--- a/rmarkdown_samtools_flagstat.xml	Wed Dec 27 15:19:43 2017 -0500
+++ b/rmarkdown_samtools_flagstat.xml	Wed Dec 27 23:29:32 2017 -0500
@@ -22,17 +22,18 @@
                     ]]></command>
   <inputs>
     <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
-    <param type="data" name="input_bam" label="BAM file" optional="False"/>
+    <param type="data" format="bam,sam" name="input_bam" label="BAM/SAM file" optional="False"/>
   </inputs>
   <outputs>
     <data name="report" format="html" label="tool name report" hidden="false"/>
     <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
   </outputs>
-  <help><![CDATA[<code>samtools flagstat in.sam|in.bam|in.cram</code>
+  <help><![CDATA[
+  samtools flagstat in.sam|in.bam|in.cram
 
 Does a full pass through the input file to calculate and print statistics to stdout]]></help>
   <citations>
-    <citation><![CDATA[
+    <citation type="bibtex"><![CDATA[
                     @article{allaire2016rmarkdown,
                         title={rmarkdown: Dynamic Documents for R, 2016},
                         author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff