--- a/uniprotxml_downloader.xml	Tue Mar 08 12:03:49 2016 -0500
+++ b/uniprotxml_downloader.xml	Wed Dec 07 16:44:14 2016 -0500
@@ -1,25 +1,26 @@
-<tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.0">
+<tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.1">
     <description>proteome</description>
     <requirements>
-        <requirement type="binary">wget</requirement>
+        <requirement type="package" version="2.7.12">python</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error downloading proteome." />
     </stdio>
-    <command interpreter="python">
+    <command>
 <![CDATA[
-uniprotxml_downloader.py -v 
-#if $taxid.choice == 'common':
---taxon $taxid.organism
-#if $taxid.reviewed:
---reviewed=$taxid.reviewed
-#end if
-#else:
-#for id in $taxid.taxons.split(','):
--t $id
-#end for
-#end if
---output="${proteome}"
+    python '$__tool_directory__/uniprotxml_downloader.py'
+        -v 
+        #if $taxid.choice == 'common':
+            --taxon '$taxid.organism'
+        #if $taxid.reviewed:
+            --reviewed=$taxid.reviewed
+        #end if
+        #else:
+        #for id in $taxid.taxons.split(','):
+            -t $id
+        #end for
+        #end if
+            --output="${proteome}"
 ]]>
     </command>
     <inputs>
@@ -61,6 +62,7 @@
     </outputs>
     <tests>
         <test>
+            <param name="choice" value="taxids"/>
             <param name="taxons" value="1566990"/>
             <output name="uniprotxml">
                 <assert_contents>