--- a/snpSift_vcfCheck.xml	Tue Jun 07 09:41:13 2016 -0400
+++ b/snpSift_vcfCheck.xml	Mon Dec 05 12:10:54 2016 -0500
@@ -1,5 +1,5 @@
-<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0">
-    <description>basic checks for Vcf specification compliance</description>
+<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1">
+    <description>basic checks for VCF specification compliance</description>
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
@@ -7,7 +7,8 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
 ]]>
     </command>
     <inputs>
@@ -18,23 +19,19 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
-            <output name="output">
-                <assert_contents>
-                    <has_text text="Errors" />
-		</assert_contents>
-            </output>
+            <param name="input" ftype="vcf" value="test_bad.vcf"/>
+            <assert_stderr>
+                <has_text text="Errors" />
+            </assert_stderr>
         </test>
     </tests>
     <help><![CDATA[
-
 Perform some basic check ups on VCF files to spot common problems.
 
 SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. 
 
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
-
 ]]>
     </help>
     <expand macro="citations" />