--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_convert_glimmer_to_gff3.xml	Mon Jun 05 02:40:30 2023 +0000
@@ -0,0 +1,40 @@
+<tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0">
+    <description>convert formats</description>
+    <macros>
+        <import>cpt-macros.xml</import>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+@GENOME_SELECTOR_PRE@
+
+'python $__tool_directory__/cpt_convert_glimmer_to_gff3.py'
+'$glimmer'
+@GENOME_SELECTOR@
+> '$data' ]]>
+</command>
+    <inputs>
+        <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/>
+        <expand macro="genome_selector"/>
+    </inputs>
+    <outputs>
+        <data format="gff3" name="data">
+		</data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_genome_source" value="history"/>
+            <param name="genome_fasta" value="ConvGlim_In.fasta"/>
+            <param name="glimmer" value="ConvGlim_In.out"/>
+            <output name="data" file="ConvGlim_Out.gff3"/>
+        </test>
+    </tests>
+    <help>
+	**What it does**
+
+	Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping 
+	around over the sequence boundary (as if circular) then it will only convert the upstream fragment and 
+	label it as "_truncated" in the resulting GFF.
+	</help>
+    <expand macro="citations"/>
+</tool>