--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_require_phage_start.xml	Mon Jun 05 02:52:41 2023 +0000
@@ -0,0 +1,50 @@
+<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>