--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie2_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,40 @@
+<macros>
+    <token name="@BOWTIE2_COMMAND@"><![CDATA[
+        #set $pattern = "% overall alignment rate"
+        @LN_FILES@
+    ]]></token>
+    <xml name="bowtie2_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="bowtie2_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="bowtie2"/>
+                    <param name="input" value="bowtie2_1.txt,bowtie2_2.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="bowtie2_se_plot"/>
+                    <has_text text="mqc-module-section-bowtie2"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="bowtie2_1_txt"/>
+                    <has_n_lines n="3"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="1"/>
+        </test>
+    </xml>
+</macros>