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+++ b/VarAmpliCNV_CallCNVs.xml	Fri Sep 25 08:30:57 2020 +0000
@@ -0,0 +1,96 @@
+<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>