# HG changeset patch
# User iuc
# Date 1773137537 0
# Node ID e17314dfcbd3ac9efa96cd69bd73df0eeceb9c49
# Parent  db4c810682eebf3adb49c7a0ec80d373edaa510f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_snpeff commit 5ed67056af2b7289fcf89e96c34afe11fa39bbdf

diff -r db4c810682ee -r e17314dfcbd3 data_manager/data_manager_snpEff_databases.xml
--- a/data_manager/data_manager_snpEff_databases.xml	Tue Nov 24 07:27:05 2020 +0000
+++ b/data_manager/data_manager_snpEff_databases.xml	Tue Mar 10 10:12:17 2026 +0000
@@ -1,7 +1,7 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3.1t" tool_type="manage_data" profile="18.09">
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="5.4.0c" tool_type="manage_data" profile="24.2">
     <description>Read the list of available SnpEff databases</description>
     <requirements>
-        <requirement type="package" version="4.3.1t">snpeff</requirement>
+        <requirement type="package" version="5.4.0c">snpeff</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
@@ -25,7 +25,7 @@
 This tool updates the list of SnpEff databases for the SnpEff Download data manager.
 It should only need to be run once for a SnpEff version, since it populates the SnpEff Download data manager from the SnpEff config file.
 
-For information about SnpEff: http://snpeff.sourceforge.net
+For information about SnpEff and its databases see: https://pcingola.github.io/SnpEff/snpeff/introduction/#databases.
     ]]></help>
     <citations>
         <citation type="doi">10.4161/fly.19695</citation>
diff -r db4c810682ee -r e17314dfcbd3 data_manager/data_manager_snpEff_download.py
--- a/data_manager/data_manager_snpEff_download.py	Tue Nov 24 07:27:05 2020 +0000
+++ b/data_manager/data_manager_snpEff_download.py	Tue Mar 10 10:12:17 2026 +0000
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+import gzip
 import json
 import optparse
 import os
@@ -61,6 +62,20 @@
     return snpeff_version
 
 
+def getSnpeffDbVersion(db_predictor_bin_file):
+    snpeff_db_version = None
+    try:
+        with gzip.open(db_predictor_bin_file, "rt") as fh:
+            buf = fh.read(100)
+            lines = buf.splitlines()
+            m = re.match(r"^(SnpEff)\s+(\d+\.\d+).*$", lines[0].strip())
+            if m:
+                snpeff_db_version = m.groups()[0] + m.groups()[1]
+    except Exception:
+        pass
+    return snpeff_db_version
+
+
 # Download human database 'hg19'
 # java -jar snpEff.jar download -v hg19
 #
@@ -87,12 +102,18 @@
     snpeff_version = getSnpeffVersion()
     key = snpeff_version + '_' + genome_version
     if os.path.isdir(genome_path):
-        for _, _, files in os.walk(genome_path):
+        for dirpath, _, files in os.walk(genome_path):
             for fname in files:
                 if fname.startswith('snpEffectPredictor'):
                     # if snpEffectPredictor.bin download succeeded
                     name = genome_version + (' : ' + organism if organism else '')
-                    data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
+                    data_table_entry = dict(
+                        key=key,
+                        version=getSnpeffDbVersion(os.path.join(dirpath, fname)) or snpeff_version,
+                        value=genome_version,
+                        name=name,
+                        path=data_dir
+                    )
                     _add_data_table_entry(data_manager_dict, 'snpeffv_genomedb', data_table_entry)
                 else:
                     m = re.match(regulation_pattern, fname)
diff -r db4c810682ee -r e17314dfcbd3 data_manager/data_manager_snpEff_download.xml
--- a/data_manager/data_manager_snpEff_download.xml	Tue Nov 24 07:27:05 2020 +0000
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Mar 10 10:12:17 2026 +0000
@@ -1,7 +1,7 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3.1t" tool_type="manage_data" profile="18.09">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="5.4.0c" tool_type="manage_data" profile="24.2">
     <description>Download a new database</description>
     <requirements>
-        <requirement type="package" version="4.3.1t">snpeff</requirement>
+        <requirement type="package" version="5.4.0c">snpeff</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/data_manager_snpEff_download.py'
@@ -9,7 +9,7 @@
 '$out_file'
     ]]></command>
     <inputs>
-        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)" help="https://snpeff-data.galaxyproject.org/databases/">
+        <param name="genome_version" type="text" value="" label="SnpEff Genome Version Name (e.g. GRCh38.76)">
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
     </inputs>
@@ -19,12 +19,12 @@
     </outputs>
     <tests>
         <test>
-            <param name="genome_version" value="GRCh38.86"/>
+            <param name="genome_version" value="ebola_zaire"/>
             <output name="out_file">
                 <assert_contents>
                     <!-- Check that a genome was added -->
-                    <has_text text="GRCh38.86" />
-                    <has_text text="snpeffv_regulationdb" />
+                    <has_text text="ebola_zaire" />
+                    <has_text text="snpeffv_genomedb" />
                 </assert_contents>
             </output>
         </test>
@@ -34,9 +34,7 @@
 
 To see the list of available SnpEff genomes, run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeffv_databases.
 
-The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
-
-For details about this tool, please go to http://snpeff.sourceforge.net
+For details about this tool, please go to https://pcingola.github.io/SnpEff/snpeff/introduction/#databases.
     ]]></help>
     <citations>
         <citation type="doi">10.4161/fly.19695</citation>