--- a/snpSift_annotate.xml	Tue Oct 13 17:31:24 2015 -0400
+++ b/snpSift_annotate.xml	Tue Jun 07 09:41:13 2016 -0400
@@ -1,6 +1,6 @@
-<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0">
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0">
     <description>SNPs from dbSnp</description>
-    <!--
+    <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
     <macros>
@@ -8,33 +8,35 @@
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd
+    <expand macro="version_command" />
+    <command><![CDATA[
+        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd 
         #if $annotate.id :
           -id
-        #elif $annotate.info_ids.__str__.strip() != '' :
+        #elif str($annotate.info_ids).strip() != '' :
           -info "$annotate.info_ids"
-        #end if
-        -q $dbSnp $input > $output
+        #end if          
+        -q "$dbSnp" "$input" > "$output" 
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
-        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
+        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
             help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
         <conditional name="annotate">
             <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
             <when value="id"/>
             <when value="info">
                 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs"
-                    help="list is a comma separated list of fields. When blank, all INFO fields are included">
+                    help="list is a comma separated list of fields. When blank, all INFO fields are included">    
                     <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
                 </param>
             </when>
         </conditional>
-        <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files">
+        <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> 
             <help>
                 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
-                Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
+                Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). 
             </help>
             </param>
     </inputs>
@@ -54,7 +56,7 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 This is typically used to annotate IDs from dbSnp.
 
@@ -92,9 +94,8 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#annotate
 
-@CITATION_SECTION@
-
-
+]]>
     </help>
+    <expand macro="citations" />
 </tool>