diff snpSift_annotate.xml @ 4:baf6602903e1

Uploaded

--- a/snpSift_annotate.xml	Thu Oct 23 06:06:25 2014 -0500
+++ b/snpSift_annotate.xml	Wed Dec 09 14:03:26 2015 -0500
@@ -1,13 +1,15 @@
-<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0">
+<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)
     -->
+    <macros>
+        <import>snpSift_macros.xml</import>
+    </macros>
     <expand macro="requirements" />
-    <macros>
-        <import>snpEff_macros.xml</import>
-    </macros>
-    <command>
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
         java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
         #if $annotate.id :
           -id
@@ -15,6 +17,7 @@
           -info "$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"/>
@@ -37,7 +40,6 @@
             </help>
             </param>
     </inputs>
-    <expand macro="stdio" />
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
@@ -54,7 +56,7 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 This is typically used to annotate IDs from dbSnp.
 
@@ -95,6 +97,7 @@
 @CITATION_SECTION@
 
 
+]]>
     </help>
 </tool>