diff snpSift_vartype.xml @ 2:bf8c1526871b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

--- a/snpSift_vartype.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_vartype.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0">
+<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.1">
     <description>Annotate with variant type</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -7,7 +7,8 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
 ]]>
     </command>
     <inputs>
@@ -33,10 +34,7 @@
 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
-
-@CITATION_SECTION@
-
+.. _MIT license: https://opensource.org/licenses/MIT
 ]]>
     </help>
     <expand macro="citations" />