Mercurial > repos > jjohnson > snpeff

diff snpEff_download.xml @ 18:36f3c82323e6

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Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
author Jim Johnson <jj@umn.edu>
date Tue, 13 Jan 2015 13:36:11 -0600
parents 3790e16a0be0
children 2e37b58fc24d
line wrap: on
line diff
--- a/snpEff_download.xml	Mon Nov 10 09:33:36 2014 -0600
+++ b/snpEff_download.xml	Tue Jan 13 13:36:11 2015 -0600
@@ -1,21 +1,22 @@
-<tool id="snpEff_download" name="SnpEff Download" version="4.0.1">
+<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.2">
     <description>Download a new database</description>
     <expand macro="requirements" />
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
     <command>
-    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genome_version > $logfile 
+<![CDATA[
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version 
+]]>
     </command>
     <inputs>
-        <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
-            <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
+        <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
+            <help>@SNPEFF_DATABASE_URL@</help>
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
     </inputs>
     <outputs>
-        <data format="txt" name="logfile" />
-        <data format="snpeffdbv4" name="snpeff_db" label="${tool.name} ${genome_version}" />
+        <data format="snpeffdbv41" name="snpeff_db" label="${tool.name} ${genome_version}" />
     </outputs>
     <expand macro="stdio" />
     <help>
@@ -25,5 +26,6 @@
 @CITATION_SECTION@
 
     </help>
+    <expand macro="citations" />
 </tool>