--- a/customProDB.xml	Thu Jan 14 18:12:22 2016 -0500
+++ b/customProDB.xml	Fri Jan 29 14:26:25 2016 -0500
@@ -4,44 +4,48 @@
     <exit_code range="1:" level="fatal" description="Job Failed" />
   </stdio>
   <command interpreter="Rscript --vanilla">PSM2SAM.R
-       #if str($input).strip() != "":
-          --passedPSM="$input"
-       #end if
-       #if str($scoreColumn).strip() != "":
-          --XScolumn="$scoreColumn"
-       #end if
-       #if str($optionalUserInput.exonAnno).strip() != "None":
-          --exon_anno="$optionalUserInput.exonAnno"
-       #end if
-       #if str($optionalUserInput.proteinSeq).strip() != "None":
-          --proteinseq="$optionalUserInput.proteinSeq"
-       #end if
-       #if str($optionalUserInput.proCodingSeq).strip() != "None":
-          --procodingseq="$optionalUserInput.proCodingSeq"
-       #end if
-       #if str($optionalUserInput.header).strip() != "None":
-          --header="$optionalUserInput.header"
-       #end if
-       #if str($output).strip() != "":
-          --OutputFile="$output"
+
+       --bam="$bamInput"
+       --vcf="$vcfInput"
+       --outputFile="$output"
+
+       #if str($genome_annotation.source) == "history":
+            --exon_anno="$genome_annotation.exonAnno"
+            --proteinseq="$genome_annotation.proteinSeq"
+            --procodingseq="$genome_annotation.proCodingSeq"
+       #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"
        #end if
 
 2&gt;&amp;1</command>
   <inputs>
-    <param name="input" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAMs">
+    <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM">
       <validator type="empty_field" message="This field is required."/>
     </param>
     <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
       <validator type="empty_field" message="This field is required."/>
     </param>
-    <conditional name="optionalUserInput">
-      <param name="optionalUserInputCondition" type="boolean" label="Override Default Exon Annotation and Coding Sequences" />
-      <when value="true">
-        <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
-        <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" />
-        <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" />
+
+    <conditional name="genome_annotation">
+      <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
+        <option value="builtin">Use a built-in genome annotation</option>
+        <option value="history">Use a genome from the history and build index</option>
+      </param>
+      <when value="builtin">
+        <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
+          <options from_data_table="customProDB">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No annotations are available for the selected input dataset"/>
+          </options>
+        </param>
       </when>
-      <when value="false">
+      <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" optional="true" />
+        <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" />
+        <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" />
       </when>
     </conditional>
   </inputs>