--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DedupRealignBAM.xml	Wed Mar 25 13:29:45 2015 -0600
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+
+<tool id="dedup_realign_bam_1" name="Deduplicate and realign a BAM file(s)">
+  <description>using samtools and GATK</description>
+  <version_string>echo 1.0.0</version_string>
+  <command interpreter="perl">prep_bams $__tool_data_path__ $messages $ref_genome\.fa ${__new_file_path__} $prepped_bam_file $input_bam_file
+      #for $i in $inputs
+        ${i.input}
+      #end for 
+  </command>
+  <inputs>
+    <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the reads were mapped"/>
+    <param format="bam" name="input_bam_file" type="data" label="Source BAM (mapped reads) file" help="Need to merge multiple input BAM files for one sample? Use controls below."/>
+    <repeat name="inputs" title="Input BAM Files">
+      <param name="input" label="Additional BAM file to merge" type="data" format="bam" />
+    </repeat>
+
+  </inputs>
+  <outputs>
+    <data name="prepped_bam_file" format="bam" type="data" label="Deduped and realigned mapped reads"/>
+    <data name="messages" format="text" type="data" label="Prep process log messages"/>
+  </outputs>
+
+  <tests/>
+
+  <help>
+  This tool runs a set of processes to first optionally merge BAMs, then deduplicate (samtools) and realign (GATK) the reads mapped to a reference genome.  
+  This is important for genotyping studies.  While these steps could be run independently in a workflow,
+  an enormous amount of intermediate data files are generated.  This tool cleans up those intermediate files.
+ </help>
+
+</tool>