diff snpEff_download.xml @ 3:b24873564cf6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31

--- a/snpEff_download.xml	Fri Feb 19 08:26:25 2016 -0500
+++ b/snpEff_download.xml	Tue Jun 07 10:03:17 2016 -0400
@@ -1,16 +1,18 @@
 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0">
     <description>Download a new database</description>
-    <expand macro="requirements" />
     <macros>
         <import>snpEff_macros.xml</import>
     </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 "$genome_version"
 ]]>
     </command>
     <inputs>
-        <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
+        <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
             <help>@SNPEFF_DATABASE_URL@</help>
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
@@ -18,13 +20,21 @@
     <outputs>
         <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
     </outputs>
-    <expand macro="stdio" />
-    <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>