--- a/snpEff_download.xml	Thu Nov 28 08:16:11 2013 -0600
+++ b/snpEff_download.xml	Fri Nov 29 09:27:22 2013 -0500
@@ -1,14 +1,15 @@
 <tool id="snpEff_download" name="SnpEff Download" version="3.4">
     <description>Download a new database</description>
-    <requirements>
-        <requirement type="package" version="3.4">snpEff</requirement>
-    </requirements>
+    <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 > $logfile 
     </command>
     <inputs>
-        <param name="genomeVersion" type="select" label="Genome Version">
+        <param name="genomeVersion" type="select" label="Select the genome version you want to download">
             <options from_data_table="snpeff_databases">
                 <filter type="sort_by" column="0" />
             </options>
@@ -18,18 +19,12 @@
         <data format="txt" name="logfile" />
         <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" />
     </outputs>
-    <stdio>
-        <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-        <exit_code range="1:"  level="fatal"   description="Error" />
-     </stdio>
+    <expand macro="stdio" />
     <help>
 
-This tool downloads a SnpEff database into the users history for use by snpEff.
+@EXTERNAL_DOCUMENTATION@
 
-For details about this tool, please go to http://snpEff.sourceforge.net
-
-Please cite:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+@CITATION_SECTION@
 
     </help>
 </tool>