| Previous changeset 55:40ea0695a0a0 (2019-05-23) Next changeset 57:8990d2675912 (2019-05-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 616f23916e8c71295e1456d6df585c351bd64f86-dirty |
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modified:
data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
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added:
test-data/kraken2_custom_data_manager.json |
| b |
| diff -r 40ea0695a0a0 -r 7d384656966e data_manager/kraken2_build_database.py --- 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 |
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| @@ -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': { |
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| diff -r 40ea0695a0a0 -r 7d384656966e data_manager/kraken2_build_database.xml --- 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 |
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| @@ -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> |
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| diff -r 40ea0695a0a0 -r 7d384656966e test-data/kraken2_custom_data_manager.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken2_custom_data_manager.json Thu May 23 15:10:16 2019 -0400 |
| [ |
| @@ -0,0 +1,1 @@ +{"data_tables": {"kraken2_databases": [{"path": "database", "name": "database", "value": "database"}]}} |