--- a/samtools_bedcov.xml	Tue May 09 11:17:25 2017 -0400
+++ b/samtools_bedcov.xml	Mon Jul 29 08:47:23 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="samtools_bedcov" name="BedCov" version="2.0.1">
+<tool id="samtools_bedcov" name="BedCov" version="2.0.2">
     <description>calculate read depth for a set of genomic intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -7,22 +7,24 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        ## Ensure simlinks have unique filenames
-        #for $i, $bam in enumerate( $input_bams ):
-            ln -s -f '${bam}' '${i}.bam' &&
-            ln -s -f '${bam.metadata.bam_index}' '${i}.bam.bai' &&
-        #end for
+        @PREPARE_IDX_MULTIPLE@
 
         samtools bedcov
+            #if $mapq:
+                -Q $mapq
+            #end if
+            $countdel
             '${input_bed}'
             #for $i in range(len( $input_bams )):
-                '${i}.bam'
+                '${i}'
             #end for
             > '${output}'
     ]]></command>
     <inputs>
         <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
         <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
+        <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" />
+        <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" />
     </inputs>
     <outputs>
         <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
@@ -38,6 +40,18 @@
             <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
             <output name="output" file="samtools_bedcov_out2.tab" />
         </test>
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
+            <param name="mapq" value="40"/>
+            <output name="output" file="samtools_bedcov_out1.tab" />
+        </test>
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
+            <param name="countdel" value="-j" />
+            <output name="output" file="samtools_bedcov_out2.tab" />
+        </test>
     </tests>
     <help>
 **What it does**