diff data_manager/bakta_build_database.xml @ 1:faae5d8ce0cb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
author pimarin
date Thu, 27 Oct 2022 13:54:13 +0000
parents 9d08486abf8e
children decc1723cf97
line wrap: on
line diff
--- a/data_manager/bakta_build_database.xml	Wed Aug 17 14:42:22 2022 +0000
+++ b/data_manager/bakta_build_database.xml	Thu Oct 27 13:54:13 2022 +0000
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+
 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description> Bakta database builder </description>
     <macros>
@@ -6,47 +6,35 @@
     </macros>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
+
     <command detect_errors="aggressive"><![CDATA[
         python '$__tool_directory__/bakta_build_database.py'
-        #if $database_command == "download"
-            download --output $output_file
-        #else if $database_command == "update"
-        #else if $database_command == "update"
-            update --db $output_file
-        #end if
+        '$output_file'
+        --database_version '$database_select'
     ]]></command>
     <inputs>
-        <conditional>
-            <param name="database_command" type="select" label="Database action" multiple="false" help="Action on bakta database. Install or update database">
-                <option value="download"> Download a prebuild bakta database</option>
-                <option value="custom"> Download a custom database</option>
-                <option value="update"> Update the databases</option>
-            </param>
-            <when value="download"/>
-            <when value="update"/>
-            <when value="custom">
-              <param name="db_link"></param>
-            </when>
-        </conditional>
+        <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)" >
+            <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" selected="true" > V4.0_2022-08-29 </option>
+            <option value="test"> database_test </option>
+        </param>
     </inputs>
     <outputs>
         <data name="output_file" format="data_manager_json" />
     </outputs>
     <tests>
-
-        <!-- TEST2 update -->
+        <!-- Test download -->
         <test expect_num_outputs="1">
-            <param name="database_command" value="update"/>
-            <output name="output_file">
-                <assert_contents>
-                    <has_text text="pangoLEARN data release 2021-04-01"/>
-                    <has_text text='"format_version": "1.0"'/>
-                </assert_contents>
-            </output>
+            <param name="database_select" value="test"/>
+            <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/>
         </test>
     </tests>
     <help><![CDATA[
-        Download, update or list bakta databases <https://github.com/oschwengers/bakta#database>
+        Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>
     ]]></help>
     <citations>
         <citation type="doi">10.1099/mgen.0.000685</citation>