diff checkm2_plugin.xml @ 30:4981b6c4f7fa draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/checkm2_plugin.xml	Thu Jan 15 20:38:43 2026 +0000
@@ -0,0 +1,47 @@
+<macros>
+    <token name="@CHECKM2_COMMAND@"><![CDATA[
+        #set $pattern = "Name\tCompleteness\tContamination\tCompleteness_Model_Used\tTranslation_Table_Used"
+        @LN_FILES@
+    ]]></token>
+    <xml name="checkm2_form">
+        <param name="input" type="data" format="tabular" multiple="true" label="Output of CheckM2" help="It should be the quality report from CheckM2"/>
+    </xml>
+    <xml name="checkm2_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="checkm2"/>
+                    <param name="input" value="checkm2.tsv"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="CheckM2"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+        <!-- This test use a Checkm2 TSV file with wrong required headers to check error handling. 
+        Some checkm2 column names are parameter-dependent and the checkm2 multiQC module rely on a specific column pattern.
+        An issue has been opened : https://github.com/MultiQC/MultiQC/issues/3466 
+        There is a stdio rule in macro that need to be removed once the issue is fixed -->
+        <test expect_failure="true" expect_exit_code="1">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="checkm2"/>
+                    <param name="input" value="checkm2-wrong.tsv"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+        </test>
+    </xml>
+</macros>