Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 19:ffeb852407d6 draft default tip
"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 6f21145d4103d33c227f52dc55a7d3dcf52f4f5d-dirty"
| author | dfornika |
|---|---|
| date | Wed, 23 Oct 2019 14:21:07 -0400 |
| parents | f005b6efd096 |
| children | |
| files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml data_manager_conf.xml |
| diffstat | 3 files changed, 32 insertions(+), 22 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Fri May 24 13:39:08 2019 -0400 +++ b/data_manager/kraken2_build_database.py Wed Oct 23 14:21:07 2019 -0400 @@ -83,13 +83,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -195,13 +196,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -250,13 +252,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', custom_database_name - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', custom_database_name + ] - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -286,6 +289,7 @@ parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)') parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='') + parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files') args = parser.parse_args() data_manager_input = json.loads(open(args.data_manager_json).read()) @@ -308,6 +312,7 @@ "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, + "clean": args.clean, } data_manager_output = kraken2_build_standard( kraken2_args, @@ -325,6 +330,7 @@ "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, + "clean": args.clean, } data_manager_output = kraken2_build_special( kraken2_args, @@ -338,6 +344,7 @@ "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, + "clean": args.clean, } data_manager_output = kraken2_build_custom( kraken2_args,
--- a/data_manager/kraken2_build_database.xml Fri May 24 13:39:08 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Wed Oct 23 14:21:07 2019 -0400 @@ -1,10 +1,11 @@ <?xml version="1.0"?> -<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta"> +<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta_galaxy1"> <macros> <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="6" label="Minimizer spaces" /> + <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> </xml> </macros> <description>database builder</description> @@ -24,12 +25,14 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + ${database_type.clean} #else if $database_type.database_type == "special" --threads \${GALAXY_SLOTS:-1} --special-database-type ${database_type.special_database_type} --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + ${database_type.clean} #else if $database_type.database_type == "custom" --threads \${GALAXY_SLOTS:-1} ${database_type.skip_maps} @@ -38,6 +41,7 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + ${database_type.clean} #end if ]]> </command> @@ -54,7 +58,7 @@ </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="v2">Version 2</option> <option value="v1">Version 1</option> </param> </when> @@ -72,7 +76,6 @@ <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> </inputs> <outputs>
--- a/data_manager_conf.xml Fri May 24 13:39:08 2019 -0400 +++ b/data_manager_conf.xml Wed Oct 23 14:21:07 2019 -0400 @@ -1,5 +1,5 @@ <data_managers> - <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta"> + <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta_galaxy1"> <data_table name="kraken2_databases"> <output> <column name="value"/>