diff snpEff_databases.xml @ 23:924af057bbca draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

--- a/snpEff_databases.xml	Wed Dec 09 10:20:13 2015 -0500
+++ b/snpEff_databases.xml	Sat Apr 09 11:51:40 2016 -0400
@@ -8,7 +8,7 @@
     <expand macro="version_command" />
     <command>
 <![CDATA[
-    java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > $snpeff_dbs
+    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > "$snpeff_dbs"
 ]]>
     </command>
     <inputs>
@@ -16,13 +16,21 @@
     <outputs>
         <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" />
     </outputs>
+    <tests>
+        <test>
+            <output name="snpeff_dbs">
+                <assert_contents>
+                    <has_text text="ebola_zaire" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help><![CDATA[
 
 @EXTERNAL_DOCUMENTATION@
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>