diff snpEff_macros.xml @ 7:7adfd0589f49 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1

--- a/snpEff_macros.xml	Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_macros.xml	Tue Apr 18 09:33:56 2017 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
+            <requirement type="package" version="4.3k">snpeff</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,22 +10,16 @@
         <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><![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
+snpEff -version
     ]]></version_command>
   </xml>
-  <token name="@WRAPPER_VERSION@">4.1</token>
-  <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
-  <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token>
+  <token name="@WRAPPER_VERSION@">4.3k</token>
+  <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
+  <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
-
-For details about this tool, please go to:
-	http://snpeff.sourceforge.net/SnpEff_manual.html
-
+For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html
   </token>
   <xml name="citations">
       <citations>