Mercurial > repos > jjohnson > snpeff

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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:51:40 -0400
parents bb0797deab78
children
line wrap: on
line diff
--- a/snpEff_download.xml	Wed Dec 09 10:20:13 2015 -0500
+++ b/snpEff_download.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 download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version
+    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version"
 ]]>
     </command>
     <inputs>
@@ -20,12 +20,20 @@
     <outputs>
         <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
     </outputs>
+    <tests>
+        <test>
+            <param name="genome_version" value="ebola_zaire"/>
+            <output name="snpeff_db">
+                <assert_contents>
+                    <has_text text="ebola_zaire" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help><![CDATA[
 
 @EXTERNAL_DOCUMENTATION@
 
-@CITATION_SECTION@
-
 ]]>
     </help>
     <expand macro="citations" />