Mercurial > repos > iuc > data_manager_build_kraken2_database
changeset 13:e9ee4d074d5d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
| author | iuc |
|---|---|
| date | Fri, 15 Nov 2024 22:31:29 +0000 |
| parents | 90b4d4f0a3a4 |
| children | 8c533e19b697 |
| files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
| diffstat | 2 files changed, 27 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Fri Oct 18 17:08:15 2024 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 15 22:31:29 2024 +0000 @@ -28,6 +28,7 @@ standard_local_build = 'standard_local_build' standard_prebuilt = 'standard_prebuilt' minikraken = 'minikraken' + special_prebuilt = 'special_prebuilt' special = 'special' custom = 'custom' @@ -64,6 +65,7 @@ pluspfp = "pluspfp" pluspfp_08gb = "pluspfp_08gb" pluspfp_16gb = "pluspfp_16gb" + eupathdb48 = "eupathdb48" def __str__(self): return self.value @@ -144,7 +146,8 @@ '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)" + 'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)", + 'eupathdb48': "EuPathDB-46", } database_value = "_".join([ @@ -408,7 +411,7 @@ parser.add_argument('--threads', dest='threads', default=1, help='threads') parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build') parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)') - parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt.') + parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt or special_prebuilt.') parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.') parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)') parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') @@ -446,7 +449,7 @@ kraken2_args, target_directory, ) - elif str(args.database_type) == 'standard_prebuilt': + elif str(args.database_type) in ('standard_prebuilt', 'special_prebuilt'): data_manager_output = kraken2_build_standard_prebuilt( str(args.prebuilt_db), str(args.prebuilt_date),
--- a/data_manager/kraken2_build_database.xml Fri Oct 18 17:08:15 2024 +0000 +++ b/data_manager/kraken2_build_database.xml Fri Nov 15 22:31:29 2024 +0000 @@ -1,9 +1,8 @@ -<?xml version="1.0"?> <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>database builder</description> <macros> <token name="@TOOL_VERSION@">2.1.3</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <token name="@PROFILE@">22.01</token> <xml name="common_params"> <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> @@ -70,6 +69,9 @@ --prebuilt-date '$database_type.prebuild.prebuilt_date' #else if $database_type.database_type == "minikraken" --minikraken2-version '$database_type.minikraken2_version' +#else if $database_type.database_type == "special_prebuilt" + --prebuilt-db '$database_type.special_prebuild.prebuilt_db' + --prebuilt-date '$database_type.special_prebuild.prebuilt_date' #else if $database_type.database_type == "special" --threads \${GALAXY_SLOTS:-1} --special-database-type '$database_type.special_database_type' @@ -98,6 +100,7 @@ <option value="standard_local_build">Standard, Local Build</option> <option value="standard_prebuilt">Pre-Built Refseq indexes</option> <option value="minikraken">MiniKraken</option> + <option value="special_prebuilt">Special Pre-Built indexes</option> <option value="special">Special</option> <option value="custom">Custom</option> </param> @@ -223,6 +226,22 @@ </when> </conditional> </when> + <when value="special_prebuilt"> + <conditional name="special_prebuild"> + <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download"> + <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option> + <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option> + </param> + <when value="eupathdb48_20230407"> + <param name="prebuilt_db" type="hidden" value="eupathdb48"/> + <param name="prebuilt_date" type="hidden" value="2023-04-07"/> + </when> + <when value="eupathdb48_20201113"> + <param name="prebuilt_db" type="hidden" value="eupathdb48"/> + <param name="prebuilt_date" type="hidden" value="2020-11-13"/> + </when> + </conditional> + </when> <when value="minikraken"> <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> <option value="v2">Version 2</option>