# HG changeset patch
# User nate
# Date 1730923239 0
# Node ID c13785ca61924cd7a3ed5258081932849c1c5db5

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a

diff -r 000000000000 -r c13785ca6192 data_manager/kraken2_build_database.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_database.py	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,502 @@
+#!/usr/bin/env python
+
+import argparse
+import datetime
+import errno
+import json
+import os
+import re
+import shutil
+import subprocess
+import sys
+import tarfile
+from enum import Enum
+
+try:
+    # Python3
+    from urllib.request import urlopen
+    from urllib.error import URLError
+except ImportError:
+    from urllib2 import urlopen
+    from urllib2 import URLError
+
+
+DATA_TABLE_NAME = "kraken2_databases"
+
+
+class KrakenDatabaseTypes(Enum):
+    standard_local_build = 'standard_local_build'
+    standard_prebuilt = 'standard_prebuilt'
+    minikraken = 'minikraken'
+    special_prebuilt = 'special_prebuilt'
+    special = 'special'
+    custom = 'custom'
+
+    def __str__(self):
+        return self.value
+
+
+class SpecialDatabaseTypes(Enum):
+    rdp = 'rdp'
+    greengenes = 'greengenes'
+    silva = 'silva'
+
+    def __str__(self):
+        return self.value
+
+
+class Minikraken2Versions(Enum):
+    v1 = 'v1'
+    v2 = 'v2'
+
+    def __str__(self):
+        return self.value
+
+
+class StandardPrebuiltSizes(Enum):
+    viral = "viral"
+    minusb = "minusb"
+    standard = "standard"
+    standard_08gb = "standard_08gb"
+    standard_16gb = "standard_16gb"
+    pluspf = "pluspf"
+    pluspf_08gb = "pluspf_08gb"
+    pluspf_16gb = "pluspf_16gb"
+    pluspfp = "pluspfp"
+    pluspfp_08gb = "pluspfp_08gb"
+    pluspfp_16gb = "pluspfp_16gb"
+    eupathdb48 = "eupathdb48"
+
+    def __str__(self):
+        return self.value
+
+
+def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
+    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+    database_value = "_".join([
+        now,
+        "standard",
+        "kmer-len", str(kraken2_args["kmer_len"]),
+        "minimizer-len", str(kraken2_args["minimizer_len"]),
+        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+        "load-factor", str(kraken2_args["load_factor"]),
+    ])
+
+    database_name = " ".join([
+        "Standard (Local Build)",
+        "(Created:",
+        now + ",",
+        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
+        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
+        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+        "load-factor", str(kraken2_args["load_factor"]),
+    ])
+
+    database_path = database_value
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--standard',
+        '--kmer-len', str(kraken2_args["kmer_len"]),
+        '--minimizer-len', str(kraken2_args["minimizer_len"]),
+        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
+        '--db', database_path
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    if kraken2_args["clean"]:
+        args = [
+            '--threads', str(kraken2_args["threads"]),
+            '--clean',
+            '--db', database_path
+        ]
+
+        subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    data_table_entry = {
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def kraken2_build_standard_prebuilt(prebuilt_db, prebuilt_date, target_directory, data_table_name=DATA_TABLE_NAME):
+
+    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+    prebuild_name = {
+        'viral': "Viral",
+        'minusb': "MinusB (archaea, viral, plasmid, human, UniVec_Core)",
+        'standard': "Standard-Full (archaea, bacteria, viral, plasmid, human,UniVec_Core)",
+        'standard_08gb': "Standard-8 (Standard with DB capped at 8 GB)",
+        'standard_16gb': "Standard-16 (Standard with DB capped at 16 GB)",
+        'pluspf': "PlusPF (Standard plus protozoa and fungi)",
+        'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
+        'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
+        'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
+        'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
+        'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)",
+        'eupathdb48': "EuPathDB-46",
+    }
+
+    database_value = "_".join([
+        now,
+        "standard_prebuilt",
+        prebuilt_db,
+        prebuilt_date
+    ])
+
+    database_name = " ".join([
+        "Prebuilt Refseq indexes: ",
+        prebuild_name[prebuilt_db],
+        "(Version: ",
+        prebuilt_date,
+        "- Downloaded:",
+        now + ")"
+    ])
+
+    database_path = database_value
+
+    # we may need to let the user choose the date when new DBs are posted.
+    date_url_str = prebuilt_date.replace('-', '')
+    # download the pre-built database
+    try:
+        download_url = 'https://genome-idx.s3.amazonaws.com/kraken/k2_%s_%s.tar.gz' % (prebuilt_db, date_url_str)
+        src = urlopen(download_url)
+    except URLError as e:
+        print('url: ' + download_url, file=sys.stderr)
+        print(e, file=sys.stderr)
+        exit(1)
+
+    with open('tmp_data.tar.gz', 'wb') as dst:
+        shutil.copyfileobj(src, dst)
+    # unpack the downloaded archive to the target directory
+    with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
+        for member in fh.getmembers():
+            if member.isreg():
+                member.name = os.path.basename(member.name)
+                fh.extract(member, os.path.join(target_directory, database_path))
+
+    data_table_entry = {
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def kraken2_build_minikraken(minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
+
+    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+    database_value = "_".join([
+        now,
+        "minikraken2",
+        minikraken2_version,
+        "8GB",
+    ])
+
+    database_name = " ".join([
+        "Minikraken2",
+        minikraken2_version,
+        "(Created:",
+        now + ")"
+    ])
+
+    database_path = database_value
+
+    # download the minikraken2 data
+    try:
+        download_url = 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' % minikraken2_version
+        src = urlopen(download_url)
+    except URLError as e:
+        print('url: ' + download_url, file=sys.stderr)
+        print(e, file=sys.stderr)
+        exit(1)
+
+    with open('tmp_data.tar.gz', 'wb') as dst:
+        shutil.copyfileobj(src, dst)
+    # unpack the downloaded archive to the target directory
+    with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
+        for member in fh.getmembers():
+            if member.isreg():
+                member.name = os.path.basename(member.name)
+                fh.extract(member, os.path.join(target_directory, database_path))
+
+    data_table_entry = {
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def kraken2_build_special(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
+
+    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+    special_database_names = {
+        "rdp": "RDP",
+        "greengenes": "Greengenes",
+        "silva": "Silva",
+    }
+
+    database_value = "_".join([
+        now,
+        kraken2_args["special_database_type"],
+        "kmer-len", str(kraken2_args["kmer_len"]),
+        "minimizer-len", str(kraken2_args["minimizer_len"]),
+        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+        "load-factor", str(kraken2_args["load_factor"]),
+    ])
+
+    database_name = " ".join([
+        special_database_names[kraken2_args["special_database_type"]],
+        "(Created:",
+        now + ",",
+        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
+        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
+        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+        "load-factor=" + str(kraken2_args["load_factor"]) + ")",
+    ])
+
+    database_path = database_value
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--special', kraken2_args["special_database_type"],
+        '--kmer-len', str(kraken2_args["kmer_len"]),
+        '--minimizer-len', str(kraken2_args["minimizer_len"]),
+        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
+        '--db', database_path
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    if kraken2_args["clean"]:
+        args = [
+            '--threads', str(kraken2_args["threads"]),
+            '--clean',
+            '--db', database_path
+        ]
+
+        subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    data_table_entry = {
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def kraken2_build_custom(kraken2_args, custom_database_name, custom_source_info, target_directory, data_table_name=DATA_TABLE_NAME):
+    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+    database_value = "_".join([
+        now,
+        re.sub(r'[^\w_.-]+', '_', custom_database_name).strip('_'),
+        "kmer-len", str(kraken2_args["kmer_len"]),
+        "minimizer-len", str(kraken2_args["minimizer_len"]),
+        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+        "load-factor", str(kraken2_args["load_factor"]),
+    ])
+
+    database_name = " ".join([
+        custom_database_name,
+        "(" + custom_source_info + ",",
+        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
+        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
+        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ",",
+        "load-factor=" + str(kraken2_args["load_factor"]) + ")",
+    ])
+
+    database_path = database_value
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--download-taxonomy',
+        '--db', database_path,
+    ]
+
+    if kraken2_args['skip_maps']:
+        args.append('--skip-maps')
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--add-to-library', kraken2_args["custom_fasta"],
+        '--db', database_path,
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--build',
+        '--kmer-len', str(kraken2_args["kmer_len"]),
+        '--minimizer-len', str(kraken2_args["minimizer_len"]),
+        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
+        '--db', database_path,
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    if kraken2_args["clean"]:
+        args = [
+            '--threads', str(kraken2_args["threads"]),
+            '--clean',
+            '--db', database_path,
+        ]
+
+        subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    data_table_entry = {
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('data_manager_json')
+    parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
+    parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
+    parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
+    parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
+    parser.add_argument('--threads', dest='threads', default=1, help='threads')
+    parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
+    parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
+    parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt or special_prebuilt.')
+    parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
+    parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
+    parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
+    parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
+    parser.add_argument('--custom-source-info', dest='custom_source_info', help='Description of how this build has been sourced (only applies to --database-type custom)')
+    parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')
+    parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
+    args = parser.parse_args()
+
+    with open(args.data_manager_json) as fh:
+        data_manager_input = json.load(fh)
+
+    target_directory = data_manager_input['output_data'][0]['extra_files_path']
+
+    try:
+        os.mkdir(target_directory)
+    except OSError as exc:
+        if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
+            pass
+        else:
+            raise
+
+    data_manager_output = {}
+
+    if str(args.database_type) == 'standard_local_build':
+        kraken2_args = {
+            "kmer_len": args.kmer_len,
+            "minimizer_len": args.minimizer_len,
+            "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
+            "threads": args.threads,
+            "clean": args.clean,
+        }
+        data_manager_output = kraken2_build_standard(
+            kraken2_args,
+            target_directory,
+        )
+    elif str(args.database_type) in ('standard_prebuilt', 'special_prebuilt'):
+        data_manager_output = kraken2_build_standard_prebuilt(
+            str(args.prebuilt_db),
+            str(args.prebuilt_date),
+            target_directory
+        )
+    elif str(args.database_type) == 'minikraken':
+        data_manager_output = kraken2_build_minikraken(
+            str(args.minikraken2_version),
+            target_directory
+        )
+    elif str(args.database_type) == 'special':
+        kraken2_args = {
+            "special_database_type": str(args.special_database_type),
+            "kmer_len": args.kmer_len,
+            "minimizer_len": args.minimizer_len,
+            "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
+            "threads": args.threads,
+            "clean": args.clean,
+        }
+        data_manager_output = kraken2_build_special(
+            kraken2_args,
+            target_directory,
+        )
+    elif str(args.database_type) == 'custom':
+        kraken2_args = {
+            "custom_fasta": args.custom_fasta,
+            "skip_maps": args.skip_maps,
+            "kmer_len": args.kmer_len,
+            "minimizer_len": args.minimizer_len,
+            "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
+            "threads": args.threads,
+            "clean": args.clean,
+        }
+        data_manager_output = kraken2_build_custom(
+            kraken2_args,
+            args.custom_database_name,
+            args.custom_source_info,
+            target_directory,
+        )
+    else:
+        sys.exit("Invalid database type")
+
+    with open(args.data_manager_json, 'w') as fh:
+        json.dump(data_manager_output, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+    main()
diff -r 000000000000 -r c13785ca6192 data_manager/kraken2_build_database.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_database.xml	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,359 @@
+<?xml version="1.0"?>
+<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>database builder</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.1.3</token>
+        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@PROFILE@">22.01</token>
+        <xml name="common_params">
+            <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
+            <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
+            <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" />
+            <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
+            <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
+        </xml>
+        <xml name="viral">
+            <option value="viral">Viral (viral; ~0.5 GB)</option>
+        </xml>
+        <xml name="minusb">
+            <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
+        </xml>
+        <xml name="standard">
+            <option value="standard">Standard-Full (archaea, bacteria, viral, plasmid, human, UniVec_Core; ~50 GB)</option>
+        </xml>
+        <xml name="standard_08gb">
+            <option value="standard_08gb">Standard-8 (Standard with DB capped at 8 GB)</option>
+        </xml>
+        <xml name="standard_16gb">
+            <option value="standard_16gb">Standard-16 (Standard with DB capped at 16 GB)</option>
+        </xml>
+        <xml name="pluspf">
+            <option value="pluspf">PlusPF (Standard plus protozoa and fungi; ~50 GB)</option>
+        </xml>
+        <xml name="pluspf_08gb">
+            <option value="pluspf_08gb">PlusPF-8 (PlusPF with DB capped at 8 GB; ~7.5 GB)</option>
+        </xml>
+        <xml name="pluspf_16gb">
+            <option value="pluspf_16gb">PlusPF-16 (PlusPF with DB capped at 16 GB; ~15 GB)</option>
+        </xml>
+        <xml name="pluspfp">
+            <option value="pluspfp">PlusPFP (Standard plus protozoa, fungi and plant; ~129 GB)</option>
+        </xml>
+        <xml name="pluspfp_08gb">
+            <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option>
+        </xml>
+        <xml name="pluspfp_16gb">
+            <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
+        </xml>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">kraken2</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
+        <requirement type="package" version="3.13">python</requirement>
+    </requirements>
+    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/kraken2_build_database.py'
+    '$out_file'
+    --database-type '$database_type.database_type'
+#if $database_type.database_type == "standard_local_build"
+    --threads \${GALAXY_SLOTS:-1}
+    --kmer-len $database_type.kmer_len
+    --minimizer-len $database_type.minimizer_len
+    --minimizer-spaces $database_type.minimizer_spaces
+    --load-factor $database_type.load_factor
+    $database_type.clean
+#else if $database_type.database_type == "standard_prebuilt"
+    --prebuilt-db '$database_type.prebuild.prebuilt_db'
+    --prebuilt-date '$database_type.prebuild.prebuilt_date'
+#else if $database_type.database_type == "minikraken"
+    --minikraken2-version '$database_type.minikraken2_version'
+#else if $database_type.database_type == "special_prebuilt"
+    --prebuilt-db '$database_type.special_prebuild.prebuilt_db'
+    --prebuilt-date '$database_type.special_prebuild.prebuilt_date'
+#else if $database_type.database_type == "special"
+    --threads \${GALAXY_SLOTS:-1}
+    --special-database-type '$database_type.special_database_type'
+    --kmer-len $database_type.kmer_len
+    --minimizer-len $database_type.minimizer_len
+    --minimizer-spaces $database_type.minimizer_spaces
+    --load-factor $database_type.load_factor
+    $database_type.clean
+#else if $database_type.database_type == "custom"
+    --threads \${GALAXY_SLOTS:-1}
+    --custom-fasta '$database_type.custom_fasta'
+    --custom-database-name '$database_type.custom_database_name'
+    --custom-source-info '$database_type.custom_source_info'
+    $database_type.skip_maps
+    --kmer-len $database_type.kmer_len
+    --minimizer-len $database_type.minimizer_len
+    --minimizer-spaces $database_type.minimizer_spaces
+    --load-factor $database_type.load_factor
+    $database_type.clean
+#end if
+]]>
+    </command>
+    <inputs>
+        <conditional name="database_type">
+            <param name="database_type" type="select" multiple="false" label="Database Type">
+                <option value="standard_local_build">Standard, Local Build</option>
+                <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
+                <option value="minikraken">MiniKraken</option>
+                <option value="special_prebuilt">Special Pre-Built indexes</option>
+                <option value="special">Special</option>
+                <option value="custom">Custom</option>
+            </param>
+            <when value="standard_local_build">
+                <expand macro="common_params" />
+            </when>
+            <when value="standard_prebuilt">
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" type="select" label="Select index build date">
+                        <option value="2024-06-05">June 5, 2024</option>
+                        <option value="2024-01-12">January 12, 2024</option>
+                        <option value="2023-06-05">June 5, 2023</option>
+                        <option value="2022-06-07">June 7, 2022</option>
+                        <option value="2021-05-17">May 17, 2021</option>
+                        <option value="2021-01-27">January 27, 2021</option>
+                        <option value="2020-12-02">December 2, 2020</option>
+                        <option value="2020-09-19">September 19, 2020</option>
+                    </param>
+                    <when value="2024-06-05">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2024-01-12">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2023-06-05">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2022-06-07">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2021-05-17">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2021-01-27">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2020-12-02">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2020-09-19">
+                        <param name="prebuilt_db" type="select" multiple="false" label="Select a prebuilt Refseq indexes to download">
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+            <when value="special_prebuilt">
+                <conditional name="special_prebuild">
+                    <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
+                        <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option>
+                        <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
+                    </param>
+                    <when value="eupathdb48_20230407">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
+                    </when>
+                    <when value="eupathdb48_20201113">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="minikraken">
+                <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
+                    <option value="v2">Version 2</option>
+                    <option value="v1">Version 1</option>
+                </param>
+            </when>
+            <when value="special">
+                <param name="special_database_type" type="select" multiple="false" label="Select database to build">
+                    <option value="greengenes">Greengenes</option>
+                    <option value="silva">Silva</option>
+                    <option value="rdp">RDP</option>
+                </param>
+                <expand macro="common_params" />
+            </when>
+            <when value="custom">
+                <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" />
+                <param name="custom_database_name" type="text" label="Name for this database" />
+                <param name="custom_source_info" type="text" label="Database source info" help="Concise description of how this build has been sourced. This description will be appended (in parentheses) to the user-facing name of the build. Example: https://doi.org/10.5281/zenodo.8339822, from v1 assembly_summary.txt sequences" />
+                <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
+                <expand macro="common_params" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="database_type">
+                <param name="database_type" value="custom" />
+                <param name="custom_fasta" value="adapter.fa" />
+                <param name="custom_database_name" value="custom_database" />
+                <param name="custom_source_info" value="from adapter.fa test data" />
+                <param name="skip_maps" value="true" />
+                <param name="kmer_len" value="35" />
+                <param name="minimizer_spaces" value="6"/>
+                <param name="load_factor" value="0.7" />
+                <param name="clean" value="true"/>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="custom_database (from adapter.fa test data, kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2022-06-07"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2022-06-07"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test with latest version -->
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2024-01-12"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2024-01-12"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test with first 2024 version -->
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2024-06-05"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2024-06-05"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s13059-019-1891-0</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r c13785ca6192 data_manager_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,18 @@
+<data_managers>
+    <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database">
+        <data_table name="kraken2_databases">
+            <output>
+                <column name="value"/>
+                <column name="name"/>
+                <column name="path" output_ref="out_file">
+                    <move type="directory">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
diff -r 000000000000 -r c13785ca6192 test-data/adapter.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adapter.fa	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,2 @@
+>sequence16|kraken:taxid|32630  Adapter sequence
+CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
diff -r 000000000000 -r c13785ca6192 test-data/adapter.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adapter.fastq	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,4 @@
+@sequence16
+CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 000000000000 -r c13785ca6192 test-data/kraken2_custom_data_manager.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken2_custom_data_manager.json	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"kraken2_databases": [{"name": "database", "path": "database", "value": "database"}]}}
\ No newline at end of file
diff -r 000000000000 -r c13785ca6192 tool-data/kraken2_databases.loc.sample
diff -r 000000000000 -r c13785ca6192 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of Kraken2 database in the required format -->
+    <table name="kraken2_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/kraken2_databases.loc" />
+    </table>
+</tables>