--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_phageqc_annotation/phage_annotation_validator.xml	Fri Jun 17 13:00:50 2022 +0000
@@ -0,0 +1,102 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt2.phage.annotation_validator" name="Phage QC" version="1.9.0" profile="16.04">
+    <description>validate phage annotations</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="1.1.7">cpt_gffparser</requirement>  
+      <requirement type="package" version="0.12.0">python-levenshtein</requirement>
+      <requirement type="package" version="2019.06.08">regex</requirement>
+      <requirement type="package">metagene_annotator</requirement>
+      <requirement type="package" version="2.10.1">jinja2</requirement>
+      <requirement type="package" version="1.11">numpy</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+@GENOME_SELECTOR_PRE@
+
+python $__tool_directory__/phage_annotation_validator.py
+$gff3_data
+@GENOME_SELECTOR@
+
+--gff3 $gff3
+
+--sd_min $sd_min
+--sd_max $sd_max
+
+--min_gene_length $min_gene
+
+--excessive_overlap_dist $eod
+--excessive_overlap_divergent_dist $eodd
+
+--excessive_gap_dist $egd
+--excessive_gap_divergent_dist $egdd
+
+--reportTemplateName $report_format
+
+> $output;
+
+#if ".tex" in str($report_format):
+    mv $output tmp.tex;
+    docker run --rm -i --user="1002:1002" --net=none -v \$PWD:/data blang/latex pdflatex tmp.tex &&
+    docker run --rm -i --user="1002:1002" --net=none -v \$PWD:/data blang/latex pdflatex tmp.tex &&
+    mv tmp.pdf $output;
+#end if
+]]></command>
+    <inputs>
+        <expand macro="gff3_input" />
+        <expand macro="genome_selector" />
+
+        <param label="Minimum distance for SDs (bp)" name="sd_min" type="integer" value="5" />
+        <param label="Maximum distance for SDs (bp)" name="sd_max" type="integer" value="15" />
+
+        <param label="Minimum length of naively called ORFs in gaps (in AAs)" name="min_gene" type="integer" value="25" />
+
+        <param label="Excessive overlap distance (non-divergent, bp)" name="eod" type="integer" value="25" />
+        <param label="Excessive overlap distance (divergent, bp)" name="eodd" type="integer" value="50" />
+
+        <param label="Excessive gap distance (non-divergent, bp)" name="egd" type="integer" value="50" />
+        <param label="Excessive gap distance (divergent, bp)" name="egdd" type="integer" value="200" />
+
+        <param label="Report Format" type="select" name="report_format">
+            <option value="phageqc_report_full.html" selected="True">Full Report</option>
+            <option value="phageqc_report_464.html">464 Report</option>
+            <option value="phageqc_report_genomea.tex">GenomeA PDF Report</option>
+            <option value="phageqc_report_genomea.html">GenomeA HTML Report</option>
+        </param>
+    </inputs>
+    <outputs>
+      <data format="html" name="output">
+          <change_format>
+            <when input="report_format" value="phageqc_report_genomea.tex" format="pdf"/>
+          </change_format>
+      </data>
+      <data format="gff3" name="gff3" label="Phage QC annotation track"/>
+    </outputs>
+    <tests>
+      <test>
+        <param name="gff3_data" value="AY216660.gff3"/>
+        <param name="genome_fasta" value="AY216660.fasta" />
+	<output name="gff3" file="PhageQC_Out.gff3"/> 
+        <output name="output" file="PhageQC_Out.html"/>
+      </test>
+    </tests>    
+    <help><![CDATA[
+**What it does**
+
+Run CPT's Phage Annotation Validator validating the following properties:
+
+-  Missing RBSs
+-  Missing Gene Features
+-  Excessive Gaps
+-  Excessive Overlaps
+-  Morons
+-  Weird Start Codons
+-  Incorrect gene model (when used with our Genbank Gene Model correction tool)
+
+        ]]></help>
+		<expand macro="citations" />
+</tool>