Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 53:21cd25cc1ab2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 1137710d16538da15bcd87e1ba382e2afc00031f-dirty
| author | dfornika |
|---|---|
| date | Wed, 08 May 2019 18:49:14 -0400 |
| parents | 86bc169b0aeb |
| children | b60b0a9523db |
| files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Wed May 08 18:39:03 2019 -0400 +++ b/data_manager/kraken2_build_database.py Wed May 08 18:49:14 2019 -0400 @@ -267,7 +267,7 @@ def main(): parser = argparse.ArgumentParser() - parser.add_argument('--extra-files-path', dest='extra_files_path', help='') + parser.add_argument('data_manager_json') parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length') parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length') parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces') @@ -281,7 +281,7 @@ data_manager_input = json.loads(open(args.data_manager_json).read()) - target_directory = args.extra_files_path + target_directory = data_manager_input['output_data'][0]['extra_files_path'] try: os.mkdir( target_directory )
--- a/data_manager/kraken2_build_database.xml Wed May 08 18:39:03 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Wed May 08 18:49:14 2019 -0400 @@ -15,7 +15,7 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/kraken2_build_database.py' - --extra-files-path '$out_file.extra_files_path' + '${out_file}' --database-type ${database_type.database_type} #if $database_type.database_type == "minikraken" --minikraken2-version ${database_type.minikraken2_version}