Mercurial > repos > iuc > data_manager_gtdbtk_database_installer
diff data_manager/gtdbtk_database_installer.xml @ 0:629464b96c2e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
author | iuc |
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date | Thu, 08 Dec 2022 19:26:49 +0000 |
parents | |
children | 2814c058a087 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/gtdbtk_database_installer.xml Thu Dec 08 19:26:49 2022 +0000 @@ -0,0 +1,48 @@ +<tool id="gtdbtk_database_installer" name="GTDB-Tk Database Installer" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description></description> + <macros> + <token name="@TOOL_VERSION@">202</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.09</token> + </macros> + <requirements> + <requirement type="package" version="3.10.2">python</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/gtdbtk_database_installer.py' + --database_id '$database_id' + --database_name '$database_name' + --url '$url' + --out_file '$out_file' + ]]> + </command> + <inputs> + <param name="database_name" type="text" value="" label="Database name or description" help="This value will be displayed in the GTDB-Tk Database select list"/> + <param name="database_id" type="text" value="" label="Database id" help="This value must be unique with nNo whitespace allowed-use underscores"/> + <param name="url" type="text" value="https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz" label="URL for downloading the selected version of the GTDB-Tk database"/> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <!-- Not actually installing a huge GTDB-Tk database --> + <param name="database_id" value="release202"/> + <param name="database_name" value="GTDB-Tk database release 202"/> + <param name="url" value="https://data.gtdb.ecogenomic.org/releases/release202/202.0/VERSION"/> + <output name="out_file"> + <assert_contents> + <has_text text="GTDB-Tk database release 202"/> + <has_text text="release202"/> + </assert_contents> + </output> + </test> + </tests> + <help> + </help> + <citations> + <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation> + <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation> + </citations> +</tool>