--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featurecounts_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,50 @@
+<macros>
+    <token name="@FEATURECOUNTS_COMMAND@"><![CDATA[
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_prefix = os.path.join($software_dir, str($identifier))
+            if grep -qw Status '$file'; then
+                ln -s '$file' '${file_prefix}.summary';
+            else
+                echo -e 'Status\t${identifier}' > '${file_prefix}.summary';
+                cat '$file' >> '${file_prefix}.summary';
+            fi &&
+        #end for
+    ]]></token>
+    <xml name="featurecounts_form">
+        <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="featurecounts_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="featureCounts"/>
+                    <param name="input" value="featureCounts.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="featureCounts_assignment_plot"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="featureCounts_mqc_generalstats_featurecounts_Assigned"/>
+                    <has_text text="accepted_hits"/>
+                    <has_text text="TopHat"/>
+                    <has_text text="featureCounts_mqc_generalstats_featurecounts_percent_assigned"/>
+                    <has_n_lines n="7"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="1"/>
+        </test>
+    </xml>
+</macros>