--- a/mafft.xml	Fri Jul 31 19:02:11 2015 -0400
+++ b/mafft.xml	Tue Aug 04 04:01:23 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="rbc_mafft" name="MAFFT" version="7.221.0">
+<tool id="rbc_mafft" name="MAFFT" version="7.221.1">
     <description>Multiple alignment program for amino acid or nucleotide sequences</description>
     <requirements>
         <requirement type="package" version="7.221">mafft</requirement>
@@ -23,6 +23,8 @@
         
         ## specify threads to use
         --thread \${GALAXY_SLOTS:-1}
+      
+        $adjustdirection
         
         #if $outputFormat.value == 'clustalw'
             --clustalout
@@ -64,6 +66,10 @@
             <when value="mafft-qinsi"/>
             <when value="mafft-xinsi"/>
         </conditional>
+        <param name="adjustdirection" type="select" display="radio" label="Direction of nucleotide sequences" help="Generate reverse complement sequences, as necessary, and align them together with the remaining sequences">
+            <option value="--adjustdirection">adjust direction</option>
+            <option value=" " selected="true">do not adjust direction</option>
+            </param>
         <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
             <option value="fasta" selected="true">FASTA</option>
             <option value="clustalw">ClustalW</option>
@@ -150,6 +156,8 @@
 
 --auto
     Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
+--adjustdirection
+    Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
     ]]>
     </help>
     <citations>