Mercurial > repos > iuc > amrfinderplus_data_manager_build

changeset 2:8fa7efc32500 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
author iuc
date Sun, 23 Nov 2025 12:21:18 +0000
parents d4e3b8d47f49
children
files data_manager/data_manager_build_amrfinderplus.py data_manager/data_manager_build_amrfinderplus.xml data_manager/macro.xml data_manager_conf.xml test-data/amrfinderplus.loc.test test-data/amrfinderplus_test_data_manager_2.json test-data/amrfinderplus_versioned.loc.test tool-data/amrfinderplus.loc.sample tool-data/amrfinderplus_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 11 files changed, 223 insertions(+), 161 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_build_amrfinderplus.py	Sun Apr 16 08:26:14 2023 +0000
+++ b/data_manager/data_manager_build_amrfinderplus.py	Sun Nov 23 12:21:18 2025 +0000
@@ -14,11 +14,13 @@
     Create the json file with database information for galaxy data manager
     """
 
-    def __init__(self,
-                 amrfinderplus_database="amrfinderplus_database",
-                 db_name="amrfinderplus-db",
-                 amrfinderplus_version="latest",
-                 date_version=None):
+    def __init__(
+        self,
+        amrfinderplus_database="amrfinderplus_versioned_database",
+        db_name="amrfinderplus-db",
+        amrfinderplus_version="latest",
+        date_version=None,
+    ):
         self.data_table_name = amrfinderplus_database
         self._db_name = db_name
         self._amrfinderplus_version = amrfinderplus_version
@@ -31,11 +33,7 @@
         Skeleton of a data_table format
         return: a data table formatted for json output
         """
-        self.data_table_entry = {
-            "data_tables": {
-                self.data_table_name: {}
-            }
-        }
+        self.data_table_entry = {"data_tables": {self.data_table_name: {}}}
         return self.data_table_entry
 
     def get_data_manager(self):
@@ -44,13 +42,19 @@
         return: The data table with database information
         """
         self.amrfinderplus_table_list = self.get_data_table_format()
-        amrfinderplus_value = f"amrfinderplus_V{self._amrfinderplus_version}" \
-                              f"_{self._amrfinderplus_date_version}"
-        amrfinderplus_name = f"V{self._amrfinderplus_version}" \
-                             f"-{self._amrfinderplus_date_version}"
-        data_info = dict(value=amrfinderplus_value,
-                         name=amrfinderplus_name,
-                         path=self._db_name)
+        amrfinderplus_value = (
+            f"amrfinderplus_V{self._amrfinderplus_version}"
+            f"_{self._amrfinderplus_date_version}"
+        )
+        amrfinderplus_name = (
+            f"V{self._amrfinderplus_version}" f"-{self._amrfinderplus_date_version}"
+        )
+        data_info = dict(
+            value=amrfinderplus_value,
+            name=amrfinderplus_name,
+            db_version=self._amrfinderplus_version,
+            path=self._db_name,
+        )
         self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
         return self.amrfinderplus_table_list
 
@@ -62,24 +66,28 @@
     Build the data manager infos for galaxy
     """
 
-    def __init__(self,
-                 output_dir=Path.cwd(),
-                 ncbi_url="ftp.ncbi.nlm.nih.gov",
-                 ftp_login="anonymous",
-                 ftp_password="anonymous",
-                 amrfinderplus_database="amrfinderplus_database",
-                 db_name="amrfinderplus-db",
-                 amrfinderplus_version="latest",
-                 json_file_path=None,
-                 date_version=None,
-                 amrfinderplus_db_path=None,
-                 test_mode=False):
+    def __init__(
+        self,
+        output_dir=Path.cwd(),
+        ncbi_url="ftp.ncbi.nlm.nih.gov",
+        ftp_login="anonymous",
+        ftp_password="anonymous",
+        amrfinderplus_database="amrfinderplus_database",
+        db_name="amrfinderplus-db",
+        amrfinderplus_version="latest",
+        json_file_path=None,
+        date_version=None,
+        amrfinderplus_db_path=None,
+        test_mode=False,
+    ):
 
         super().__init__()
         self.json_file_path = json_file_path
         self._output_dir = output_dir
         self._ncbi_ftp_url = ncbi_url
-        self._ncbi_database_path = "pathogen/Antimicrobial_resistance/AMRFinderPlus/database"
+        self._ncbi_database_path = (
+            "pathogen/Antimicrobial_resistance/AMRFinderPlus/database"
+        )
         self._login = ftp_login
         self._password = ftp_password
         self._amrfinderplus_database = amrfinderplus_database
@@ -102,42 +110,61 @@
         [cmd.append(i) for i in args]
         proc = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
         if proc.returncode != 0:
-            print(f'Error type {proc.returncode} with : \n {proc}')
+            print(f"Error type {proc.returncode} with : \n {proc}")
 
     def download_amrfinderplus_db(self):
         """
         Download the amrfinderplus database from the ncbi ftp server
         """
-        self.amrfinderplus_db_path = f'{self._output_dir}/{self._db_name}'
+        self.amrfinderplus_db_path = f"{self._output_dir}/{self._db_name}"
         os.makedirs(self.amrfinderplus_db_path)
-        if self._amrfinderplus_version == 'latest':
+
+        if self._amrfinderplus_version == "latest":
             self.get_amrfinderplus_version()
 
-        amrfinderplus_ftp_path = f"ftp://{self._login}:" \
-                                 f"{self._password}@{self._ncbi_ftp_url}/" \
-                                 f"{self._ncbi_database_path}/" \
-                                 f"{self._amrfinderplus_version}/" \
-                                 f"{self._amrfinderplus_date_version}"
+        amrfinderplus_ftp_path = (
+            f"ftp://{self._login}:"
+            f"{self._password}@{self._ncbi_ftp_url}/"
+            f"{self._ncbi_database_path}/"
+            f"{self._amrfinderplus_version}/"
+            f"{self._amrfinderplus_date_version}"
+        )
+
+        if self._amrfinderplus_version == "3.12":
+            taxa_group_file = "taxgroup.tab"
+            test_dna_fasta = "AMR_DNA-Escherichia"
+        else:
+            taxa_group_file = "taxgroup.tsv"
+            test_dna_fasta = "AMR_DNA-Escherichia.fa"
         if self.test_mode is True:
-            file_list = ["AMR_DNA-Escherichia", "version.txt", "taxgroup.tab", "database_format_version.txt"]
+            file_list = [
+                test_dna_fasta,
+                "version.txt",
+                taxa_group_file,
+                "database_format_version.txt",
+            ]
             output_option = "-O"
             for file in file_list:
-                self.subprocess_cmd("wget",
-                                    "-nd",
-                                    "-np",
-                                    "-r",
-                                    f"{amrfinderplus_ftp_path}/{file}",
-                                    output_option,
-                                    f"{self.amrfinderplus_db_path}/{file}")
+                self.subprocess_cmd(
+                    "wget",
+                    "-nd",
+                    "-np",
+                    "-r",
+                    f"{amrfinderplus_ftp_path}/{file}",
+                    output_option,
+                    f"{self.amrfinderplus_db_path}/{file}",
+                )
         else:
             output_option = "-P"
-            self.subprocess_cmd("wget",
-                                "-nd",
-                                "-np",
-                                "-r",
-                                amrfinderplus_ftp_path,
-                                output_option,
-                                self.amrfinderplus_db_path)
+            self.subprocess_cmd(
+                "wget",
+                "-nd",
+                "-np",
+                "-r",
+                amrfinderplus_ftp_path,
+                output_option,
+                self.amrfinderplus_db_path,
+            )
 
     def make_hmm_profile(self):
         """
@@ -154,27 +181,48 @@
         Extract le list of species which have file in the database
         return: a filtered species list of available species in the database
         """
-        taxa_group_path = Path(f"{self.amrfinderplus_db_path}/taxgroup.tab")
+        if self._amrfinderplus_version == "3.12":
+            taxa_group_file = "taxgroup.tab"
+        else:
+            taxa_group_file = "taxgroup.tsv"
+        taxa_group_path = Path(f"{self.amrfinderplus_db_path}/{taxa_group_file}")
         if Path.exists(taxa_group_path):
             taxa_table = pd.read_table(taxa_group_path)
-            taxa_table.columns = ["taxgroup", "gpipe_taxgroup", "number_of_nucl_ref_genes"]
-            taxa_df = taxa_table[taxa_table.number_of_nucl_ref_genes > 0].filter(items=["taxgroup"], axis=1)
+            taxa_table.columns = [
+                "taxgroup",
+                "gpipe_taxgroup",
+                "number_of_nucl_ref_genes",
+            ]
+            taxa_df = taxa_table[taxa_table.number_of_nucl_ref_genes > 0].filter(
+                items=["taxgroup"], axis=1
+            )
             if self.test_mode is True:
                 taxa_df = taxa_df[taxa_df.taxgroup == "Escherichia"].taxgroup
             else:
                 taxa_df = taxa_df.taxgroup
             self.species_list = list(taxa_df)
         else:
-            print("taxgroup.tab file is missing to list available species")
+            print(f"{taxa_group_file} file is missing to list available species")
 
     def make_blastdb(self):
         """
         Index fasta file for blast
         """
         self.extract_filelist_makeblast()
-        nucl_file_db_list = [f'{self.amrfinderplus_db_path}/AMR_DNA-{specie}' for specie in self.species_list]
-        amr_dna = f'{self.amrfinderplus_db_path}/AMR_CDS'
-        amr_prot = f'{self.amrfinderplus_db_path}/AMRProt'
+        if self._amrfinderplus_version == "3.12":
+            nucl_file_db_list = [
+                f"{self.amrfinderplus_db_path}/AMR_DNA-{specie}"
+                for specie in self.species_list
+            ]
+            amr_dna = f"{self.amrfinderplus_db_path}/AMR_CDS"
+            amr_prot = f"{self.amrfinderplus_db_path}/AMRProt"
+        else:
+            nucl_file_db_list = [
+                f"{self.amrfinderplus_db_path}/AMR_DNA-{specie}.fa"
+                for specie in self.species_list
+            ]
+            amr_dna = f"{self.amrfinderplus_db_path}/AMR_CDS.fa"
+            amr_prot = f"{self.amrfinderplus_db_path}/AMRProt.fa"
         os.chdir(self.amrfinderplus_db_path)
         if Path(amr_dna).exists():
             nucl_file_db_list.append(amr_dna)
@@ -184,10 +232,16 @@
             self.subprocess_cmd("makeblastdb", "-in", amr_prot, "-dbtype", "prot")
         else:
             print("No file AMRProt detected for indexing")
-        [self.subprocess_cmd("makeblastdb", "-in", file, "-dbtype", "nucl") for file in nucl_file_db_list]
+        [
+            self.subprocess_cmd("makeblastdb", "-in", file, "-dbtype", "nucl")
+            for file in nucl_file_db_list
+        ]
 
-    def get_amrfinderplus_version(self, version_file="version.txt",
-                                  database_version_file="database_format_version.txt"):
+    def get_amrfinderplus_version(
+        self,
+        version_file="version.txt",
+        database_version_file="database_format_version.txt",
+    ):
         """
         Check the version when latest if provided and update the number
         param version_file: name of the file containing version information
@@ -198,11 +252,14 @@
         ftp.cwd(f"{self._ncbi_database_path}/{self._amrfinderplus_version}")
         db_version = BytesIO()
         db_date_version = BytesIO()
-        ftp.retrbinary(f'RETR {version_file}', db_version.write)
-        ftp.retrbinary(f'RETR {database_version_file}', db_date_version.write)
-        self._amrfinderplus_date_version = db_version.getvalue().decode("utf-8").splitlines()[0]
-        self._amrfinderplus_version = '.'.join(
-            db_date_version.getvalue().decode("utf-8").splitlines()[0].split(".")[:2])
+        ftp.retrbinary(f"RETR {version_file}", db_version.write)
+        ftp.retrbinary(f"RETR {database_version_file}", db_date_version.write)
+        self._amrfinderplus_date_version = (
+            db_version.getvalue().decode("utf-8").splitlines()[0]
+        )
+        self._amrfinderplus_version = ".".join(
+            db_date_version.getvalue().decode("utf-8").splitlines()[0].split(".")[:2]
+        )
 
     def read_json_input_file(self):
         """
@@ -210,7 +267,7 @@
         """
         with open(self.json_file_path) as fh:
             params = json.load(fh)
-        target_dir = params['output_data'][0]['extra_files_path']
+        target_dir = params["output_data"][0]["extra_files_path"]
         os.makedirs(target_dir)
         self._output_dir = target_dir
 
@@ -218,7 +275,7 @@
         """
         Write in the imported json file
         """
-        with open(self.json_file_path, 'w') as fh:
+        with open(self.json_file_path, "w") as fh:
             json.dump(self.get_data_manager(), fh, sort_keys=True)
 
 
@@ -229,23 +286,32 @@
     """
     # parse options and arguments
     arg_parser = argparse.ArgumentParser()
-    arg_parser.add_argument("data_manager_json",
-                            help="json file from galaxy")
-    arg_parser.add_argument("--db_version", default="latest",
-                            help="select the major version of the database (e.g. 3.10, 3.8), default is latest")
-    arg_parser.add_argument("--db_date",
-                            help="select the date into the database version (e.g. 2022-10-11.2)")
-    arg_parser.add_argument("--test", action='store_true',
-                            help="option to test the script with an lighted database")
+    arg_parser.add_argument("data_manager_json", help="json file from galaxy")
+    arg_parser.add_argument(
+        "--db_version",
+        default="latest",
+        help="select the major version of the database (e.g. 3.10, 3.8), default is latest",
+    )
+    arg_parser.add_argument(
+        "--db_date",
+        help="select the date into the database version (e.g. 2022-10-11.2)",
+    )
+    arg_parser.add_argument(
+        "--test",
+        action="store_true",
+        help="option to test the script with an lighted database",
+    )
     return arg_parser.parse_args()
 
 
 def main():
     all_args = parse_arguments()
-    amrfinderplus_download = DownloadAmrFinderPlusDatabase(amrfinderplus_version=all_args.db_version,
-                                                           date_version=all_args.db_date,
-                                                           json_file_path=all_args.data_manager_json,
-                                                           test_mode=all_args.test)
+    amrfinderplus_download = DownloadAmrFinderPlusDatabase(
+        amrfinderplus_version=all_args.db_version,
+        date_version=all_args.db_date,
+        json_file_path=all_args.data_manager_json,
+        test_mode=all_args.test,
+    )
     amrfinderplus_download.read_json_input_file()
     amrfinderplus_download.download_amrfinderplus_db()
     amrfinderplus_download.make_hmm_profile()
@@ -253,5 +319,5 @@
     amrfinderplus_download.write_json_infos()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
--- a/data_manager/data_manager_build_amrfinderplus.xml	Sun Apr 16 08:26:14 2023 +0000
+++ b/data_manager/data_manager_build_amrfinderplus.xml	Sun Nov 23 12:21:18 2025 +0000
@@ -1,66 +1,38 @@
 <tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>AMRfinderplus database builder</description>
+    <description>AMRFinderPlus database builder</description>
     <macros>
         <import>macro.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
       <![CDATA[
-        python '$__tool_directory__/data_manager_build_amrfinderplus.py'
-        '$output_file'
-        --db_version '$database_list.database_version_select'
-        #if $database_list.database_version_select != 'latest':
-            --db_date '$database_list.database_date_select'
-        #end if
-        $test_data_manager
+python '$__tool_directory__/data_manager_build_amrfinderplus.py'
+    '$output_file'
+    --db_version '$database_list.database_version_select'
+    #if $database_list.database_version_select != 'latest':
+    --db_date '$database_list.database_date_select'
+    #end if
+    $test_data_manager
       ]]></command>
     <inputs>
         <conditional name="database_list">
             <param name="database_version_select" type="select" label="Database version">
-                <option value="latest" selected="true">Latest available version</option>
-                <option value="3.10">V3.10</option>
-                <option value="3.9">V3.9</option>
-                <option value="3.8">V3.8</option>
-                <option value="3.6">V3.6</option>
+                <option value="4.0">V4.0</option>
+                <option value="3.12">V3.12</option>
             </param>
-            <when value="latest">
-            </when>
-            <when value="3.10">
+            <when value="4.0">
                 <param name="database_date_select" type="select" label="Date version">
-                <option value="2022-10-11.2" selected="true">2022-10-11.2</option>
-                <option value="2022-08-09.1">2022-08-09.1</option>
-                <option value="2022-05-26.1">2022-05-26.1</option>
-                <option value="2022-04-04.1">2022-04-04.1</option>
-                <option value="2021-12-21.1">2021-12-21.1</option>
-                <option value="2021-09-30.1">2021-09-30.1</option>
-                <option value="2021-09-30.1">2021-08-11.1</option>
-                <option value="2021-09-30.1">2021-06-01.1</option>
-                <option value="2021-09-30.1">2021-03-01.1</option>
+                    <option value="2025-07-16.1">2025-07-16.1</option>
                 </param>
             </when>
-            <when value="3.9">
-                <param name="database_date_select" type="select" label="Date version">
-                <option value="2020-11-09.1" selected="true">2020-11-09.1</option>
-                <option value="2020-12-17.1">2020-12-17.1</option>
-                </param>
-            </when>
-             <when value="3.8">
+            <when value="3.12">
                 <param name="database_date_select" type="select" label="Date version">
-                <option value="2020-09-30.1" selected="true">2020-09-30.1</option>
-                <option value="2020-09-22.2">2020-09-22.2</option>
-                <option value="2020-07-16.2">2020-07-16.2</option>
-                <option value="2020-06-11.1">2020-06-11.1</option>
-                <option value="2020-05-04.1">2020-05-04.1</option>
-                </param>
-            </when>
-            <when value="3.6">
-                <param name="database_date_select" type="select" label="Date version">
-                <option value="2020-01-22.1" selected="true">2020-01-22.1</option>
-                <option value="2020-03-20.1">2020-03-20.1</option>
+                    <option value="2024-05-02.2">2024-05-02.2</option>
+                    <option value="2024-01-31.1">2024-01-31.1</option>
                 </param>
             </when>
         </conditional>
-         <param name="test_data_manager" type="hidden" value=""/>
+        <param name="test_data_manager" type="hidden" value=""/>
     </inputs>
     <outputs>
         <data name="output_file" format="data_manager_json"/>
@@ -73,24 +45,47 @@
                 <assert_contents>
                     <has_n_lines n="1"/>
                     <has_text text="{&quot;data_tables&quot;"/>
-                    <has_text text="amrfinderplus_database"/>
+                    <has_text text="amrfinderplus_versioned_database"/>
                 </assert_contents>
             </output>
         </test>
-        <!-- Test_2 DB 3.2 -->
+        <!-- Test_2 DB 3.12 2024-01-31.1 -->
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
             <conditional name="database_list">
-                <param name="database_version_select" value="3.6"/>
-                <param name="database_date_select" value="2020-03-20.1"/>
+                <param name="database_version_select" value="3.12"/>
+                <param name="database_date_select" value="2024-01-31.1"/>
             </conditional>
-            <output name="output_file" value="amrfinderplus_test_data_manager_2.json"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_text text="{&quot;data_tables&quot;"/>
+                    <has_text text="amrfinderplus_versioned_database"/>
+                    <has_text text='"name": "V3.12-2024-01-31.1"'/>
+                    <has_text text='"db_version": "3.12"'/>
+                </assert_contents>
+            </output>
         </test>
-
-
+        <!-- Test_3 DB 4.0 2025-07-16.1 -->
+        <test expect_num_outputs="1">
+            <param name="test_data_manager" value="--test"/>
+            <conditional name="database_list">
+                <param name="database_version_select" value="4.0"/>
+                <param name="database_date_select" value="2025-07-16.1"/>
+            </conditional>
+            <output name="output_file">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_text text="{&quot;data_tables&quot;"/>
+                    <has_text text="amrfinderplus_versioned_database"/>
+                    <has_text text='"name": "V4.0-2025-07-16.1"'/>
+                    <has_text text='"db_version": "4.0"'/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
-        Download amrfinderplus database from the NCBI server
+Download AMRFinderPlus database from the NCBI server
     ]]></help>
     <citations>
         <citation type="doi">10.1038/s41598-021-91456-0</citation>
--- a/data_manager/macro.xml	Sun Apr 16 08:26:14 2023 +0000
+++ b/data_manager/macro.xml	Sun Nov 23 12:21:18 2025 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">3.10.45</token>
-    <token name="@PYTHON_VERSION@">3.10.6</token>
-    <token name="@PANDAS@">1.5.1</token>
+    <token name="@TOOL_VERSION@">4.0.23</token>
+    <token name="@PYTHON_VERSION@">3.11.14</token>
+    <token name="@PANDAS@">2.3.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="requirements">
--- a/data_manager_conf.xml	Sun Apr 16 08:26:14 2023 +0000
+++ b/data_manager_conf.xml	Sun Nov 23 12:21:18 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <data_managers>
     <data_manager tool_file="data_manager/data_manager_build_amrfinderplus.xml" id="data_manager_build_amrfinderplus">
-        <data_table name="amrfinderplus_database">
+        <data_table name="amrfinderplus_versioned_database">
             <output>
                 <column name="value" />
                 <column name="name" />
--- a/test-data/amrfinderplus.loc.test	Sun Apr 16 08:26:14 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-# this is a tab separated file describing the location of amrfinderplus database
-#
-# the columns are:
-# value, name, path
-#
-# for example
-amrfinderplus_V3.10_2022-10-11.2	V3.10-2022-10-11.2	amrfinderplus-db
-amrfinderplus_V3.6_2020-03-20.1	V3.6-2020-03-20.1	amrfinderplus-db
--- a/test-data/amrfinderplus_test_data_manager_2.json	Sun Apr 16 08:26:14 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"data_tables": {"amrfinderplus_database": [{"name": "V3.6-2020-03-20.1", "path": "amrfinderplus-db", "value": "amrfinderplus_V3.6_2020-03-20.1"}]}}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amrfinderplus_versioned.loc.test	Sun Nov 23 12:21:18 2025 +0000
@@ -0,0 +1,10 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, db_version, path
+#
+# for example
+amrfinderplus_V3.12_2024-05-02.2	V3.12-2024-05-02.2	3.12	amrfinderplus-db
+amrfinderplus_V3.12_2024-01-31.1	V3.12-2024-01-31.1	3.12	amrfinderplus-db
+amrfinderplus_V3.12_2024-05-02.2	V3.12-2024-05-02.2	3.12	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp3d_yq23a/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-05-02.2
+amrfinderplus_V3.12_2024-01-31.1	V3.12-2024-01-31.1	3.12	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp3d_yq23a/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-01-31.1
--- a/tool-data/amrfinderplus.loc.sample	Sun Apr 16 08:26:14 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# this is a tab separated file describing the location of amrfinderplus database
-#
-# the columns are:
-# value, name, path
-#
-# for example
-#amrfinderplus_V3.6_2020-03-20.1    V3.6-2020-03-20.1    amrfinderplus-db
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/amrfinderplus_versioned.loc.sample	Sun Nov 23 12:21:18 2025 +0000
@@ -0,0 +1,7 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, db_version, path
+#
+# for example
+#amrfinderplus_V3.12_2024-05-02.2	V3.12-2024-05-02.2	3.12    amrfinderplus-db
--- a/tool_data_table_conf.xml.sample	Sun Apr 16 08:26:14 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Nov 23 12:21:18 2025 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of amrfinderplus database in the required format -->
-    <table name="amrfinderplus_database" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/amrfinderplus.loc" />
+    <table name="amrfinderplus_versioned_database" comment_char="#">
+        <columns>value, name, db_version, path</columns>
+        <file path="tool-data/amrfinderplus_versioned.loc" />
     </table>
 </tables>
\ No newline at end of file
--- a/tool_data_table_conf.xml.test	Sun Apr 16 08:26:14 2023 +0000
+++ b/tool_data_table_conf.xml.test	Sun Nov 23 12:21:18 2025 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of amrfinderplus database in the required format -->
-    <table name="amrfinderplus_database" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="${__HERE__}/test-data/amrfinderplus.loc.test"/>
+    <table name="amrfinderplus_versioned_database" comment_char="#">
+        <columns>value, name, db_version, path</columns>
+        <file path="${__HERE__}/test-data/amrfinderplus_versioned.loc.test"/>
     </table>
 </tables>