--- a/customProDB.xml	Mon May 09 12:55:26 2016 -0400
+++ b/customProDB.xml	Wed Jun 08 14:04:54 2016 -0400
@@ -16,12 +16,24 @@
             --proteinseq="$genome_annotation.proteinSeq"
             --procodingseq="$genome_annotation.proCodingSeq"
             --ids="$genome_annotation.ids"
+            #if str($genome_annotation.dbsnpInCoding) != "None":
+                --dbsnpinCoding="$genome_annotation.dbsnpInCoding"
+            #end if
+            #if str($genome_annotation.cosmic) != "None":
+                --cosmic="$genome_annotation.cosmic"
+            #end if
        #else:
             #set index_path = $genome_annotation.builtin.fields.path
             --exon_anno="$index_path/exon_anno.RData"
             --proteinseq="$index_path/proseq.RData"
             --procodingseq="$index_path/procodingseq.RData"
             --ids="$index_path/ids.RData"
+            #if $genome_annotation.dbsnpInCoding:
+                --dbsnpinCoding="$index_path/dbsnpinCoding.RData"
+            #end if
+            #if $genome_annotation.cosmic:
+                --cosmic="$index_path/cosmic.RData"
+            #end if
        #end if
 
 2&gt;&amp;1</command>
@@ -50,6 +62,8 @@
             <validator type="unspecified_build" />
             <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
         </param>
+        <param name="labelrsid" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" />
+        <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
       </when>
       <when value="history">
         <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
@@ -63,6 +77,8 @@
             <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
         </param>
         <param name="vcfInput" type="data" format="vcf" label="VCF file" />
+        <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
+        <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
       </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." />