--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VarAmpliCNV_Count.xml	Fri Sep 25 08:30:57 2020 +0000
@@ -0,0 +1,54 @@
+<tool id="VarAmpliCNV_Count" name="Count Aligned Amplicons" version="0.1.0" >
+    <requirements>
+	<container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ##prepare input and indices 
+        ln -s '$bam' infile &&
+        #if $bam.is_of_type('bam'):
+            #if str( $bam.metadata.bam_index ) != "None":
+                ln -s '${bam.metadata.bam_index}' infile.bai &&
+            #else:
+                samtools index infile infile.bai &&
+            #end if
+        #elif $bam.is_of_type('cram'):
+            #if str( $bam.metadata.cram_index ) != "None":
+                ln -s '${bam.metadata.cram_index}' infile.crai &&
+            #else:
+                samtools index infile infile.crai &&
+            #end if
+        #end if
+
+	## Run Counter.
+	parseBAM.py '$bed' 'infile' '$counts' '$unmapped' '$stats' 
+
+	]]></command>
+    <inputs>
+	<param name="bed" type="data" format="BED" optional="false" label="Unique Amplicons (BED)" help="This file is created by the VarAmpliCNV 'Annotate Amplicons' tool." />
+	<param name="bam" type="data" format="bam" optional="false" label="BAM file" help="Sequencing data file" />
+    </inputs>
+    <outputs>
+	<data name="counts" format="tabular" label="VarAmpliCNV on ${on_string}: Counts" />
+	<data name="unmapped" format="bam" label="VarAmpliCNV on ${on_string}: UnMapped Reads" />
+	<data name="stats" format="txt" label="VarAmpliCNV on ${on_string}: Statistics" />
+    </outputs>
+    <help>
+**VarAmpliCNV : Counting**
+
+BAM files are parsed for readpairs exactly matching specified amplicons, based on start and end position. 
+
+**Parameters are :** 
+
+* Amplicon Design File (BED) : The de-duplicated amplicon list, generated by "varAmpliCNV Annotate".
+* Sample Data (BAM) : The sample read data, provided as a single BAM file, or a collection of BAM files. 
+
+**Output files :**
+
+* Count file (txt): the amplicon-read table. 
+* Unmapped (BAM)  : Reads not matching amplicons. This bam file can be used to investigate issues.
+* Stats (txt): Overview of the matching performance. Use it to investigate issues.
+
+In case a collection of BAM files is provided, the output files will be grouped in collections as well. 
+
+    </help>
+</tool>