--- a/tools/align_back_trans/align_back_trans.xml	Wed Jun 04 08:42:23 2014 -0400
+++ b/tools/align_back_trans/align_back_trans.xml	Wed Aug 05 10:52:56 2015 -0400
@@ -1,18 +1,18 @@
-<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.4">
+<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.6">
     <description>Gives a codon aware alignment</description>
     <requirements>
         <requirement type="package" version="1.63">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_command interpreter="python">align_back_trans.py --version</version_command>
-    <command interpreter="python">
-align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">align_back_trans.py --version</version_command>
+    <command interpreter="python">
+align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
+    </command>
     <inputs>
         <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
         <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
@@ -38,7 +38,7 @@
         <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
     </inputs>
     <outputs>
-        <data name="out_nuc_align" format="input" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
+        <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
     </outputs>
     <tests>
         <test>
@@ -122,4 +122,8 @@
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>