<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>