--- a/snpSift_annotate.xml	Mon Dec 05 12:11:18 2016 -0500
+++ b/snpSift_annotate.xml	Mon Jun 12 10:25:32 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.1">
+<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)
@@ -10,22 +10,23 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        @CONDA_SNPSIFT_JAR_PATH@ &&
-        java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" $annotate_cmd
-        #if $annotate.id :
-          -id
-        #elif str($annotate.info_ids).strip() != '' :
-          -info "$annotate.info_ids"
-        #end if
-        -q "$dbSnp" "$input" > "$output"
-]]>
-    </command>
+SnpSift annotate
+#if $annotate.id == 'id':
+    -id
+#elif str($annotate.info_ids).strip() != '':
+    -info "$annotate.info_ids"
+#end if
+-q '$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 name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
+        <param name="dbSnp" type="data" format="vcf" 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=""/>
+            <param name="id" type="select" label="Fields to annotate">
+                <option value="id">Only annotate ID field (no INFO fields will be added)</option>
+                <option value="info">Add also INFO fields</option>
+            </param>
             <when value="id"/>
             <when value="info">
                 <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included">
@@ -33,22 +34,15 @@
                 </param>
             </when>
         </conditional>
-        <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).
-            </help>
-            </param>
     </inputs>
     <outputs>
-        <data format="vcf" name="output" />
+        <data name="output" format="vcf" />
     </outputs>
     <tests>
         <test>
             <param name="input" ftype="vcf" value="annotate_1.vcf"/>
             <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
-            <param name="annotate_cmd" value="False"/>
-            <param name="id" value="True"/>
+            <param name="id" value="id"/>
             <output name="output">
                 <assert_contents>
                     <has_text text="rs76166080" />
@@ -57,7 +51,6 @@
         </test>
     </tests>
     <help><![CDATA[
-
 This is typically used to annotate IDs from dbSnp.
 
 Annotatating only the ID field from dbSnp137.vcf ::
@@ -74,8 +67,6 @@
     22      16346045    rs56234788   T    C    0.0    FAIL    NS=244
     22      16350245    rs2905295    C    A    0.0    FAIL    NS=192
 
-
-
 Annotatating both the ID and INFO fields from dbSnp137.vcf ::
 
     Input VCF:
@@ -90,12 +81,8 @@
     22      16346045    rs56234788   T    C    0.0    FAIL    NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO
     22      16350245    rs2905295    C    A    0.0    FAIL    NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO
 
-
 @EXTERNAL_DOCUMENTATION@
-	http://snpeff.sourceforge.net/SnpSift.html#annotate
-
-]]>
-    </help>
+- http://snpeff.sourceforge.net/SnpSift.html#annotate
+    ]]></help>
     <expand macro="citations" />
 </tool>
-