--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pairtools_plugin.xml	Tue Feb 18 23:18:25 2025 +0000
@@ -0,0 +1,55 @@
+<macros>
+    <token name="@PAIRTOOLS_COMMAND@"><![CDATA[
+        #set $pattern = "total_single_sided_mapped"
+        #set file_paths = []
+        #for $file in $repeat.software_cond.input:
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier))
+            #if $file_path in $file_paths
+                #set $file_path += '_' + str($file_paths.count($file_path))
+            #end if
+            #set $file_paths += [$file_path]
+            grep -Pzq "(?s)(?=.*total_single_sided_mapped\t)(?=.*cis\t)(?=.*trans\t)(?=.*pair_types/)" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
+            ln -s '$file' '$file_path'  &&
+        #end for
+    ]]></token>
+    <xml name="pairtools_form">
+        <param name="input" type="data" format="tabular" multiple="true" label="Output of Pairtools"/>
+    </xml>
+    <xml name="pairtools_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="pairtools"/>
+                    <param name="input" value="output_dedup_pairs.stats"/>
+                </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="output_dedup_pairs"/>
+                    <has_text text="Pairs by alignment status"/>
+                    <has_text text="Fraction of read pairs by strand orientation"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="pairtools-total"/>
+                    <has_text text="pairtools-frac_unmapped"/>
+                    <has_text text="0.001992"/>
+                    <has_text text="45.88353413654618"/>
+                    <has_text text="pairtools-frac_dups"/>
+                    <has_text text="0.4518072289156626"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="8"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="5"/>
+        </test>
+    </xml>
+</macros>