Mercurial > repos > nate > data_manager_build_kraken2_database
changeset 0:c13785ca6192 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
| author | nate |
|---|---|
| date | Wed, 06 Nov 2024 20:00:39 +0000 |
| parents | |
| children | |
| files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml data_manager_conf.xml test-data/adapter.fa test-data/adapter.fastq test-data/kraken2_custom_data_manager.json tool-data/kraken2_databases.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 7 files changed, 894 insertions(+), 0 deletions(-) [+] |
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--- /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()
--- /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>
--- /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>
--- /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
--- /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
--- /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
--- /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>