--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/template_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,59 @@
+<macros>
+    <!--
+    This is the TEMPLATE macro for MultiQC
+    1. please copy this template_plugin.xml to your own file e.g. trimmomatic_plugin.xml
+    2. Replace `TEMPLATE` with the name of the plugin, e.g. `fastqc`. The tokens and xml-names need to be called `trimmomatic_form` or `TRIMMOMATIC_COMMAND`
+    3. import your new *_plugin.xml macro into the main multiqc.xml file at the top of the file
+    4. add a new option to the main select element, e.g. `<option value="trimmomatic">Trimmomatic</option>`
+    5. add the *_COMMAND token to the <command> section.
+    6. add the *_test macro to the test section.
+    7. remove all unused comments from your new file
+-->
+    <token name="@TEMPLATE_COMMAND@"><![CDATA[
+        <!--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@f
+    ]]></token>
+    <xml name="TEMPLATE_form">
+        <!-- Please add here your input forms specific to your plugin. Keep the name as `input` if you have a single input.
+            If you have multiple inputs have a look at other plugins, e.g. fastqc 
+        -->
+        <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="TEMPLATE_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="cutadapt_trimmed_sequences_plot"/>
+                    <has_text text="All-in-one FASTQ preprocessor"/>
+                    <has_text text="trimmomatic_plot"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="dataset_33"/>
+                    <has_text text="R1_fq"/>
+                    <has_text text="result_right"/>
+                    <has_text text="25839_merged"/>
+                    <has_text text="C2"/>
+                    <has_n_lines n="11"/>
+                    <has_n_columns n="22"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="29"/>
+        </test>
+    </xml>
+</macros>