--- a/customProDB.xml	Wed Feb 03 12:37:47 2016 -0500
+++ b/customProDB.xml	Fri May 06 15:56:07 2016 -0400
@@ -8,6 +8,7 @@
        --bam="$genome_annotation.bamInput"
        --bai="${genome_annotation.bamInput.metadata.bam_index}"
        --vcf="$genome_annotation.vcfInput"
+       --rpkmCutoff=$rpkmCutoff
        --outputFile="${output_rpkm}"
 
        #if str($genome_annotation.source) == "history":
@@ -64,6 +65,7 @@
         <param name="vcfInput" type="data" format="vcf" label="VCF file" />
       </when>
     </conditional>
+    <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />
   </inputs>
   <outputs>
     <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>