--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fix-aragorn-gff3.xml	Mon Jun 05 02:42:12 2023 +0000
@@ -0,0 +1,32 @@
+<tool id="edu.tamu.cpt.external.aragorn-gff3" name="Fix tRNA model" version="19.1.0.0">
+  <description/>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+'$__tool_directory__/fix-aragorn-gff3.py'
+@INPUT_GFF@
+> '$default']]></command>
+  <inputs>
+    <expand macro="gff3_input"/>
+  </inputs>
+  <outputs>
+    <data format="gff3" name="default"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="gff3_data" value="FixAra_In.gff3"/>
+      <output name="default" file="FixAra_Out.gff3"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+For an input GFF3 file with tRNAs from the Aragorn or converted from the tRNAscan-SE tools, this tool modifies 
+the gene model to reflect a gene-tRNA-exon hierarchy. That change is needed 
+to allow for creation of proper tRNA features in Apollo.
+      ]]></help>
+  <expand macro="citations"/>
+</tool>