--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_req_phage_start/gff3_require_phage_start.xml	Fri May 13 05:31:56 2022 +0000
@@ -0,0 +1,52 @@
+<tool id="edu.tamu.cpt.gff3.require_phage_start" name="GFF3 Filter: Require Phage Start" version="19.1.0.0">
+  <description>ensures start is ATG, TTG, or GTG</description>
+  <macros>
+    <import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+@GENOME_SELECTOR_PRE@
+
+python $__tool_directory__/gff3_require_phage_start.py
+
+@GENOME_SELECTOR@
+$gff3_data
+
+> $stdout
+
+]]></command>
+  <inputs>
+    <expand macro="genome_selector" />
+    <expand macro="gff3_input" />
+  </inputs>
+  <outputs>
+    <data format="gff3" name="stdout" label="$gff3_data.name filtered for start codon"/>
+  </outputs>
+  <tests>
+      <test>
+			<param name="reference_genome_source" value="history" />
+			<param name="genome_fasta" value="T7_ReqPhageIn.fasta" />
+			<param name="gff3_data" value="T7_ReqPhageIn.gff3" />
+
+          <output name="stdout" file="T7_ReqPhageOut.gff3" />
+      </test>
+      <test>
+			<param name="reference_genome_source" value="history" />
+			<param name="genome_fasta" value="Miro_ReqPhageIn.fa" />
+			<param name="gff3_data" value="Miro_ReqPhageIn.gff3" />
+
+          <output name="stdout" file="Miro_ReqPhageOut.gff3" />
+      </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Removes any CDS from the GFF3 whose start codon is **not** ATG, TTG, or GTG.
+
+.. class:: warningmark
+
+The tool only retains *gene* and *CDS* features that pass this filter. 
+      ]]></help>
+		<expand macro="citations" />
+</tool>