Mercurial > repos > iuc > snpeff

diff snpEff_download.xml @ 7:7adfd0589f49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
author iuc
date Tue, 18 Apr 2017 09:33:56 -0400
parents 698ef30638a8
children 68693743661e
line wrap: on
line diff
--- a/snpEff_download.xml	Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_download.xml	Tue Apr 18 09:33:56 2017 -0400
@@ -6,14 +6,11 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-<![CDATA[
-    @CONDA_SNPEFF_JAR_PATH@ &&
-    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version"
-]]>
-    </command>
+    <command><![CDATA[
+snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version'
+    ]]></command>
     <inputs>
-        <param name="genome_version" type="text" 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. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)">
             <help>@SNPEFF_DATABASE_URL@</help>
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
@@ -32,11 +29,7 @@
         </test>
     </tests>
     <help><![CDATA[
-
 @EXTERNAL_DOCUMENTATION@
-
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
-