--- a/samtools_bedcov.xml	Tue Apr 21 15:05:45 2015 -0400
+++ b/samtools_bedcov.xml	Tue May 09 11:17:25 2017 -0400
@@ -1,36 +1,31 @@
-<tool id="samtools_bedcov" name="BedCov" version="2.0">
-  <description>calculate read depth for a set of genomic intervals</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
+<tool id="samtools_bedcov" name="BedCov" version="2.0.1">
+    <description>calculate read depth for a set of genomic intervals</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
     <command><![CDATA[
-        for bamfile in 
-        #for dataset in $input_bams:
-            "${dataset}"
+        ## 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}' '${i}.bam.bai' &&
         #end for
-        ; do
-            if [ ! -f \$bamfile.bai ] ; then
-                ln -s \$bamfile && samtools index `basename \$bamfile` ;
-            else
-                ln -s \$bamfile && ln -s \$bamfile.bai ;
-            fi ;
-        done ;
-        samtools bedcov "${input_bed}"
-        #for dataset in $input_bams:
-            `basename "${dataset}"`
-        #end for
-        > "${output}"
-        ]]>
-    </command>
+
+        samtools bedcov
+            '${input_bed}'
+            #for $i in range(len( $input_bams )):
+                '${i}.bam'
+            #end for
+            > '${output}'
+    ]]></command>
     <inputs>
-        <param name="input_bed" type="data" format="bed" label="BED file" />
-        <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
+        <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
+        <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
     </inputs>
     <outputs>
-        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
@@ -50,8 +45,6 @@
 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
 
  samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
-
     </help>
-    <expand macro="citations"></expand>
+    <expand macro="citations"/>
 </tool>
-