--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VarAmpliCNV_GC.xml	Fri Sep 25 08:30:57 2020 +0000
@@ -0,0 +1,43 @@
+<tool id="VarAmpliCNV_GC" name="Get Amplicon GC-Content" version="0.1.0" python_template_version="2.7">
+    <requirements>
+	<container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+	getGCAmplicon.py 
+
+	## amplicon input file
+	-a '$input' 
+
+	## output file 
+	-o '$gcOut' 
+
+	## 2bit reference gene file
+	-f $index
+	 
+	]]></command>
+    <inputs>
+	<param name="input" type="data" format="bed" optional="false" label="Amplicon Design File (BED)" help="This file is the HaloPlex design file, containing individual amplicons." />
+	<param name="index" type="select">
+		<options from_data_table="TwoBitDocker" />
+	</param>
+    </inputs>
+    <outputs>
+	<data name="gcOut" format="tabular" label="VarAmpliCNV on ${on_string}: GC-content" />
+	<!--<data name="ampliconOut" format="tabular" label="Amplicon Gene annotations" />-->
+    </outputs>
+    <help>
+**VarAmpliCNV : GC-calculation**
+
+Calculate the GC-content of entries in a BED file. 
+
+**Parameters are :** 
+
+* Amplicon Design File (BED) : The de-duplicated amplicon list, generated by "varAmpliCNV Annotate".
+* Genome Build : Select a genome build from the configured options to extract GC content from. 
+
+**Output files :**
+
+* GC-content (txt) : Tabular file containing GC information per region. 
+
+</help>
+</tool>