--- a/mafft.xml	Tue Jun 16 10:54:16 2015 -0400
+++ b/mafft.xml	Fri Jul 31 19:00:37 2015 -0400
@@ -16,20 +16,23 @@
     <![CDATA[
         #if $cond_flavour.flavourType != 'custom'
             $cond_flavour.flavourType
-        #else
+        #elif $cond_flavour.flavourType == 'custom'
             ### full parameter options
             mafft
         #end if
         
-        #if $cond_outformat.outputFormat == 'clustalw'
+        ## specify threads to use
+        --thread \${GALAXY_SLOTS:-1}
+        
+        #if $outputFormat.value == 'clustalw'
             --clustalout
         #end if
         
         $inputSequences > 
         
-        #if $cond_outformat.outputFormat == 'fasta'
+        #if $outputFormat.value == 'fasta'
             $outputFasta
-        #else ## $cond_outformat.outputFormat == 'clustalw'
+        #elif $outputFormat.value == 'clustalw'
             $outputClustalW
         #end if
     ]]>
@@ -39,6 +42,7 @@
         <conditional name="cond_flavour">
             <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
                 <option value="mafft-fftns" selected="true">fftns</option>
+                <option value="mafft --auto">auto</option>
                 <option value="mafft-fftnsi">fftnsi</option>
                 <option value="mafft-nwns">nwns</option>
                 <option value="mafft-nwnsi">nwnsi</option>
@@ -47,9 +51,10 @@
                 <option value="mafft-linsi">linsi</option>
                 <option value="mafft-qinsi">qinsi</option>
                 <option value="mafft-xinsi">xinsi</option>
-                <option value="custom">Custom Parameters</option>
+                <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters -->
             </param>
             <when value="mafft-fftns"/>
+            <when value="mafft --auto"/>
             <when value="mafft-fftnsi"/>
             <when value="mafft-nwns"/>
             <when value="mafft-nwnsi"/>
@@ -58,31 +63,32 @@
             <when value="mafft-linsi"/>
             <when value="mafft-qinsi"/>
             <when value="mafft-xinsi"/>
-            <when value="custom"/>
         </conditional>
-        <conditional name="cond_outformat">
-            <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>
-            </param>
-            <when value="fasta"/>
-            <when value="clustalw"/>
-        </conditional>
+        <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>
+        </param>
     </inputs>
     <outputs>
         <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">
-            <filter>(cond_outformat['outputFormat'] == 'fasta')</filter>
+            <filter>outputFormat == 'fasta'</filter>
         </data>
         <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">
-            <filter>(cond_outformat['outputFormat'] == 'clustalw')</filter>
+            <filter>outputFormat == 'clustalw'</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="inputSequences" value="sample"/>
-            <param name="flavourType" value="fftns"/>
+            <param name="inputSequences" value="sample.fa"/>
+            <param name="flavourType" value="mafft-fftns"/>
             <param name="outputFormat" value="fasta"/>
-            <output name="outputFasta" file="sample.fftns2"/>
+            <output name="outputFasta" ftype="fasta" file="mafft_fftns_result.aln"/>
+        </test>
+        <test>
+            <param name="inputSequences" value="sample.fa"/>
+            <param name="flavourType" value="mafft-nwns"/>
+            <param name="outputFormat" value="clustalw"/>
+            <output name="outputClustalW" ftype="clustal" file="mafft_nwns_result.aln"/>
         </test>
     </tests>
     <help>
@@ -139,19 +145,14 @@
 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
 
     - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
-    
+
+**Options:**
+
+--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)
     ]]>
     </help>
     <citations>
         <citation type="doi">10.1093/molbev/mst010</citation>
-        <citation type="doi">10.1093/nar/gkt389</citation>
-        <citation type="doi">10.1093/bioinformatics/bts578</citation>
-        <citation type="doi">10.1093/bioinformatics/btq224</citation>
-        <citation type="doi">10.1007/978-1-59745-251-9_3</citation>
-        <citation type="doi">10.1186/1471-2105-9-212</citation>
-        <citation type="doi">10.1093/bib/bbn013</citation>
-        <citation type="doi">10.1093/bioinformatics/btl592</citation>
-        <citation type="doi">10.1093/nar/gki198</citation>
-        <citation type="doi">10.1093/nar/gkf436</citation>
     </citations>
 </tool>