diff data_manager/gtdbtk_database_installer.xml @ 7:3b1d503c6260 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
author iuc
date Thu, 03 Oct 2024 12:42:22 +0000
parents df84aaed4769
children 750d902de22c
line wrap: on
line diff
--- a/data_manager/gtdbtk_database_installer.xml	Mon Sep 09 09:01:39 2024 +0000
+++ b/data_manager/gtdbtk_database_installer.xml	Thu Oct 03 12:42:22 2024 +0000
@@ -2,7 +2,7 @@
     <description></description>
     <macros>
         <token name="@TOOL_VERSION@">202</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
         <token name="@PROFILE@">20.09</token>
     </macros>
     <requirements>
@@ -10,18 +10,16 @@
     </requirements>
     <command>
     <![CDATA[
-        python '$__tool_directory__/gtdbtk_database_installer.py'
-          --database_name '$database_name'
-          --release '$release'
-          --out_file '$out_file'
-          $meta
-          $test
+python '$__tool_directory__/gtdbtk_database_installer.py'
+    --release '$release'
+    --out_file '$out_file'
+    $meta
+    $test
     ]]>
     </command>
     <inputs>
-	    <param name="database_name" type="text" value="" label="Database name or description" help="This value will be displayed in the GTDB-Tk Database select list"/>
-        <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " />
-        <param name="test" type="hidden" value="" checked="false" label="Run a dry test run !" />
+	    <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " />
+        <param name="test" type="hidden" value="" checked="false" label="Run a dry test run!" />
         <param name="release" type="select" multiple="false" label="GTDB Release">
             <option value="202">202</option>
             <option value="207">207</option>
@@ -34,40 +32,36 @@
     </outputs>
     <tests>
         <test>
-            <!-- TODO -->
             <!-- Not actually installing a huge GTDB-Tk database -->
             <!-- but it will check if all urls exist -->
             <param name="release" value="202"/>
-            <param name="database_name" value="GTDB-Tk database release 202"/>
             <param name="test" value="--test"/>
             <output name="out_file">
                 <assert_contents>
-                    <has_text text="GTDB-Tk database release 202"/>
-                    <has_text text="release_202"/>
+                    <has_text text="Full Database - release 202 "/>
+                    <has_text text="full_database_release_202_downloaded"/>
                 </assert_contents>
             </output>
         </test>
         <test>
             <!-- Test meta data download with tsv.gz-->
             <param name="release" value="220"/>
-            <param name="database_name" value="GTDB-Tk database release 220 metadata"/>
             <param name="meta" value="true"/>
             <output name="out_file">
                 <assert_contents>
-                    <has_text text="GTDB-Tk database release 220 metadata"/>
-                    <has_text text="release_220"/>
+                    <has_text text="Metadata Tables - release 220"/>
+                    <has_text text="metadata_tables_release_220_downloaded_"/>
                 </assert_contents>
             </output>
         </test>
         <test>
             <!-- Test meta data download with tar.gz -->
             <param name="release" value="207"/>
-            <param name="database_name" value="GTDB-Tk database release 207 metadata"/>
             <param name="meta" value="true"/>
             <output name="out_file">
                 <assert_contents>
-                    <has_text text="GTDB-Tk database release 207 metadata"/>
-                    <has_text text="release_207"/>
+                    <has_text text="Metadata Tables - release 207"/>
+                    <has_text text="metadata_tables_release_207_downloaded_"/>
                 </assert_contents>
             </output>
         </test>