Mercurial > repos > pimarin > data_manager_bakta
changeset 12:7bd60bfa8ffc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
| author | pimarin |
|---|---|
| date | Wed, 02 Nov 2022 14:35:26 +0000 |
| parents | c50e8b4f74d7 |
| children | 8f63e424da2b |
| files | data_manager/bakta_build_database.xml data_manager/macro.xml test-data/bakta_test_data_manager.json |
| diffstat | 3 files changed, 7 insertions(+), 21 deletions(-) [+] |
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--- a/data_manager/bakta_build_database.xml Wed Nov 02 11:06:36 2022 +0000 +++ b/data_manager/bakta_build_database.xml Wed Nov 02 14:35:26 2022 +0000 @@ -5,14 +5,16 @@ <import>macro.xml</import> </macros> <expand macro="requirements"/> - <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ + <command detect_errors="exit_code"> + <![CDATA[ python '$__tool_directory__/bakta_build_database.py' '$output_file' --database_version '$database_select' - '$test_data_manager' - ]]></command> + #if '$test_data_manager' != '' + '$test_data_manager' + #end if + ]]></command> <inputs> <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)"> <option value="latest" selected="true">Latest available version</option>
--- a/data_manager/macro.xml Wed Nov 02 11:06:36 2022 +0000 +++ b/data_manager/macro.xml Wed Nov 02 14:35:26 2022 +0000 @@ -5,11 +5,7 @@ <token name="@PROFILE@">21.05</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@TOOL_VERSION@">bakta</requirement> <requirement type="package" version="@PYTHON_VERSION@">python</requirement> </requirements> </xml> - <xml name="version_command"> - <version_command><![CDATA[bakta --version]]></version_command> - </xml> </macros>
--- a/test-data/bakta_test_data_manager.json Wed Nov 02 11:06:36 2022 +0000 +++ b/test-data/bakta_test_data_manager.json Wed Nov 02 14:35:26 2022 +0000 @@ -1,13 +1,1 @@ -{ - "data_tables": { - "bakta_database": [ - { - "bakta_version": "0.0", - "database_record": "7197299", - "dbkey": "date_test", - "path": "/tmp/tmpu_ccwfs9/job_working_directory/000/1/working/dataset_fb48f154-bf1b-4974-8759-e4f0e230e917_files/bakta_test", - "value": "bakta_0.0" - } - ] - } -} +{"data_tables":{"bakta_database": [{"bakta_version": "0.0","database_record": "7197299","dbkey": "date_test","path": "/tmp/tmpu_ccwfs9/job_working_directory/000/1/working/dataset_fb48f154-bf1b-4974-8759-e4f0e230e917_files/bakta_test","value": "bakta_0.0"}]}}