Mercurial > repos > iuc > snpeff

diff snpEff_download.xml @ 7:aaa749ea91a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:40:10 -0400
parents 9ec1cb6f760d
children 1501e66908de
line wrap: on
line diff
--- a/snpEff_download.xml	Tue Oct 13 17:30:57 2015 -0400
+++ b/snpEff_download.xml	Tue Jun 07 09:40:10 2016 -0400
@@ -5,9 +5,10 @@
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
+    <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 "$genome_version"
 ]]>
     </command>
     <inputs>
@@ -19,12 +20,21 @@
     <outputs>
         <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
     </outputs>
-    <help>
+    <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" />
 </tool>