Mercurial > repos > iuc > data_manager_build_kraken2_database
changeset 17:4877dfefaacc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit 797b5fc5c1b1eb7903c2ab681f399777b77501e3
| author | iuc |
|---|---|
| date | Thu, 19 Feb 2026 12:13:41 +0000 |
| parents | 54871a78828e |
| children | |
| files | data_manager/kraken2_build_database.xml |
| diffstat | 1 files changed, 41 insertions(+), 21 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.xml Wed Nov 05 13:32:18 2025 +0000 +++ b/data_manager/kraken2_build_database.xml Thu Feb 19 12:13:41 2026 +0000 @@ -1,7 +1,7 @@ <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="@TOOL_VERSION@">2.17.1</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">24.0</token> <xml name="common_params"> @@ -56,7 +56,7 @@ #import datetime #import re -#set now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") +#set now = datetime.datetime.now(datetime.UTC).strftime("%Y-%m-%dT%H%M%SZ") #set commands = [] mkdir '$out_file.extra_files_path' && @@ -75,6 +75,7 @@ '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)", @@ -144,24 +145,21 @@ #end if #if $database_type.database_type == "custom" - #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"', - "--download-taxonomy", + #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 = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"', - "--add-to-library", "'" + str($database_type.custom_fasta) + "'", + #silent command = ["k2", "add-to-library", "--threads", '"${GALAXY_SLOTS:-1}"', + "--file", "'" + str($database_type.custom_fasta) + "'", "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"] #silent commands.append(" ".join(command)) #end if - #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"'] + #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)]) - #else if $database_type.database_type == "custom" - #silent command.append("--build") #end if #silent command.extend([ "--kmer-len", str($database_type.kmer_len), @@ -172,8 +170,7 @@ #silent commands.append(" ".join(command)) #if $database_type.clean - #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"', - "--clean", + #silent command = ["k2", "clean", "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"] #silent commands.append(" ".join(command)) #end if @@ -208,6 +205,7 @@ <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> @@ -220,6 +218,21 @@ <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"/> @@ -374,6 +387,7 @@ <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> @@ -382,6 +396,10 @@ <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"/> @@ -460,13 +478,13 @@ <expand macro="common_params" /> </when> </conditional> - <param name="run_test_command" type="hidden"/> + <param name="run_test_command" type="hidden" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> - <!-- standard_local_build --> + <!-- standard_local_build - test 1 --> <test expect_num_outputs="1"> <conditional name="database_type"> @@ -487,7 +505,7 @@ </output> </test> - <!-- standard_prebuilt --> + <!-- standard_prebuilt - test 2 --> <test> <conditional name="database_type"> <param name="database_type" value="standard_prebuilt" /> @@ -508,7 +526,7 @@ </assert_contents> </output> </test> - <!-- test with latest version --> + <!-- test with latest version - test 3 --> <test> <conditional name="database_type"> <param name="database_type" value="standard_prebuilt" /> @@ -529,7 +547,7 @@ </assert_contents> </output> </test> - <!-- test with first 2024 version --> + <!-- test with first 2024 version - test 4 --> <test> <conditional name="database_type"> <param name="database_type" value="standard_prebuilt" /> @@ -551,7 +569,7 @@ </output> </test> - <!-- minikraken --> + <!-- minikraken - test 5 --> <test> <conditional name="database_type"> @@ -570,7 +588,7 @@ </output> </test> - <!-- special_prebuilt --> + <!-- special_prebuilt - test 6 --> <test> <conditional name="database_type"> @@ -594,7 +612,7 @@ </output> </test> - <!-- amplicon_prebuilt --> + <!-- amplicon_prebuilt - test 7 --> <test> <conditional name="database_type"> @@ -615,7 +633,7 @@ </output> </test> - <!-- special --> + <!-- special - test 8 --> <test expect_num_outputs="1"> <conditional name="database_type"> @@ -636,6 +654,8 @@ </assert_contents> </output> </test> + + <!-- special - test 9 --> <test expect_num_outputs="1"> <conditional name="database_type"> <param name="database_type" value="special" /> @@ -656,7 +676,7 @@ </output> </test> - <!-- custom --> + <!-- custom - test 10 --> <test expect_num_outputs="1"> <conditional name="database_type">