--- a/multiCov.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/multiCov.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,53 +6,70 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
-        bedtools multicov
-        -bed $input1
-        -bam 
-        #for $bam in $bams:
-            $bam.input
+<![CDATA[
+        #for $i, $bam in enumerate( $bams ):
+            ln -s -f $bam ${i}.bam &&
+            ln -s -f $bam.metadata.bam_index ${i}.bam.bai &&
         #end for
-        $strand
-        -f $overlap
-        $reciprocal
-        $split
-        -q $mapq
-        $duplicate
-        $failed
-        $proper
-        &gt; $output
+
+        bedtools multicov
+            -bed $input
+            -bams
+            #for $i, $bam in enumerate( $bams ):
+                ${i}.bam
+            #end for
+            $strand
+            -f $overlap
+            $reciprocal
+            $split
+            -q $q
+            $duplicate
+            $failed
+            $proper
+            > $output
+]]>
     </command>
     <inputs>
-        <param name="input1" format="bed" type="data" label="First sorted BED file" />
+        <param name="input" format="bed" type="data" label="Sorted BED file" />
         <!-- Additional files, if the user needs more -->
-        <repeat name="bams" title="Add BAM files" >
-            <param name="input" format="bam" type="data" label="BAM file" />
-        </repeat>
+        <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />
+
         <expand macro="strand2" />
         <expand macro="overlap" />
-        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Require that the fraction overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B." />
+        <expand macro="reciprocal" />
         <expand macro="split" />
-
-        <param name="duplicate" type="boolean" checked="false" truevalue="-D" falsevalue="" label="Include duplicate reads. Default counts non-duplicates only" />
-        <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" label=" 	Include failed-QC reads. Default counts pass-QC reads only" />
-        <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Only count proper pairs. Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field." />
+        <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" />
+        <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue=""
+            label="Include duplicate reads"
+            help="Default counts non-duplicates only. (-D)" />
+        <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
+            label="Include failed-QC reads" 
+            help="Default counts pass-QC reads only (-F)"/>
+        <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
+            label="Only count proper pairs"
+            help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" />
     </inputs>
-
     <outputs>
-        <data format="bed" name="output" label="" />
+        <data name="output" metadata_source="input" format_source="input" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="multiCov1.bed" ftype="bed" />
+            <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/>
+            <param name="q" value="1"/>
+            <param name="split" value="False"/>
+            <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-    
+<![CDATA[
 **What it does**
 
 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
 
-.. class:: infomark
-
-bedtools multicov depends upon index BAM files in order to count the number of overlaps in each BAM file. As such, each BAM file should be position sorted (samtool sort aln.bam aln.sort) and indexed (samtools index aln.sort.bam) with either samtools or bamtools.
 
 @REFERENCES@
-
+]]>
     </help>
     <expand macro="citations" />
 </tool>