diff data_manager/checkm2_datamanager.xml @ 0:4abc306ec842 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/checkm2_datamanager.xml	Tue Jan 14 20:27:00 2025 +0000
@@ -0,0 +1,62 @@
+<tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>database builder</description>
+    <macros>
+        <!-- on update run a local test setting `test` to something else than "true" -->
+        <token name="@TOOL_VERSION@">1.0.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
+    </requirements>
+    <version_command>checkm2 --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p '$out_file.extra_files_path' &&
+        #if $test != "true"
+            checkm2 database --download --path  '$out_file.extra_files_path'/ &&
+            mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
+        #else
+            touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
+        #end if
+        cp '$dmjson' '$out_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+{
+  "data_tables":{
+    "checkm2":[
+      {
+        "path":"uniref100.KO.1.dmnd",
+        "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@",
+        "version":"@TOOL_VERSION@",
+        "value":"@TOOL_VERSION@"
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="test" type="hidden"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="test" value="true"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"value":"@TOOL_VERSION@"'/>
+                    <has_text text='"name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Download and extract CheckM2 reference data.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41592-023-01940-w</citation>
+    </citations>
+</tool>