# HG changeset patch
# User iuc
# Date 1474310635 14400
# Node ID 9ba6e2c298ab9f2f1cab35736b3c0ce69dd3ed28
# Parent  0af41de4eda1ff0dc0ed1e3874736742d7e4bd74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504

diff -r 0af41de4eda1 -r 9ba6e2c298ab snpSift_geneSets.xml
--- a/snpSift_geneSets.xml	Tue Jun 07 10:05:20 2016 -0400
+++ b/snpSift_geneSets.xml	Mon Sep 19 14:43:55 2016 -0400
@@ -10,6 +10,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
+        @CONDA_SNPEFF_JAR_PATH@ &&
         java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v
         #if $db_opts.db_opts_selector == "db"
           "${db_opts.database.fields.path}"
diff -r 0af41de4eda1 -r 9ba6e2c298ab snpSift_macros.xml
--- a/snpSift_macros.xml	Tue Jun 07 10:05:20 2016 -0400
+++ b/snpSift_macros.xml	Mon Sep 19 14:43:55 2016 -0400
@@ -10,8 +10,13 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
+  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
   <xml name="version_command">
-    <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command>
+    <version_command><![CDATA[
+    if [ -z "$SNPEFF_JAR_PATH" ]; then
+        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
+    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
+    ]]></version_command>
   </xml>
   <token name="@WRAPPER_VERSION@">4.1</token>
   <token name="@EXTERNAL_DOCUMENTATION@">