<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>