<tool id="VarAmpliCNV_CallCNVs" name="Call CNVs" version="0.1.0" >
    <requirements>
	<container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
    </requirements>
     <command detect_errors="exit_code"><![CDATA[
	## make output folder.
	mkdir Output 

	&& 
	
	varAmpliCNV.R  

	## counts object
	-i $RData

	## deduped amplicons.
	-b $BedFile

	## Gene information
	-r $RoiFile

	## GC content
	-c $GcFile

	## genders (if specified)
        #if $GenderFile 
                -s $GenderFile
        #end if

	## output folder
	-o Output

	## variance to remove
	-p $VarProp

	## analysis type
	-n $aTypeSelect.aType

	## thresholds
	-d $aTypeSelect.delT
	-D $aTypeSelect.dupT
	
	]]></command>
    <inputs>
	<param name="RData" type="data" format="rdata" optional="false" label="Sample Amplicon Counts" help="This file is created by the VarAmpliCNV 'Merge Counts' tool." />
	<param name="BedFile" type="data" format="bed" optional="false" label="Amplicon BED file (duplicates removed)" help="This file is created by the VarAmpliCNV 'annotate' tool." />
	<param name="RoiFile" type="data" format="bed" optional="false" label="ROI-Amplicon file" help="This file is created by the VarAmpliCNV 'annotate' tool." />
	<param name="GcFile" type="data" format="txt" optional="false" label="Amplicon GC content" help="This file is created by the VarAmpliCNV 'Get GC Content' tool."/>
	<param name="GenderFile" type="data" format="txt" optional="true" label="Sample Genders" help="Sample genders for handling X-CNVs. See Documentation for format information"/>
	<param name="VarProp" type="float" value="0.8" label="Fraction of Variance to remove during MDS" help="Default: 0.8" />	
	<conditional name="aTypeSelect">
	   <param name="aType" type="select" label="Analysis Type" help="Use 'Direct' Segmentation (pure CBS), or apply post-segmentation 'AOF' (Amplicon Overlap Filtering)">
		<option value='0'>Direct Segmentation</option>
		<option value='1' selected="TRUE">Amplicon Overlap Filtering</option>
	   </param>
	   <when value='0'>
	    <param name="delT" value='-0.5' label="LogR Threshold for Deletions" type='float'/>
		<param name="dupT" value="0.5" label="LogR Threshold for Duplications" type='float'/>
	   </when>
       <when value='1'>
	    <param name="delT" value="-0.2" label="LogR Threshold for Deletions" type='float'/>
		<param name="dupT" value="0.38" label="LogR Threshold for Duplications" type='float'/>
	   </when>
	</conditional>
    </inputs>
    <outputs>
	<data name="outfile" format="pdf" label="VarAmpliCNV on ${on_string}: Results" >
		<discover_datasets pattern="__designation_and_ext__" directory="Output" visible="true" assign_primary_output="true" />
	</data>
    </outputs>
    <help>
**VarAmpliCNV : Call CNVs**

During CNV calling read counts are normalized over all samples inluced during "count merging", a set fraction of variance is removed and circular binary segmentation is applied to identify CNVs. If specified, a post-processing step is applied to take amplicon size and overlap into account to estimate reliability of the event. Passing CNVs are plotted gene-by-gene. 

**Parameters are :** 

* Sample Amplicon Counts (RData) : The result from the 'Merge Counts' tool. It contains a raw sample-by-amplicon count matrix. 
* Amplicon BED file (BED) : This is the *exact* BED file provided by HaloPlex for the used library, with duplicates removed using the VarAmpliCNV "Annotate" tool.
* ROI file (BED) : This is the *exact* BED file provided by HaloPlex for the used library, with duplicates removed and annotated with gene symbols using the VarAmpliCNV "Annotate" tool.
* Amplicon GC Content (txt) : GC-content of individual amplicons, used for count correction. Generated using VarAmpliCNV 'Amplicon GC-Content' tool. 
* Sample Genders (txt) : Optional. If specified, build gender-specific normalization sets for X and Y chromosomes. Format is tab-separated : SamplenName&lt;tab&gt;M/F/U
* Fraction of Variance to Remove : Using an approach similar to Principal component analysis, a preset fraction of noise is removed from the data. Higher values typically result in less CNVs. 
* Analysis Type : Direct Segmentation applies only CBS and will not plot results. Amplicon Overlap Filtering is a post-processing filter to improve specificity, and will also enable plotting. The full CBS-results are always returned for manual inspection. 
* Thresholds : Set mininal values for LogR-based filtering of the called Segments. 


**Output files :**

* Parameter_settings : Overview of set and derived settings + a list of discarded samples
* Plots.Quality_Measures : Quality metrics: coverage, variance by PC, GC-coverage-correlation
* Plots.Results : Gene-based CNV plots for segments passing the filters (if AOF is activated)
* Table.Results.Full : Full CBS results
* Table.Results.Filtered : Filtered CBS results (on LogR).  
</help>
</tool>