--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/mapseq_db_fetcher.xml	Thu Mar 26 20:22:36 2026 +0000
@@ -0,0 +1,52 @@
+<tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Fetches the DB required for mapseq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        python '$__tool_directory__/data_manager_fetch_mapseq_db.py' 
+        --out '${out_file}' 
+        --version '${select_version.version}' 
+        --database-type '${database_type}'
+    ]]>
+    </command>
+    <inputs>
+        <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" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    Downloads preformatted DBs form MGnify that can be used for mapseq. 
+    The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/
+    </help>
+    <expand macro="citations" />
+    <expand macro="creator" />
+</tool>
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