--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VarAmpliCNV_MergeCounts.xml	Fri Sep 25 08:30:57 2020 +0000
@@ -0,0 +1,39 @@
+<tool id="VarAmpliCNV_MergeCounts" name="Merge Counts" version="0.1.0" >
+    <requirements>
+	<container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
+    </requirements>
+ 
+   <command detect_errors="exit_code"><![CDATA[
+	mkdir -p infiles 
+        
+	#for $element in $inputFile:
+      	   && bname=\$(basename ${element}) 
+           && ln -s "${element}" "infiles/\$bname.txt" 
+    	#end for	
+	
+	&& 
+	
+	MergeCounts.py -d 'infiles' -o "$outfile"
+	
+	]]></command>
+    <inputs>
+	<param name="inputFile" type="data" format="txt" optional="false" multiple="True" label="Sample Amplicon Counts" help="This file is created by the VarAmpliCNV 'Count' tool." />
+    </inputs>
+    <outputs>
+	<data name="outfile" format="rdata" label="VarAmpliCNV on ${on_string}: Aggregated Counts" />
+    </outputs>
+    <help>
+**VarAmpliCNV : Merge Count files**
+
+Merge a list of count files from "varAmpliCNV Count" into a single cohort for CNV-calling.
+
+**Parameters are :** 
+
+* Count file (txt) : A list or collection of count files from "varAmpliNCV Count".
+
+
+**Output files :**
+
+* Count-by-Sample Matrix (Rdata) : Rdata object containing counts for all provided samples.   
+    </help>
+</tool>