diff snpSift_vcfCheck.xml @ 4:baf6602903e1

Uploaded

--- a/snpSift_vcfCheck.xml	Thu Oct 23 06:06:25 2014 -0500
+++ b/snpSift_vcfCheck.xml	Wed Dec 09 14:03:26 2015 -0500
@@ -1,11 +1,14 @@
-<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0">
+<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0">
     <description>basic checks for Vcf specification compliance</description>
-    <expand macro="requirements" />
     <macros>
-        <import>snpEff_macros.xml</import>
+        <import>snpSift_macros.xml</import>
     </macros>
-    <command>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
       java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
@@ -13,7 +16,6 @@
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
             <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
@@ -24,7 +26,7 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 Perform some basic check ups on VCF files to spot common problems.
 
@@ -35,5 +37,6 @@
 
 @CITATION_SECTION@
 
+]]>
     </help>
 </tool>