Mercurial > repos > thanhlv > data_manager_build_ariba_database
changeset 9:218301fbbb99 draft default tip
"planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 3a0b92d1a2dcd5c5b75e5b63727850139af21ace-dirty"
| author | thanhlv |
|---|---|
| date | Fri, 02 Oct 2020 11:43:36 +0000 |
| parents | fb4da292b6d0 |
| children | |
| files | data_manager/ariba_database_builder.py data_manager/ariba_database_builder.xml data_manager/macros.xml data_manager_conf.xml |
| diffstat | 4 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/data_manager/ariba_database_builder.py Sun May 19 09:09:24 2019 -0400 +++ b/data_manager/ariba_database_builder.py Fri Oct 02 11:43:36 2020 +0000 @@ -7,7 +7,7 @@ import os import shutil import errno - +from pprint import pprint data_table_name = "ariba_databases" @@ -158,6 +158,7 @@ genes_dict = { "card" : "CARD", + "ncbi" : "ncbi", "resfinder" : "Resfinder", "plasmidfinder" : "Plasmidfinder", "megares" : "Megares", @@ -212,7 +213,7 @@ name = args.db_name params = json.loads(open(args.params).read()) - + pprint(params) target_directory = params['output_data'][0]['extra_files_path'] if not os.path.isdir(target_directory):
--- a/data_manager/ariba_database_builder.xml Sun May 19 09:09:24 2019 -0400 +++ b/data_manager/ariba_database_builder.xml Fri Oct 02 11:43:36 2020 +0000 @@ -25,6 +25,7 @@ <when value="curated"> <param name="db" type="select" multiple="false" label="Select partial library to download"> <option value="card">CARD</option> + <option value="ncbi">ncbi</option> <option value="resfinder">Resfinder</option> <option value="plasmidfinder">Plasmidfinder</option> <option value="megares">Megares</option>
--- a/data_manager/macros.xml Sun May 19 09:09:24 2019 -0400 +++ b/data_manager/macros.xml Fri Oct 02 11:43:36 2020 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.13.2</token> + <token name="@VERSION@">2.14.6</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">ariba</requirement>
--- a/data_manager_conf.xml Sun May 19 09:09:24 2019 -0400 +++ b/data_manager_conf.xml Fri Oct 02 11:43:36 2020 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/ariba_database_builder.xml" id="ariba_database_builder" version="0.1.0"> + <data_manager tool_file="data_manager/ariba_database_builder.xml" id="ariba_database_builder" version="2.14.6"> <data_table name="ariba_databases"> <output> <column name="value" />