view data_manager/kraken2_build_database.xml @ 13:150ea60a4ebc draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852

<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@">2.1.6</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">24.0</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="false" label="Clean up extra files. Note: If the extra files are removed this DB cannot be used to build a bracken DB!" />
        </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>
    </requirements>
    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
    <command detect_errors="exit_code"><![CDATA[
#import datetime
#import re

#set now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
#set commands = []
mkdir '$out_file.extra_files_path' &&

#if  $database_type.database_type == "standard_prebuilt" or $database_type.database_type == "special_prebuilt" or $database_type.database_type == "amplicon_prebuilt"
    #set prebuilt_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)",
    }
    #set special_name = {
        "core_nt_20250609": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (July, 2025)",
        "core_nt_20241228": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (December, 2024)",
        "core_nt_20240904": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (September, 2024)",
        "gtdb_genome_reps_20250609": "GTDB v226 (Bacterial and archaeal)",
        "gtdb_genome_reps_20241109": "GTDB v220 (Bacterial and archaeal)",
        "eupathdb48_20230407": "EuPathDB-46 (April 18, 2023)",
        "eupathdb48_20201113": "EuPathDB-46 (November 13, 2020)"
    }
    #set amplicon_name = {
        "16S_Greengenes13.5_20200326": "Greengenes 13.5",
        "16S_RDP11.5_20200326": "RDP 11.5",
        "16S_Silva132_20200326": "Silva 132",
        "16S_Silva138_20200326": "Silva 138"
    }

    #set date_url_str = str($database_type.prebuilt.prebuilt_date).replace('-', '')
    #set display_name = prebuilt_name.get(str($database_type.prebuilt.prebuilt_db))
    #if not display_name
        #set display_name = special_name.get(str($database_type.prebuilt.prebuilt_db)+"_"+date_url_str)
    #end if
    #if not display_name
        #set display_name = amplicon_name.get(str($database_type.prebuilt.prebuilt_db)+"_"+date_url_str)
    #end if

    #set database_value = "_".join([now, "standard_prebuilt", str($database_type.prebuilt.prebuilt_db), str($database_type.prebuilt.prebuilt_date)])
    #set database_name = " ".join(["Prebuilt Refseq indexes: ", display_name, "(Version: ", str($database_type.prebuilt.prebuilt_date), "- Downloaded:", now + ")"])

    ## the 16S dbs have a different link and file name 
    ## and are stored in a subfolder
    #if $database_type.database_type == "amplicon_prebuilt"
        #silent commands.append("wget https://genome-idx.s3.amazonaws.com/kraken/" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tgz")
        #silent commands.append("mkdir -p '" + $out_file.extra_files_path + "/" + database_value + "'/tmp_extract")
        #silent commands.append("tar -xzf " + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tgz -C '" + $out_file.extra_files_path + "/" + database_value + "'/tmp_extract")
        #silent commands.append("topdir=$(find '" + $out_file.extra_files_path + "/" + database_value + "/tmp_extract' -mindepth 1 -maxdepth 1 -type d | head -n 1)")
        #silent commands.append("if [ -n \"$topdir\" ]")
        #silent commands.append("then")
        #silent commands.append("    mv \"$topdir\"/* '" + $out_file.extra_files_path + "/" + database_value + "/'")
        #silent commands.append("fi")
        #silent commands.append("rm -rf '" + $out_file.extra_files_path + "/" + database_value + "/tmp_extract'")
    #else
        #silent commands.append("wget https://genome-idx.s3.amazonaws.com/kraken/k2_" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tar.gz")
        #silent commands.append("mkdir -p '" + $out_file.extra_files_path + "/" + database_value + "'")
        #silent commands.append("tar -xzf k2_" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tar.gz -C '" + $out_file.extra_files_path + "/" + database_value + "'")
    #end if

#else if $database_type.database_type == "minikraken"
    #set database_value = "_".join([now, "minikraken2", str($database_type.minikraken2_version), "8GB"])
    #set database_name = " ".join(["Minikraken2", str($database_type.minikraken2_version), "(Created:", now + ")"])

    #silent commands.append("wget 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_" + str($database_type.minikraken2_version) + "_8GB_201904.tgz'")
    #silent commands.append("mkdir -p '" + $out_file.extra_files_path + "'/'" + database_value + "'")
    #silent commands.append("tar -xzf 'minikraken2_" + str($database_type.minikraken2_version) + "_8GB_201904.tgz' -C '" + $out_file.extra_files_path + "'/'" + database_value + "'")
#else
    #if $database_type.database_type == "standard_local_build"
        #set database_value = "_".join([now, "standard", "kmer-len", str($database_type.kmer_len), "minimizer-len", str($database_type.minimizer_len), "minimizer-spaces", str($database_type.minimizer_spaces), "load-factor", str($database_type.load_factor)])
        #set database_name = " ".join(["Standard (Local Build)", "Created:", now + ",", "kmer-len=" + str($database_type.kmer_len) + ",", "minimizer-len=" + str($database_type.minimizer_len) + ",", "minimizer-spaces=" + str($database_type.minimizer_spaces) + ",", "load-factor=" + str($database_type.load_factor) + ")"])
    #else if $database_type.database_type == "special"
        #set special_database_names = {"rdp": "RDP", "greengenes": "Greengenes", "silva": "Silva"}
        #set database_value = "_".join([now, str($database_type.special_database_type), "kmer-len", str($database_type.kmer_len), "minimizer-len", str($database_type.minimizer_len), "minimizer-spaces", str($database_type.minimizer_spaces), "load-factor", str($database_type.load_factor)])
        #set database_name = " ".join([special_database_names[str($database_type.special_database_type)], "(Created:", now + ",", "kmer-len=" + str($database_type.kmer_len) + ",", "minimizer-len=" + str($database_type.minimizer_len) + ",", "minimizer-spaces=" + str($database_type.minimizer_spaces) + ",", "load-factor=" + str($database_type.load_factor) + ")"])
    #else if $database_type.database_type == "custom"
        #set custom_database_name = re.sub(r'[^\w_.-]+', '_', str($database_type.custom_database_name)).strip('_')
        #set database_name = " ".join([custom_database_name, "(" + str($database_type.custom_source_info) + ",", "kmer-len=" + str($database_type.kmer_len) + ",", "minimizer-len=" + str($database_type.minimizer_len) + ",", "minimizer-spaces=" + str($database_type.minimizer_spaces) + ",", "load-factor=" + str($database_type.load_factor) + ")"])
        #set database_value = "_".join([now, custom_database_name, "kmer-len", str($database_type.kmer_len), "minimizer-len", str($database_type.minimizer_len), "minimizer-spaces", str($database_type.minimizer_spaces), "load-factor", str($database_type.load_factor)])
    #else
        >&2 echo "invalid database_type: $database_type.database_type"
    #end if

    #if $database_type.database_type == "custom"
        #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
            "--download-taxonomy",
            "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'",
            str($database_type.skip_maps)]
        #silent commands.append(" ".join(command))
        #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
            "--add-to-library", "'" + str($database_type.custom_fasta) + "'",
            "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
        #silent commands.append(" ".join(command))
    #end if

    #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"']
    #if $database_type.database_type == "standard_local_build"
        #silent command.append("--standard")
    #else if $database_type.database_type == "special"
        #silent command.extend(["--special", str($database_type.special_database_type)])
    #else if $database_type.database_type == "custom"
        #silent command.append("--build")
    #end if
    #silent command.extend([
        "--kmer-len", str($database_type.kmer_len),
        "--minimizer-len", str($database_type.minimizer_len),
        "--minimizer-spaces", str($database_type.minimizer_spaces),
        "--load-factor", str($database_type.load_factor),
        "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"])
    #silent commands.append(" ".join(command))

    #if $database_type.clean
        #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
            "--clean",
            "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
        #silent commands.append(" ".join(command))
    #end if
#end if

#for command in commands
    ## In test mode the tool executes `echo COMMAND` instead of `COMMAND`
    #if $run_test_command == "false"
        echo
    #end if
    #echo command
    &&
#end for

echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name": "$database_name", "path": "$database_value"}]}}' > '$out_file'
]]>
    </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="amplicon_prebuilt">16S 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="prebuilt">
                    <param name="prebuilt_date" type="select" label="Select index build date">
                        <option value="2025-07-14">July 14, 2025</option>
                        <option value="2024-12-28">December 28, 2024</option>
                        <option value="2024-09-04">September 4, 2024</option>
                        <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="2025-07-14">
                        <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="2024-12-28">
                        <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="2024-09-04">
                        <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"/>
                        </param>
                    </when>
                    <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="prebuilt">
                    <param name="xyz" type="select" multiple="false" label="Select pre-built database to download">
                        <option value="core_nt_20250609">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (July, 2025)</option>
                        <option value="core_nt_20241228">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (December, 2024)</option>
                        <option value="core_nt_20240904">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (September, 2024)</option>
                        <option value="gtdb_genome_reps_20250609">GTDB v226 (Bacterial and archaeal; ~497 GB) (July, 2025)</option>
                        <option value="gtdb_genome_reps_20241109">GTDB v220 (Bacterial and archaeal; ~644 GB) (December 13, 2024)</option>
                        <option value="eupathdb48_20230407">EuPathDB-46 (April 18, 2023)</option>
                        <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
                    </param>
                    <when value="core_nt_20250609">
                        <param name="prebuilt_db" type="hidden" value="core_nt"/>
                        <param name="prebuilt_date" type="hidden" value="20250609"/>
                    </when>
                    <when value="core_nt_20241228">
                        <param name="prebuilt_db" type="hidden" value="core_nt"/>
                        <param name="prebuilt_date" type="hidden" value="20241228"/>
                    </when>
                    <when value="core_nt_20240904">
                        <param name="prebuilt_db" type="hidden" value="core_nt"/>
                        <param name="prebuilt_date" type="hidden" value="20240904"/>
                    </when>
                    <when value="gtdb_genome_reps_20250609">
                        <param name="prebuilt_db" type="hidden" value="gtdb_genome_reps"/>
                        <param name="prebuilt_date" type="hidden" value="2025-06-09"/>
                    </when>
                    <when value="gtdb_genome_reps_20241109">
                        <param name="prebuilt_db" type="hidden" value="gtdb_genome_reps"/>
                        <param name="prebuilt_date" type="hidden" value="2024-11-09"/>
                    </when>
                    <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="amplicon_prebuilt">
                <conditional name="prebuilt">
                    <param name="xyz" type="select" multiple="false" label="Select pre-built database to download">
                        <option value="16S_Greengenes13.5_20200326">Greengenes 13.5</option>
                        <option value="16S_RDP11.5_20200326">RDP 11.5</option> 
                        <option value="16S_Silva132_20200326">Silva 132</option> 
                        <option value="16S_Silva138_20200326">Silva 138</option> 
                    </param>
                    <when value="16S_Greengenes13.5_20200326">
                        <param name="prebuilt_db" type="hidden" value="16S_Greengenes13.5"/>
                        <param name="prebuilt_date" type="hidden" value="20200326"/>
                    </when>
                    <when value="16S_RDP11.5_20200326">
                        <param name="prebuilt_db" type="hidden" value="16S_RDP11.5"/>
                        <param name="prebuilt_date" type="hidden" value="20200326"/>
                    </when>
                    <when value="16S_Silva132_20200326">
                        <param name="prebuilt_db" type="hidden" value="16S_Silva132"/>
                        <param name="prebuilt_date" type="hidden" value="20200326"/>
                    </when>
                    <when value="16S_Silva138_20200326">
                        <param name="prebuilt_db" type="hidden" value="16S_Silva138"/>
                        <param name="prebuilt_date" type="hidden" value="20200326"/>
                    </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> https://github.com/DerrickWood/kraken2/issues/736 -->
                </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>
        <param name="run_test_command" type="hidden"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <!-- standard_local_build -->

        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="standard_local_build" />
                <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>
            <param name="run_test_command" value="false"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="Standard (Local Build)"/>
                    <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
                </assert_contents>
            </output>
        </test>

        <!-- standard_prebuilt -->
        <test>
            <conditional name="database_type">
                <param name="database_type" value="standard_prebuilt" />
                <conditional name="prebuilt">
                    <param name="prebuilt_date" value="2022-06-07"/>
                    <param name="prebuilt_db" value="viral"/>
                </conditional>
            </conditional>
            <param name="run_test_command" value="true"/>
            <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="prebuilt">
                    <param name="prebuilt_date" value="2024-01-12"/>
                    <param name="prebuilt_db" value="viral"/>
                </conditional>
            </conditional>
            <param name="run_test_command" value="true"/>
            <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="prebuilt">
                    <param name="prebuilt_date" value="2024-06-05"/>
                    <param name="prebuilt_db" value="viral"/>
                </conditional>
            </conditional>
            <param name="run_test_command" value="true"/>
            <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>

        <!-- minikraken -->

        <test>
            <conditional name="database_type">
                <param name="database_type" value="minikraken" />
                <param name="minikraken2_version" value="v1"/>
            </conditional>
            <param name="run_test_command" value="false"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="Minikraken2"/>
                    <has_text text="v1"/>
                    <has_text text="Created"/>
                </assert_contents>
            </output>
        </test> 

        <!-- special_prebuilt -->

       <test>
            <conditional name="database_type">
                <param name="database_type" value="special_prebuilt" />
                <conditional name="prebuilt">
                    <param name="xyz" value="eupathdb48_20201113"/>
                    <param name="prebuilt_date" value="2020-11-13"/>
                    <param name="prebuilt_db" value="eupathdb48"/>
                </conditional>
            </conditional>
            <param name="run_test_command" value="false"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="Prebuilt Refseq indexes:  EuPathDB-46"/>
                    <has_text text="standard_prebuilt_eupathdb48_2020-11-13"/>
                    <has_text text="Prebuilt Refseq indexes"/>
                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test> 

        <!-- amplicon_prebuilt -->

       <test>
            <conditional name="database_type">
                <param name="database_type" value="amplicon_prebuilt" />
                <conditional name="prebuilt">
                    <param name="xyz" value="16S_Greengenes13.5_20200326"/>
                    <param name="prebuilt_date" value="20200326"/>
                    <param name="prebuilt_db" value="16S_Greengenes13.5"/>
                </conditional>
            </conditional>
            <param name="run_test_command" value="false"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="16S_Greengenes13.5"/>
                </assert_contents>
            </output>
        </test> 

        <!-- special -->

        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="special" />
                <param name="special_database_type" value="greengenes" />
                <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>
            <param name="run_test_command" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="Greengenes"/>
                    <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="special" />
                <param name="special_database_type" value="silva" />
                <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>
            <param name="run_test_command" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="Silva"/>
                    <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
                </assert_contents>
            </output>
        </test>

        <!-- custom -->

        <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>
            <param name="run_test_command" value="true"/>
            <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>


    </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>