--- a/emboss_wobble.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_wobble.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,21 +1,18 @@
-<tool id="EMBOSS: wobble108" name="wobble" version="5.0.0">
-  <description>Wobble base plot</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -window "$window" -bases "$bases" -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>Sequence</label>
-    </param>
-    <param name="window" type="text" value="30">
-      <label>Window size, in codons</label>
-    </param>
-    <param name="bases" type="text" value="GC">
-      <label>Bases used</label>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="png" name="ofile1" />
-    <data format="wobble" name="ofile2" />
+<tool id="EMBOSS: wobble108" name="wobble" version="5.0.0.1">
+  <description>Wobble base plot</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' wobble -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -window $window -bases '$bases' -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequence" />
+    <param name="window" type="integer" value="30" label="Window size, in codons" />
+    <param name="bases" type="text" value="GC" label="Bases used" />
+  </inputs>
+  <outputs>
+    <data name="ofile1" format="png" />
+    <data name="ofile2" format="wobble" />
   </outputs>
   <tests>
     <test>
@@ -24,25 +21,17 @@
       <param name="bases" value="GC"/>
       <output name="ofile2" file="emboss_wobble_out.wobble"/>
     </test>
-  </tests>
+  </tests>
   <help>
+.. class:: warningmark
 
-.. class:: warningmark 
+The input dataset needs to be sequences.
 
-The input dataset needs to be sequences. 
-
------ 
+-----
 
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wobble.html
-
-------
-
-**Citation**
 
-For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
-
-If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wobble.html
   </help>
+  <expand macro="citations" />
 </tool>