--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft.xml	Thu Jun 18 08:59:56 2015 -0400
@@ -0,0 +1,152 @@
+<tool id="rbc_mafft" name="MAFFT" version="7.221.0">
+    <description>Multiple alignment program for amino acid or nucleotide sequences</description>
+    <requirements>
+        <requirement type="package" version="7.221">mafft</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <version_command>
+    <![CDATA[
+        mafft --version
+    ]]>
+    </version_command>
+    <command>
+    <![CDATA[
+        #if $cond_flavour.flavourType != 'custom'
+            $cond_flavour.flavourType
+        #elif $cond_flavour.flavourType == 'custom'
+            ### full parameter options
+            mafft
+        #end if
+        
+        ## specify threads to use
+        --thread \${GALAXY_SLOTS:-1}
+        
+        #if $outputFormat.value == 'clustalw'
+            --clustalout
+        #end if
+        
+        $inputSequences > 
+        
+        #if $outputFormat.value == 'fasta'
+            $outputFasta
+        #elif $outputFormat.value == 'clustalw'
+            $outputClustalW
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
+        <conditional name="cond_flavour">
+            <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
+                <option value="mafft-fftns" selected="true">fftns</option>
+                <option value="mafft-fftnsi">fftnsi</option>
+                <option value="mafft-nwns">nwns</option>
+                <option value="mafft-nwnsi">nwnsi</option>
+                <option value="mafft-einsi">einsi</option>
+                <option value="mafft-ginsi">ginsi</option>
+                <option value="mafft-linsi">linsi</option>
+                <option value="mafft-qinsi">qinsi</option>
+                <option value="mafft-xinsi">xinsi</option>
+                <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters -->
+            </param>
+            <when value="mafft-fftns"/>
+            <when value="mafft-fftnsi"/>
+            <when value="mafft-nwns"/>
+            <when value="mafft-nwnsi"/>
+            <when value="mafft-einsi"/>
+            <when value="mafft-ginsi"/>
+            <when value="mafft-linsi"/>
+            <when value="mafft-qinsi"/>
+            <when value="mafft-xinsi"/>
+        </conditional>
+        <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
+            <option value="fasta" selected="true">FASTA</option>
+            <option value="clustalw">ClustalW</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">
+            <filter>outputFormat == 'fasta'</filter>
+        </data>
+        <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">
+            <filter>outputFormat == 'clustalw'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputSequences" value="sample.fa"/>
+            <param name="flavourType" value="mafft-fftns"/>
+            <param name="outputFormat" value="fasta"/>
+            <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>
+    <![CDATA[
+**What it does**
+
+MAFFT is a multiple sequence alignment program for unix-like operating systems.  
+It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), 
+FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
+
+From the MAFFT man page, an overview of the different predefined flavours of the tool.
+
+**Accuracy-oriented methods:**
+
+- L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
+    
+    - mafft --localpair --maxiterate 1000 input [> output]
+
+- G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
+    
+    - mafft --globalpair --maxiterate 1000 input [> output]
+
+- E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
+    
+    - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps. 
+
+
+**Speed-oriented methods:**
+
+- FFT-NS-i (iterative refinement method; two cycles only):
+
+    - mafft --retree 2 --maxiterate 2 input [> output]
+
+- FFT-NS-i (iterative refinement method; max. 1000 iterations):
+
+    - mafft --retree 2 --maxiterate 1000 input [> output]
+
+- FFT-NS-2 (fast; progressive method):
+
+    - mafft --retree 2 --maxiterate 0 input [> output]
+
+- FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
+
+    - mafft --retree 1 --maxiterate 0 input [> output]
+
+- NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
+
+    - mafft --retree 2 --maxiterate 2 --nofft input [> output]
+
+- NW-NS-2 (fast; progressive method without the FFT approximation):
+
+    - mafft --retree 2 --maxiterate 0 --nofft input [> output]
+
+- 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]
+    
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/molbev/mst010</citation>
+    </citations>
+</tool>