--- a/bamtools.xml	Wed Aug 26 13:26:01 2015 -0400
+++ b/bamtools.xml	Wed Nov 11 12:33:26 2015 -0500
@@ -1,19 +1,19 @@
 <?xml version="1.0"?>
-<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1">
+<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.2">
   <description>BAM datasets and perform other transformations</description>
   <requirements>
     <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
-  
+
   <command>
    ##set up input files
-  
+
   #for $bam_count, $input_bam in enumerate( $input_bams ):
-    ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
-    ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
+    ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
+    ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
   #end for
-   
+
   #if str( $analysis_type.analysis_type_selector ) == "convert":
     #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
       #set $reference_fasta_filename = "localref.fa"
@@ -27,83 +27,81 @@
   #end if
 
     ##finished setting up inputs
-    
+
     ##start bamtools commandline
-    
+
     bamtools
-    
+
     #if str( $analysis_type.analysis_type_selector ) == "convert":
-    
+
     convert
-    
+
     -format ${analysis_type.format_type.format_type_selector}
-    
+
       #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
-    
+
       ${analysis_type.format_type.mapqual}
       -fasta "${reference_fasta_filename}"
-    
+
       #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
-    
+
       ${analysis_type.format_type.noheader}
-    
+
       #end if
-      
+
     -out $out_file1
-    
+
     #elif str( $analysis_type.analysis_type_selector ) == "count":
-    
+
     count
     > $out_file1
-    
+
     #elif str( $analysis_type.analysis_type_selector ) == "coverage":
-    
+
     coverage
     -out $out_file1
-    
+
     #elif str( $analysis_type.analysis_type_selector ) == "header":
-    
+
     header
     > $out_file1
-    
+
     #elif str( $analysis_type.analysis_type_selector ) == "merge":
-    
+
     merge
     -out $out_file1
-    
+
     #elif str( $analysis_type.analysis_type_selector ) == "random":
-    
+
     random
     -n ${analysis_type.count}
     -seed ${analysis_type.seed}
     -out $out_file1
-    
+
     #elif str( $analysis_type.analysis_type_selector ) == "revert":
-    
+
     revert
     ${analysis_type.keepDuplicate}
     ${analysis_type.keepQualities}
     -out $out_file1
-    
+
     #elif str( $analysis_type.analysis_type_selector ) == "sort":
-    
+
     sort
     ${analysis_type.byname}
     -out $out_file1
-    
+
     #end if
-    
+
     #for $bam_count, $input_bam in enumerate( $input_bams ):
         -in "localbam_${bam_count}.bam"
     #end for
-    
-   
+
+
   </command>
   <inputs>
-    
-    <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
-          <param name="input_bam" type="data" format="bam" label="BAM dataset" />
-    </repeat>
+
+    <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
 
     <conditional name="analysis_type">
       <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
@@ -179,7 +177,7 @@
         <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
       </when>
     </conditional>
-    
+
     </inputs>
     <outputs>
       <data format="txt" name="out_file1">
@@ -195,11 +193,11 @@
           <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
           <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
         </change_format>
-      </data>  
+      </data>
     </outputs>
     <tests>
       <test>
-        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
         <param name="analysis_type_selector" value="convert"/>
         <param name="format_type_selector" value="pileup"/>
         <param name="reference_source_selector" value="history" />
@@ -208,26 +206,26 @@
         <output name="output_bam" file="bamtools-convert-pileup.pu" />
       </test>
       <test>
-        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
         <param name="analysis_type_selector" value="count"/>
         <output name="output_bam" file="bamtools-count.tab" />
       </test>
       <test>
-        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
         <param name="analysis_type_selector" value="coverage"/>
         <output name="output_bam" file="bamtools-coverage.tab" />
       </test>
       <test>
-        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
         <param name="analysis_type_selector" value="header"/>
         <output name="output_bam" file="bamtools-header.txt" />
       </test>
     </tests>
-  
+
   <stdio>
     <exit_code range="1:" />
   </stdio>
-  
+
   <help>
 
 **What is does**