data_manager_build_kraken2_database: data_manager/kraken2_build

comparison 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

author	iuc
date	Wed, 05 Nov 2025 13:31:52 +0000
parents	bf7f964a12b7
children

comparison

equal deleted inserted replaced

-:bf7f964a12b7
+: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@">2.1.3</token>
+<token name="@TOOL_VERSION@">2.1.6</token>
-<token name="@VERSION_SUFFIX@">6</token>
+<token name="@VERSION_SUFFIX@">0</token>
-<token name="@PROFILE@">22.01</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="true" label="Clean up extra files" />
+<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">
 <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>
-<xml name="core_nt">
-<option value="core_nt">core_nt (Very large collection, inclusive of GenBank, RefSeq, TPA and PDB; ~182 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'
+#import datetime
-'$out_file'
+#import re
---database-type '$database_type.database_type'
-#if $database_type.database_type == "standard_local_build"
+#set now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
---threads \${GALAXY_SLOTS:-1}
+#set commands = []
---kmer-len $database_type.kmer_len
+mkdir '$out_file.extra_files_path' &&
---minimizer-len $database_type.minimizer_len
---minimizer-spaces $database_type.minimizer_spaces
+#if  $database_type.database_type == "standard_prebuilt" or $database_type.database_type == "special_prebuilt" or $database_type.database_type == "amplicon_prebuilt"
---load-factor $database_type.load_factor
+#set prebuilt_name = {
-$database_type.clean
+'viral': "Viral",
-#else if $database_type.database_type == "standard_prebuilt"
+'minusb': "MinusB (archaea, viral, plasmid, human, UniVec_Core)",
---prebuilt-db '$database_type.prebuild.prebuilt_db'
+'standard': "Standard-Full (archaea, bacteria, viral, plasmid, human,UniVec_Core)",
---prebuilt-date '$database_type.prebuild.prebuilt_date'
+'standard_08gb': "Standard-8 (Standard with DB capped at 8 GB)",
+'standard_16gb': "Standard-16 (Standard with DB capped at 16 GB)",
+'pluspf': "PlusPF (Standard plus protozoa and fungi)",
+'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
+'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
+'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
+'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
+'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)",
+}
+#set special_name = {
+"core_nt_20250609": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (July, 2025)",
+"core_nt_20241228": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (December, 2024)",
+"core_nt_20240904": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (September, 2024)",
+"gtdb_genome_reps_20250609": "GTDB v226 (Bacterial and archaeal)",
+"gtdb_genome_reps_20241109": "GTDB v220 (Bacterial and archaeal)",
+"eupathdb48_20230407": "EuPathDB-46 (April 18, 2023)",
+"eupathdb48_20201113": "EuPathDB-46 (November 13, 2020)"
+}
+#set amplicon_name = {
+"16S_Greengenes13.5_20200326": "Greengenes 13.5",
+"16S_RDP11.5_20200326": "RDP 11.5",
+"16S_Silva132_20200326": "Silva 132",
+"16S_Silva138_20200326": "Silva 138"
+}
+#set date_url_str = str($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 $database_type.database_type == "minikraken"
---minikraken2-version '$database_type.minikraken2_version'
+#set database_value = "_".join([now, "minikraken2", str($database_type.minikraken2_version), "8GB"])
-#else if $database_type.database_type == "special_prebuilt"
+#set database_name = " ".join(["Minikraken2", str($database_type.minikraken2_version), "(Created:", now + ")"])
---prebuilt-db '$database_type.special_prebuild.prebuilt_db'
---prebuilt-date '$database_type.special_prebuild.prebuilt_date'
+#silent commands.append("wget 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_" + str($database_type.minikraken2_version) + "_8GB_201904.tgz'")
-#else if $database_type.database_type == "special"
+#silent commands.append("mkdir -p '" + $out_file.extra_files_path + "'/'" + database_value + "'")
---threads \${GALAXY_SLOTS:-1}
+#silent commands.append("tar -xzf 'minikraken2_" + str($database_type.minikraken2_version) + "_8GB_201904.tgz' -C '" + $out_file.extra_files_path + "'/'" + database_value + "'")
---special-database-type '$database_type.special_database_type'
+#else
---kmer-len $database_type.kmer_len
+#if $database_type.database_type == "standard_local_build"
---minimizer-len $database_type.minimizer_len
+#set database_value = "_".join([now, "standard", "kmer-len", str($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)])
---minimizer-spaces $database_type.minimizer_spaces
+#set database_name = " ".join(["Standard (Local Build)", "Created:", now + ",", "kmer-len=" + str($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) + ")"])
---load-factor $database_type.load_factor
+#else if $database_type.database_type == "special"
-$database_type.clean
+#set special_database_names = {"rdp": "RDP", "greengenes": "Greengenes", "silva": "Silva"}
-#else if $database_type.database_type == "custom"
+#set database_value = "_".join([now, str($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)])
---threads \${GALAXY_SLOTS:-1}
+#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($database_type.load_factor) + ")"])
---custom-fasta '$database_type.custom_fasta'
+#else if $database_type.database_type == "custom"
---custom-database-name '$database_type.custom_database_name'
+#set custom_database_name = re.sub(r'[^\w_.-]+', '_', str($database_type.custom_database_name)).strip('_')
---custom-source-info '$database_type.custom_source_info'
+#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($database_type.load_factor) + ")"])
-$database_type.skip_maps
+#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)])
---kmer-len $database_type.kmer_len
+#else
---minimizer-len $database_type.minimizer_len
+>&2 echo "invalid database_type: $database_type.database_type"
---minimizer-spaces $database_type.minimizer_spaces
+#end if
---load-factor $database_type.load_factor
-$database_type.clean
+#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="prebuild">
+<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="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="pluspf_08gb"/>
 <expand macro="pluspf_16gb"/>
 <expand macro="pluspfp"/>
 <expand macro="pluspfp_08gb"/>
 <expand macro="pluspfp_16gb"/>
-<expand macro="core_nt"/>
 </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="pluspf"/>
 <expand macro="pluspf_08gb"/>
 <expand macro="pluspf_16gb"/>
 <expand macro="pluspfp"/>
 <expand macro="pluspfp_08gb"/>
-<expand macro="core_nt"/>
 </param>
 </when>
 <when value="2024-06-05">
 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
 <expand macro="viral"/>
 </param>
 </when>
 </conditional>
 </when>
 <when value="special_prebuilt">
-<conditional name="special_prebuild">
+<conditional name="prebuilt">
-<param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
+<param name="xyz" type="select" multiple="false" label="Select pre-built database to download">
-<option value="gtdb_genome_reps_20241109">GTDB v220 (Bacterial and archaeal; ~497 GB) (December 13, 2024)</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_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_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">
 </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>
+<!-- <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_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="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>
-<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>

Mercurial > repos > iuc > data_manager_build_kraken2_database

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