comparison data_manager/kraken2_build_database.xml @ 14:1663e897c832 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit 797b5fc5c1b1eb7903c2ab681f399777b77501e3

13:150ea60a4ebc

<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" />

    <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 = {

        '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)",

    #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

                <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="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"/>

                </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="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" />

                    <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"/>

                    <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"/>

                    <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"/>

                    <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"/>

                    <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">

                    <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">

                    <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" />

                    <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" />

                    <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" />

14:1663e897c832

<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@">2.17.1</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" />

    <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.now(datetime.UTC).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 = {

        '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_20251015": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (October, 2025)",
        "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)",

    #else
        >&2 echo "invalid database_type: $database_type.database_type"
    #end if

    #if $database_type.database_type == "custom"
        #silent command = ["k2", "download-taxonomy",
            "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'",
            str($database_type.skip_maps)]
        #silent commands.append(" ".join(command))
        #silent command = ["k2", "add-to-library", "--threads", '"${GALAXY_SLOTS:-1}"',
            "--file", "'" + str($database_type.custom_fasta) + "'",
            "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
        #silent commands.append(" ".join(command))
    #end if

    #silent command = ["k2", "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)])
    #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 = ["k2", "clean",
            "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
        #silent commands.append(" ".join(command))
    #end if
#end if

                <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="2025-10-15">October 15, 2025</option>
                        <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="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="2025-10-15">
                        <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="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"/>

                </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_20251015">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (October, 2025)</option>
                        <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_20251015">
                        <param name="prebuilt_db" type="hidden" value="core_nt"/>
                        <param name="prebuilt_date" type="hidden" value="20251015"/>
                    </when>
                    <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="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 1 -->

        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="standard_local_build" />
                <param name="kmer_len" value="35" />

                    <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
                </assert_contents>
            </output>
        </test>

        <!-- standard_prebuilt - test 2 -->
        <test>
            <conditional name="database_type">
                <param name="database_type" value="standard_prebuilt" />
                <conditional name="prebuilt">
                    <param name="prebuilt_date" value="2022-06-07"/>

                    <has_text text="Version"/>
                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test>
        <!-- test with latest version - test 3 -->
        <test>
            <conditional name="database_type">
                <param name="database_type" value="standard_prebuilt" />
                <conditional name="prebuilt">
                    <param name="prebuilt_date" value="2024-01-12"/>

                    <has_text text="Version"/>
                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test>
        <!-- test with first 2024 version - test 4 -->
        <test>
            <conditional name="database_type">
                <param name="database_type" value="standard_prebuilt" />
                <conditional name="prebuilt">
                    <param name="prebuilt_date" value="2024-06-05"/>

                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test>

        <!-- minikraken - test 5 -->

        <test>
            <conditional name="database_type">
                <param name="database_type" value="minikraken" />
                <param name="minikraken2_version" value="v1"/>

                    <has_text text="Created"/>
                </assert_contents>
            </output>
        </test> 

        <!-- special_prebuilt - test 6 -->

       <test>
            <conditional name="database_type">
                <param name="database_type" value="special_prebuilt" />
                <conditional name="prebuilt">

                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test> 

        <!-- amplicon_prebuilt - test 7 -->

       <test>
            <conditional name="database_type">
                <param name="database_type" value="amplicon_prebuilt" />
                <conditional name="prebuilt">

                    <has_text text="16S_Greengenes13.5"/>
                </assert_contents>
            </output>
        </test> 

        <!-- special - test 8 -->

        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="special" />
                <param name="special_database_type" value="greengenes" />

                    <has_text text="Greengenes"/>
                    <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
                </assert_contents>
            </output>
        </test>

        <!-- special - test 9 -->
        <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" />

                    <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
                </assert_contents>
            </output>
        </test>

        <!-- custom - test 10 -->

        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="custom" />
                <param name="custom_fasta" value="adapter.fa" />