--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastp_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,47 @@
+<macros>
+    <token name="@FASTP_COMMAND@"><![CDATA[
+        #set $pattern = "report_title"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
+            ln -s '$file' '$file_path' &&
+            grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
+        #end for
+    ]]></token>
+    <xml name="fastp_form">
+        <param name="input" type="data" format="json" label="Output of fastp" help="It should be the json report from fastp containing 'report_title" multiple="true"/>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="fastp_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="fastp"/>
+                    <param name="input" value="fastp1.json.txt,fastp2.json.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="All-in-one FASTQ preprocessor"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="fastp_mqc_generalstats_fastp_pct_duplication"/>
+                    <has_text text="R1_fq"/>
+                    <has_text text="fastp_mqc_generalstats_fastp_after_filtering_q30_rate"/>
+                    <has_text text="bwa-mem-fastq1_fq"/>
+                    <has_n_lines n="3"/>
+                    <has_n_columns n="8"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="15"/>
+        </test>
+    </xml>
+</macros>