--- a/snpEff_download.xml	Tue Oct 21 14:40:44 2014 -0500
+++ b/snpEff_download.xml	Thu Oct 23 05:09:26 2014 -0500
@@ -5,49 +5,17 @@
         <import>snpEff_macros.xml</import>
     </macros>
     <command>
-    #if $snpDb.genomeSrc == "named":
-      #set genomeVersion = $snpDb.genome_version
-      #set data_dir = $snpeff_db_named.extra_files_path
-    ## echo $snpDb.genome_version > $snpeff_db_named; 
-    ## java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db_named.extra_files_path -v $snpDb.genome_version > $logfile 
-    #else
-      #set genomeVersion = $snpDb.genome_databases.fields.value
-      #set data_dir = $snpeff_db_cached.extra_files_path
-    ## echo $snpeff_db_cached.extra_files_path > $snpeff_db_cached; 
-    ## java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db_cached.extra_files_path -v $snpeff_db_cached.extra_files_path > $logfile 
-    #end if
-    ## echo $genomeVersion > $snpeff_db; 
-    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $data_dir -v $genomeVersion > $logfile 
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genome_version > $logfile 
     </command>
     <inputs>
-        <conditional name="snpDb">
-            <param name="genomeSrc" type="select" label="Genome List">
-                <option value="named">By Name</option>
-                <option value="cached">Select from list</option>
-            </param>
-            <when value="named">
-                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
-                <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
-                <validator type="regex" message="A genome version name is required">\S+</validator>
-                </param>
-            </when>
-            <when value="cached">
-                <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
-                    <options from_data_table="snpeff4_databases">
-                        <filter type="sort_by" column="0" />
-                    </options>
-                </param>
-            </when>
-        </conditional>
+        <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
+            <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
+            <validator type="regex" message="A genome version name is required">\S+</validator>
+        </param>
     </inputs>
     <outputs>
         <data format="txt" name="logfile" />
-        <data format="snpeffdb" name="snpeff_db_named" label="${tool.name} ${snpDb.genome_version}" >
-            <filter>snpDb['genomeSrc'] == "named"</filter>
-        </data>
-        <data format="snpeffdb" name="snpeff_db_cached" label="${tool.name} ${snpDb.genome_databases.fields.value}">
-            <filter>snpDb['genomeSrc'] == "cached"</filter>
-        </data>
+        <data format="snpeffdbv4" name="snpeff_db" label="${tool.name} ${genome_version}" />
     </outputs>
     <expand macro="stdio" />
     <help>