diff snpSift_int.xml @ 1:98708b88af9f draft

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

--- a/snpSift_int.xml	Thu Jan 22 08:39:07 2015 -0500
+++ b/snpSift_int.xml	Tue Jun 07 10:04:09 2016 -0400
@@ -1,14 +1,17 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0">
+<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
     <description>Filter variants using intervals</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
-    <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
-    <command>
-        java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+        java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -19,7 +22,6 @@
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
             <param name="input" ftype="vcf" value="annotate_5.vcf"/>
@@ -44,14 +46,14 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 You can filter using intervals (BED file).
 
 @EXTERNAL_DOCUMENTATION@
     http://snpeff.sourceforge.net/SnpSift.html#intervals
 
-@CITATION_SECTION@
-
+]]>
     </help>
+    <expand macro="citations" />
 </tool>