diff snpEff_databases.xml @ 7:7adfd0589f49 draft

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

--- a/snpEff_databases.xml	Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_databases.xml	Tue Apr 18 09:33:56 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0">
+<tool id="snpEff_databases" name="SnpEff available databases" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -6,12 +6,9 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-<![CDATA[
-    @CONDA_SNPEFF_JAR_PATH@ &&
-    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > "$snpeff_dbs"
-]]>
-    </command>
+    <command><![CDATA[
+snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/  *//g' > '$snpeff_dbs'
+    ]]></command>
     <inputs>
     </inputs>
     <outputs>
@@ -27,11 +24,8 @@
         </test>
     </tests>
     <help><![CDATA[
-
 @EXTERNAL_DOCUMENTATION@
-
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>