Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

diff data_manager/plasmidfinder_fetch_database.xml @ 5:60cfd33bc2fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 0a3992c5be846fc9f18b7ca18f0adcd78f5b9396-dirty
author pimarin
date Mon, 24 Jul 2023 10:00:33 +0000
parents 5ffc68b4ec04
children 4e933a39094f
line wrap: on
line diff
--- a/data_manager/plasmidfinder_fetch_database.xml	Fri Feb 17 14:07:54 2023 +0000
+++ b/data_manager/plasmidfinder_fetch_database.xml	Mon Jul 24 10:00:33 2023 +0000
@@ -1,4 +1,3 @@
-
 <tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>plasmidfinder database builder</description>
     <macros>
@@ -10,38 +9,30 @@
         python '$__tool_directory__/plasmidfinder_fetch_database.py'
         --db_version '$database_select'
         '$output_file'
+        && cat '$output_file'
       ]]></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="2.1">V2.1_2019-08-28</option>
-        </param>param>
+        </param>
     </inputs>
     <outputs>
         <data name="output_file" format="data_manager_json"/>
     </outputs>
     <tests>
-        <!-- Test_1 DB latest -->
+        <!-- Test_2 DB 2.1 -->
         <test expect_num_outputs="1">
-            <param name="database_select" value="latest"/>
-            <output name="output_file" value="plasmidfinder_test_data_manager_latest.json">
-                <assert_contents>
-                    <has_text_matching expression="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;\:\ \[\{&quot;date&quot;\:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;\:\ &quot;\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;\:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;\:\ &quot;plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d&quot;\}\]\}\}"/>
-                </assert_contents>
-            </output>
-        </test>
-         <!-- Test_2 DB 2.1 -->
-        <test expect_num_outputs="1">
-            <param name="database_select" value="2.1"/>
-            <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
-                <assert_contents>
-                    <has_text_matching expression="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;:\ \[\{&quot;date&quot;\:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;\:\ &quot;2.1_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;\:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;\:\ &quot;plasmidfinder_1307168b1ce7_\d\d\d\d-\d\d-\d\d&quot;\}\]\}\}"/>
-                </assert_contents>
-            </output>
+           <param name="database_select" value="2.1"/>
+           <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
+               <assert_contents>
+                   <has_text text="2019_08_28"/>
+               </assert_contents>
+           </output>
         </test>
     </tests>
     <help><![CDATA[
-        Download plasmidfinder database from the bitbucket repository
+        Download plasmidfinder database from the bitbucket repository: https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master/
     ]]></help>
     <citations>
         <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>