Mercurial > repos > pimarin > data_manager_bakta

diff data_manager/bakta_build_database.xml @ 11:c50e8b4f74d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
author pimarin
date Wed, 02 Nov 2022 11:06:36 +0000
parents 683b09c92299
children 7bd60bfa8ffc
line wrap: on
line diff
--- a/data_manager/bakta_build_database.xml	Thu Oct 27 15:56:22 2022 +0000
+++ b/data_manager/bakta_build_database.xml	Wed Nov 02 11:06:36 2022 +0000
@@ -1,6 +1,6 @@
 
 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description> Bakta database builder </description>
+    <description>Bakta database builder</description>
     <macros>
         <import>macro.xml</import>
     </macros>
@@ -8,31 +8,30 @@
     <expand macro="version_command"/>
 
     <command detect_errors="aggressive"><![CDATA[
-        mkdir './output_dir_json' &&
-        ln -s '$output_file' './output_dir_json/json_output.json' &&
         python '$__tool_directory__/bakta_build_database.py'
-        './output_dir_json/json_output.json'
+        '$output_file'
         --database_version '$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="test"> database_test </option>
+        <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>
         </param>
+        <param name="test_data_manager" type="hidden" value=""/>
     </inputs>
     <outputs>
-        <data name="output_file" format="data_manager_json" from_work_dir="./output_dir_json/json_output.json"/>
+        <data name="output_file" format="data_manager_json"/>
     </outputs>
     <tests>
         <!-- Test download -->
         <test expect_num_outputs="1">
-            <param name="database_select" value="test"/>
+            <param name="test_data_manager" value="--test"/>
             <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/>
         </test>
     </tests>