Mercurial > repos > iuc > data_manager_gtdbtk_database_installer

diff data_manager/gtdbtk_database_installer.xml @ 0:629464b96c2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
author iuc
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>