Mercurial > repos > iuc > data_manager_gtdbtk_database_installer
diff data_manager/gtdbtk_database_installer.xml @ 7:3b1d503c6260 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
| author | iuc |
|---|---|
| date | Thu, 03 Oct 2024 12:42:22 +0000 |
| parents | df84aaed4769 |
| children | 750d902de22c |
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--- a/data_manager/gtdbtk_database_installer.xml Mon Sep 09 09:01:39 2024 +0000 +++ b/data_manager/gtdbtk_database_installer.xml Thu Oct 03 12:42:22 2024 +0000 @@ -2,7 +2,7 @@ <description></description> <macros> <token name="@TOOL_VERSION@">202</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.09</token> </macros> <requirements> @@ -10,18 +10,16 @@ </requirements> <command> <![CDATA[ - python '$__tool_directory__/gtdbtk_database_installer.py' - --database_name '$database_name' - --release '$release' - --out_file '$out_file' - $meta - $test +python '$__tool_directory__/gtdbtk_database_installer.py' + --release '$release' + --out_file '$out_file' + $meta + $test ]]> </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="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " /> - <param name="test" type="hidden" value="" checked="false" label="Run a dry test run !" /> + <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " /> + <param name="test" type="hidden" value="" checked="false" label="Run a dry test run!" /> <param name="release" type="select" multiple="false" label="GTDB Release"> <option value="202">202</option> <option value="207">207</option> @@ -34,40 +32,36 @@ </outputs> <tests> <test> - <!-- TODO --> <!-- Not actually installing a huge GTDB-Tk database --> <!-- but it will check if all urls exist --> <param name="release" value="202"/> - <param name="database_name" value="GTDB-Tk database release 202"/> <param name="test" value="--test"/> <output name="out_file"> <assert_contents> - <has_text text="GTDB-Tk database release 202"/> - <has_text text="release_202"/> + <has_text text="Full Database - release 202 "/> + <has_text text="full_database_release_202_downloaded"/> </assert_contents> </output> </test> <test> <!-- Test meta data download with tsv.gz--> <param name="release" value="220"/> - <param name="database_name" value="GTDB-Tk database release 220 metadata"/> <param name="meta" value="true"/> <output name="out_file"> <assert_contents> - <has_text text="GTDB-Tk database release 220 metadata"/> - <has_text text="release_220"/> + <has_text text="Metadata Tables - release 220"/> + <has_text text="metadata_tables_release_220_downloaded_"/> </assert_contents> </output> </test> <test> <!-- Test meta data download with tar.gz --> <param name="release" value="207"/> - <param name="database_name" value="GTDB-Tk database release 207 metadata"/> <param name="meta" value="true"/> <output name="out_file"> <assert_contents> - <has_text text="GTDB-Tk database release 207 metadata"/> - <has_text text="release_207"/> + <has_text text="Metadata Tables - release 207"/> + <has_text text="metadata_tables_release_207_downloaded_"/> </assert_contents> </output> </test>
