diff data_manager/bakta_build_database.xml @ 0:9d08486abf8e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bakta_build_database.xml	Wed Aug 17 14:42:22 2022 +0000
@@ -0,0 +1,54 @@
+<?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>
+        <import>macro.xml</import>
+    </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
+    ]]></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>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+
+        <!-- TEST2 update -->
+        <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>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Download, update or list bakta databases <https://github.com/oschwengers/bakta#database>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1099/mgen.0.000685</citation>
+    </citations>
+</tool>