Mercurial > repos > iuc > amrfinderplus_data_manager_build
view data_manager/data_manager_build_amrfinderplus.xml @ 2:a5921c09b7b7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
author | iuc |
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date | Thu, 30 May 2024 13:06:37 +0000 |
parents | 592ef3959907 |
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<tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>AMRFinderPlus database builder</description> <macros> <import>macro.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/data_manager_build_amrfinderplus.py' '$output_file' --db_version '$database_list.database_version_select' #if $database_list.database_version_select != 'latest': --db_date '$database_list.database_date_select' #end if $test_data_manager ]]></command> <inputs> <conditional name="database_list"> <param name="database_version_select" type="select" label="Database version"> <option value="3.12">V3.12</option> </param> <when value="3.12"> <param name="database_date_select" type="select" label="Date version"> <option value="2024-05-02.2">2024-05-02.2</option> <option value="2024-01-31.1">2024-01-31.1</option> </param> </when> </conditional> <param name="test_data_manager" type="hidden" value=""/> </inputs> <outputs> <data name="output_file" format="data_manager_json"/> </outputs> <tests> <!-- Test_1 DB latest --> <test expect_num_outputs="1"> <param name="test_data_manager" value="--test"/> <output name="output_file"> <assert_contents> <has_n_lines n="1"/> <has_text text="{"data_tables""/> <has_text text="amrfinderplus_versioned_database"/> <has_text text='"db_version": "3.12"'/> </assert_contents> </output> </test> <!-- Test_2 DB 3.12 2024-01-31.1 --> <test expect_num_outputs="1"> <param name="test_data_manager" value="--test"/> <conditional name="database_list"> <param name="database_version_select" value="3.12"/> <param name="database_date_select" value="2024-01-31.1"/> </conditional> <output name="output_file"> <assert_contents> <has_n_lines n="1"/> <has_text text="{"data_tables""/> <has_text text="amrfinderplus_versioned_database"/> <has_text text='"name": "V3.12-2024-01-31.1"'/> <has_text text='"db_version": "3.12"'/> </assert_contents> </output> </test> </tests> <help><![CDATA[ Download AMRFinderPlus database from the NCBI server ]]></help> <citations> <citation type="doi">10.1038/s41598-021-91456-0</citation> </citations> </tool>