--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_intron_detect/intron_detection.xml	Fri May 13 05:08:54 2022 +0000
@@ -0,0 +1,57 @@
+<?xml version="1.1"?>
+<tool id="edu.tamu.cpt2.phage.intron_detection" name="Interrupted gene detection tool" version="19.1.0.0">
+  <description>based on nearby protein blast results</description>
+  <macros>
+    <import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+  </macros>
+  <requirements>
+    <requirement type="package" version="3.6">python</requirement>
+    <requirement type="package" version="1.77">biopython</requirement>
+    <requirement type="package" version="1.1.3">cpt_gffparser</requirement>  
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+python $__tool_directory__/intron_detection.py
+
+"$gff3_data"
+"$blast"
+--minimum $minimum
+--maximum $maximum
+--idThresh $idThresh
+> $output]]></command>
+  <inputs>
+    <expand macro="gff3_input" />
+    <param label="Blastp Results" name="blast" type="data" format="blastxml"/>
+    <param label="Separation Minimum" name="minimum" type="text" value="-1"
+        help="Minimum number of amino acids a CDS pair must be separated by to detect an intron. Set to a negative number to instead allow CDS to overlap by up to that many AAs."/>
+    <param label="Separation Maximum" name="maximum" type="integer" value="10000"
+        help="Maximum number of bases a CDS pair may be separated by to detect an intron (eg, distance from end of 1 cds to the start of another)."/>
+    <param label="Percent Identity Threshold" name="idThresh" type="float" value=".30"
+        help="Minimum Identity Percentage for HSP to be considered for intron comparison (0.00 to 1.00)"/>
+  </inputs>
+  <outputs>
+    <data format="gff3" name="output" label="Potential interrupted genes"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="gff3_data" value="T7_CLEAN.gff3"/>
+          <param name="blast" value="T7_NR.blastxml"/>
+          <param name="minimum" value="10" />
+          <param name="maximum" value="2000" />
+          <param name="idThresh" value="0.3" />
+          <output name="output" file="T7_INTRON.gff3"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+This tool parses BLAST XML results and returns potential intron regions by 
+identifying query proteins with BLAST hits to the same target protein within 
+the maximum number of bases set above. This distance will also wraparound the 
+ends of the genome. The list of hits is returned as a gff3.
+
+(Tool formerly named Intron Detection, updated Nov 2020)
+
+      ]]></help>
+		<expand macro="citations-2020" />
+</tool>