--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_req_sd/gff3_require_sd.xml	Fri May 13 05:35:34 2022 +0000
@@ -0,0 +1,53 @@
+<tool id="edu.tamu.cpt.gff3.require_sd" name="Gff3 Filter: Require SD" version="19.1.0.0">
+  <description>ensures CDSs have an SD</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_sd.py
+
+@GENOME_SELECTOR@
+@INPUT_GFF@
+
+> $stdout
+
+]]></command>
+  <inputs>
+    <expand macro="genome_selector" />
+    <expand macro="gff3_input" />
+  </inputs>
+  <outputs>
+    <data format="gff3" name="stdout" label="$gff3_data.name filtered for SD presence"/>
+  </outputs>
+  <tests>
+      <test>
+			<param name="reference_genome_source" value="history" />
+			<param name="genome_fasta" value="T7_ReqSDIn.fasta" />
+			<param name="gff3_data" value="T7_ReqSDIn.gff3" />
+
+          <output name="stdout" file="T7_ReqSDOut.gff3" />
+      </test>
+      <test>
+			<param name="reference_genome_source" value="history" />
+			<param name="genome_fasta" value="Miro_ReqSDIn.fa" />
+			<param name="gff3_data" value="Miro_ReqSDIn.gff3" />
+
+          <output name="stdout" file="Miro_ReqSDOut.gff3" />
+      </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Ensures every CDS has an upstream Shine-Dalgarno site defined. ShineFind is used to add SD subfeatures to CDSs without one.
+
+.. class:: warningmark 
+
+This tool removes non-CDS type features, and CDS features without an SD site (RBS features are ignored). 
+
+      ]]></help>
+		<expand macro="citations" />
+</tool>