--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,40 @@
+<macros>
+    <token name="@TRIMMOMATIC_COMMAND@">
+        <!--This pattern is used to check the file content in the @CHECK_LN_FILE@ token. The pattern should be included in the file. -->
+    #set $pattern = "Trimmomatic"
+    @LN_FILES@
+</token>
+    <xml name="trimmomatic_form">
+        <param name="input" type="data" format="txt,tabular,tsv,csv" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic" multiple="true"/>
+    </xml>
+    <xml name="trimmomatic_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="trimmomatic"/>
+                    <param name="input" value="trimmomatic.txt"/>
+                </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="trimmomatic_plot"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="Trimmomatic_mqc_generalstats_trimmomatic_dropped_pct"/>
+                    <has_text text="C2"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="1"/>
+        </test>
+    </xml>
+</macros>