From 0258fd33c9e425e545ad074eef9db8a31b5bc29c Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Thu, 5 Dec 2024 14:46:54 +0100
Subject: [PATCH 1/2] Update MAPseq DM

---
 .../data_manager/macros.xml                   |  2 +-
 .../data_manager/mapseq_db_fetcher.xml        | 41 +++++++++++--------
 2 files changed, 25 insertions(+), 18 deletions(-)

diff --git a/data_managers/data_manager_mapseq/data_manager/macros.xml b/data_managers/data_manager_mapseq/data_manager/macros.xml
index 4cbc7e347a8..c1681b2eb44 100644
--- a/data_managers/data_manager_mapseq/data_manager/macros.xml
+++ b/data_managers/data_manager_mapseq/data_manager/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>
diff --git a/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml b/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml
index 383b3020ce0..198df5de923 100644
--- a/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml
+++ b/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml
@@ -9,31 +9,38 @@
     <![CDATA[
         python '$__tool_directory__/data_manager_fetch_mapseq_db.py' 
         --out '${out_file}' 
-        --version '${version}' 
+        --version '${select_version.version}' 
         --database-type '${database_type}'
         $test_data_manager_v5
-        $test_data_manager_v6
     ]]>
     </command>
     <inputs>
         <!-- <param name="test_data_manager" type="hidden" /> -->
         <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v5." />
         <param name="test_data_manager_v6" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v6." />
-    
-        <param name="database_type" type="select" multiple="false" label="Database Type">
-            <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
-            <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
-            <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
-            <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
-            <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
-            <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
-            <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
-            <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
-            <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
-        </param>
-    
-        <!-- <param name="test_data_manager" type="text" value=""/> -->
-        <param argument="--version" type="text" value="6.0" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/amplicon-pipeline) for the version."/>
+        <conditional name="select_version">
+            <param argument="--version" type="select" label="Select MGnify version">
+                <option value="5.0">v5.0</option>
+                <option value="6.0">v6.0</option>
+            </param>
+            <when value="5.0">
+                <param name="database_type" type="select" multiple="false" label="Database Type">
+                    <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
+                    <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
+                    <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
+                    <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
+                </param>
+            </when>
+            <when value="6.0">
+                <param name="database_type" type="select" multiple="false" label="Database Type">
+                    <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
+                    <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
+                    <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
+                    <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
+                    <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="data_manager_json" name="out_file" />

From 24cbe6656cadeff49c5489fbdfd40bb908471c7b Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Fri, 6 Dec 2024 16:23:39 +0100
Subject: [PATCH 2/2] removing testv6 from inputs and tests sections

---
 .../data_manager/mapseq_db_fetcher.xml               | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml b/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml
index 198df5de923..4a7c41162e8 100644
--- a/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml
+++ b/data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml
@@ -17,7 +17,6 @@
     <inputs>
         <!-- <param name="test_data_manager" type="hidden" /> -->
         <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v5." />
-        <param name="test_data_manager_v6" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v6." />
         <conditional name="select_version">
             <param argument="--version" type="select" label="Select MGnify version">
                 <option value="5.0">v5.0</option>
@@ -57,17 +56,6 @@
             </assert_contents>
         </output>
     </test>
-    <test expect_num_outputs="1">
-        <param name="test_data_manager_v6" value="--test"/>
-        <param name="version" value="6.0"/>
-        <param name="database_type" value="mgnify_v6_pr2"/>
-        <output name="out_file">
-            <assert_contents>
-                <has_text text="mgnify_v6_pr2"/>
-                <has_text text="6.0"/>
-            </assert_contents>
-        </output>
-    </test>
     </tests>
     <help>
     Downloads preformatted DBs form MGnify that can be used for mapseq.