-20)</option>
         </param>
         <param name="test_data_manager" type="hidden" value=""/>
     </inputs>
@@ -33,19 +33,40 @@
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
             <param name="database_select" value="1.0"/>
-            <output name="output_file" value="bakta_test_data_manager1.json" />
+            <output name="output_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text="data_tables"/>
+                    <has_text text="bakta_database"/>
+                    <has_text text="bakta_version"/>
+                    <has_text text="V1.0_2022-10-12"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test 2 with the latest option -->
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
-            <param name="database_select" value="latest"/>
-            <output name="output_file" value="bakta_test_data_manager2.json" />
+            <param name="database_select" value="5.1_light"/>
+            <output name="output_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text="data_tables"/>
+                    <has_text text="bakta_database"/>
+                    <has_text text="bakta_version"/>
+                    <has_text text="V5.1light_2024-01-19"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test 3 with light db -->
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
             <param name="database_select" value="5.0_light"/>
-            <output name="output_file" value="bakta_test_data_manager3.json" />
+            <output name="output_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text="data_tables"/>
+                    <has_text text="bakta_database"/>
+                    <has_text text="bakta_version"/>
+                    <has_text text="V5.0light_2023-06-08"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[