diff snpEff_download.xml @ 1:500832f27cbc draft

Uploaded

--- a/snpEff_download.xml	Wed Dec 11 08:53:32 2013 -0500
+++ b/snpEff_download.xml	Thu Jan 22 08:28:37 2015 -0500
@@ -1,23 +1,22 @@
-<tool id="snpEff_download" name="SnpEff Download" version="3.4">
+<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>
     <command>
-    echo $genomeVersion > $snpeff_db; 
-    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile 
+<![CDATA[
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version 
+]]>
     </command>
     <inputs>
-        <param name="genomeVersion" type="select" label="Select the genome version you want to download">
-            <options from_data_table="snpeff_databases">
-                <filter type="sort_by" column="0" />
-            </options>
+        <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
+            <help>@SNPEFF_DATABASE_URL@</help>
+            <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
     </inputs>
     <outputs>
-        <data format="txt" name="logfile" />
-        <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" />
+        <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
     </outputs>
     <expand macro="stdio" />
     <help>
@@ -27,5 +26,6 @@
 @CITATION_SECTION@
 
     </help>
+    <expand macro="citations" />
 </tool>