Mercurial > repos > iuc > data_manager_gtdbtk_database_installer

changeset 9:1a049e50e6b8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit c63b1bff90ebc5b5df0a4cbd9a294fc1d51583c7
author iuc
date Thu, 09 Oct 2025 08:23:46 +0000
parents 6a6175006cb9
children
files data_manager/gtdbtk_database_installer.py data_manager/gtdbtk_database_installer.xml
diffstat 2 files changed, 19 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/gtdbtk_database_installer.py	Mon Oct 21 15:49:43 2024 +0000
+++ b/data_manager/gtdbtk_database_installer.py	Thu Oct 09 08:23:46 2025 +0000
@@ -33,6 +33,14 @@
         "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/ar53_metadata_r220.tsv.gz",
         "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/bac120_metadata_r220.tsv.gz",
     },
+    "226": {
+        "full": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz",
+        "meta_ar": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/ar53_metadata_r226.tsv.gz",
+        "meta_bac": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/bac120_metadata_r226.tsv.gz",
+    },
+    "mocked": {
+        "full": "https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_package/mockup_db/mockup.tar.gz",
+    },
 }
 
 
@@ -174,7 +182,10 @@
     data_manager_entry["value"] = (
         f"{database_name.replace(' ', '_').lower()}_release_{release}_downloaded_{time}"
     )
-    data_manager_entry["name"] = f"{database_name} - release {release} ({time})"
+    if release == "mocked_226":
+        data_manager_entry["name"] = "Mocked GTBD DB (226)"
+    else:
+        data_manager_entry["name"] = f"{database_name} - release {release} ({time})"
     data_manager_entry["path"] = file_path
     data_manager_entry["version"] = release
     return data_manager_entry
--- a/data_manager/gtdbtk_database_installer.xml	Mon Oct 21 15:49:43 2024 +0000
+++ b/data_manager/gtdbtk_database_installer.xml	Thu Oct 09 08:23:46 2025 +0000
@@ -1,8 +1,8 @@
 <tool id="gtdbtk_database_installer" name="GTDB-Tk Database Installer" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description></description>
     <macros>
-        <token name="@TOOL_VERSION@">202</token>
-        <token name="@VERSION_SUFFIX@">4</token>
+        <token name="@TOOL_VERSION@">226</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@PROFILE@">20.09</token>
     </macros>
     <requirements>
@@ -25,6 +25,8 @@
             <option value="207">207</option>
             <option value="214">214</option>
             <option value="220">220</option>
+            <option value="226">226</option>
+            <option value="mocked_226">mocked DB (226)</option>
         </param>
     </inputs>
     <outputs>
@@ -43,8 +45,9 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test meta data download with tsv.gz-->
+        <!-- to large .. takes to much time
         <test>
-            <!-- Test meta data download with tsv.gz-->
             <param name="release" value="220"/>
             <param name="meta" value="true"/>
             <output name="out_file">
@@ -53,7 +56,7 @@
                     <has_text text="metadata_tables_release_220_downloaded_"/>
                 </assert_contents>
             </output>
-        </test>
+        </test> -->
         <test>
             <!-- Test meta data download with tar.gz -->
             <param name="release" value="207"/>