--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VarAmpliCNV_Anno.xml	Fri Sep 25 08:30:57 2020 +0000
@@ -0,0 +1,51 @@
+<tool id="VarAmpliCNV_Anno" name="Annotate Amplicons" version="0.1.0" python_template_version="3.5">
+    <requirements>
+	<container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
+
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+	processAmpliconRegion.py
+	
+	## input amplicon file
+	-a '$AmpInput' 
+
+	## ROI input
+	-r '$roiInput'
+
+	## snpInput (probes to discard)
+	#if $snpInput
+		-s $snpInput
+        #end if
+
+	## output files
+	-D '$dedupOut'
+	-R '$roiOut'
+	
+	
+	]]></command>
+    <inputs>
+	<param name="AmpInput" type="data" format="bed" optional="false" label="Amplicon Design File (BED)" help="This file is the HaloPlex design file, containing individual amplicons." />
+	<param name="roiInput" type="data" format="bed" optional="false" label="ROI file (BED)" help="Region of Interest definition. Typically one line per Exon of the target genes bis." />
+	<param name="snpInput" type="data" format="bed" optional="true" label="Ignore List (BED)" help="A subset of amplicons you do not want to analyze (e.g. a co-enriched panel)." />
+    </inputs>
+    <outputs>
+	<data name="dedupOut" format="bed" label="VarAmpliCNV on ${on_string}: DeDuplicated Amplicon List" />
+	<data name="roiOut" format="bed" label="VarAmpliCNV on ${on_string}: ROI-Annotated Amplicon List" />
+    </outputs>
+<help>
+**VarAmpliCNV : BED file PreProcessing**
+
+Preprocessing includes removing SNP (unwanted amplicons) coordinates and duplicate coordinates. It also adds Region annotations to input region of interest (ROI) used during plotting.
+
+**Parameters are :** 
+
+* Amplicon Design File (BED) : This is the *exact* BED file provided by HaloPlex, containing the restriction fragments.
+* ROI file (BED) : Typically the file provided *to* HaloPlex as the basis of the design. Names in column 4 are used to annotate CNV plots
+* Ignore list (BED) : (optional) Provide amplicons present in amplicon design, to exclude during the analysis
+
+**Output files :**
+
+* DeDuplicated amplicon List (BED) : Use this file in subsequent steps (GC and Counting).
+* ROI-Annotated List : This file is needed during CNV-calling.
+</help>
+</tool>