Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 56:7d384656966e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 616f23916e8c71295e1456d6df585c351bd64f86-dirty
author | dfornika |
---|---|
date | Thu, 23 May 2019 15:10:16 -0400 |
parents | 40ea0695a0a0 |
children | 8990d2675912 |
files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml test-data/kraken2_custom_data_manager.json |
diffstat | 3 files changed, 12 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Thu May 23 14:16:37 2019 -0400 +++ b/data_manager/kraken2_build_database.py Thu May 23 15:10:16 2019 -0400 @@ -227,7 +227,7 @@ ] if kraken2_args['skip_maps']: - args += '--skip-maps' + args.append('--skip-maps') subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) @@ -256,7 +256,7 @@ '--db', custom_database_name ] - subprocess.check_call(['kraken2-build'] + args, target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': {
--- a/data_manager/kraken2_build_database.xml Thu May 23 14:16:37 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Thu May 23 15:10:16 2019 -0400 @@ -78,6 +78,15 @@ <outputs> <data name="out_file" format="data_manager_json" /> </outputs> + <tests> + <test> + <param name="database_type" value="custom" /> + <param name="custom_fasta" value="adapter.fa" /> + <param name="custom_database_name" value="database" /> + <param name="skip_maps" value="true" /> + <output name="out_file" value="kraken2_custom_data_manager.json" /> + </test> + </tests> <help> </help> <citations>