--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_gff.xml	Thu May 19 08:23:55 2022 +0000
@@ -0,0 +1,39 @@
+<tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" python_template_version="3.5">
+    <requirements>
+        <requirement type="package">bioconductor-rtracklayer</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        $__tool_directory__/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name'
+        &&
+        cp annotation_overlap_long.csv '$out_long'
+        &&
+        cp annotation_overlap.csv '$out_wide'
+
+    ]]></command>
+    <inputs>
+      <param type="data" name="input1_gff" format="gff" label="First GFF">
+        <sanitizer invalid_char="">
+          <valid initial="string.ascii_letters,string.digits">
+            <add value="_" />
+          </valid>
+        </sanitizer>
+      </param>
+      <param type="data" name="input2_gff" format="gff" label="Second GFF">
+        <sanitizer invalid_char="">
+          <valid initial="string.ascii_letters,string.digits">
+            <add value="_" />
+          </valid>
+        </sanitizer>
+      </param>
+        <param type="text" name="attribute_name" label="Name of attribute to summarize"/>
+    </inputs>
+    <outputs>
+        <data name="out_long" format="tabular" label="Overlap of annotations
+        ${input1_gff.hid} and ${input1_gff.hid} (as matrix)"  />
+        <data name="out_wide" format="tabular" label="Overlap of annotations
+        ${input1_gff.hid} and ${input1_gff.hid} (as table)"/>
+    </outputs>
+    <help><![CDATA[
+        Compare overlaps in two GFF3 by selected attribute. Overlap is reported a number of bases. It expects not overlap within individuals GFF3.
+    ]]></help>
+</tool>