diff snpSift_vcfCheck.xml @ 1:98708b88af9f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31

--- a/snpSift_vcfCheck.xml	Thu Jan 22 08:39:07 2015 -0500
+++ b/snpSift_vcfCheck.xml	Tue Jun 07 10:04:09 2016 -0400
@@ -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>snpSift_macros.xml</import>
     </macros>
-    <command>
-      java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$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.
 
@@ -33,7 +35,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
 
-@CITATION_SECTION@
-
+]]>
     </help>
+    <expand macro="citations" />
 </tool>