Mercurial > repos > ufz > data_manager_eukcc

diff data_manager/eukcc.xml @ 0:7f11e0da0e4f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
author: ufz
date: Fri, 25 Jul 2025 10:54:08 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/eukcc.xml	Fri Jul 25 10:54:08 2025 +0000
@@ -0,0 +1,60 @@
+<tool id="data_manager_eukcc" name="EukCC data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
+    <macros>
+        <token name="@TOOL_VERSION@">2.1.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">eukcc</requirement>
+    </requirements>
+    <version_command>eukcc --version | cut -d" " -f3</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir '$output_file.extra_files_path' &&
+        wget http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/eukcc2_db_ver_${version}.tar.gz &&
+        tar -xvf eukcc2_db_ver_${version}.tar.gz &&
+        rm eukcc2_db_ver_${version}.tar.gz &&
+        mv eukcc2_db_ver_${version}/* '$output_file.extra_files_path'/ &&
+        cp '$dmjson' '$output_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+    {
+      "data_tables":{
+        "eukcc":[
+          {
+            "value":"$version",
+            "name":"EukCC DB ${version}",
+            "version":"${version}",
+            "path":"$output_file.extra_files_path"
+          }
+        ]
+      }
+    }]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="version" type="select" label="DB version">
+            <option value="1.2">1.2</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <!-- data to large for test in CI
+        <test>
+            <param name="version" value="1.2"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="EukCC DB"/>
+                    <has_text text="1.2"/>
+                    <has_text text="eukcc"/>
+                </assert_contents>
+            </output>
+        </test> -->
+    </tests>
+    <help><![CDATA[
+        This data managers fetches EukCC reference data from http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s13059-020-02155-4</citation>
+    </citations>
+</tool>