--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,48 @@
+<macros>
+    <token name="@CUTADAPT_COMMAND@"><![CDATA[
+        #set $pattern = "This is cutadapt"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
+            ln -s '$file' '$file_path' &&
+            ## replace header for old cutadapt release
+            sed -i.old 's/You are running/This is/' '$file_path' &&
+            grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" &&
+        #end for
+    ]]></token>
+    <xml name="cutadapt_form">
+        <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/>
+    </xml>
+    <xml name="cutadapt_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="cutadapt"/>
+                    <param name="input" value="cutadapt.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"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="Cutadapt"/>
+                    <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/>
+                    <has_text text="10"/>
+                    <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="2"/>
+        </test>
+    </xml>
+</macros>