--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_fix_sixpack.xml	Mon Jun 05 02:42:28 2023 +0000
@@ -0,0 +1,37 @@
+<tool id="edu.tamu.cpt.gff3.fixsixpack" name="GFF3 Add Gene to CDS for Sixpack" version="19.1.0.0">
+  <description>Properly formats naive ORF caller output for Apollo</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+'$__tool_directory__/gff3_fix_sixpack.py'
+@INPUT_GFF@
+> '$output']]></command>
+  <inputs>
+    <expand macro="gff3_input"/>
+  </inputs>
+  <outputs>
+    <data format="gff3" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="gff3_data" value="miro.gff3"/>
+      <output name="output" file="miro.6pfix.gff3"/>
+    </test>
+    <test>
+      <param name="gff3_data" value="miro.cds.gff3"/>
+      <output name="output" file="miro.cds6pfix.gff3"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+This tool **strips ALL the mRNA features** in a GFF3 file. It specifically formats 
+the output of the naïve ORF call Sixpack such that it will be compatible with 
+Apollo via JBrowse.
+
+      ]]></help>
+  <expand macro="citations"/>
+</tool>