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<tool id="mafft1" name="MAFFT">
	<description>, a progressive multiple alignment builder</description>
	<command interpreter="bash">./mafft --quiet
#if $datatype_condition.type == "nt": 
 --nuc
#end if
#if $datatype_condition.type == "aa": 
 --amino
#end if
#if $datatype_condition.type != "nt": 
	#if $datatype_condition.PAM_value_condition.matrix == "bl30": 
 --bl 30
	#end if
	#if $datatype_condition.PAM_value_condition.matrix == "bl45": 
 --bl 45
	#end if	
	#if $datatype_condition.PAM_value_condition.matrix == "bl62": 
 --bl 62
	#end if	
	#if $datatype_condition.PAM_value_condition.matrix == "bl80": 
 --bl 80
	#end if	
	#if $datatype_condition.PAM_value_condition.matrix == "PAM": 
 --jtt $datatype_condition.PAM_value_condition.PAM_value
	#end if		
#end if
 --maxiterate $iterations --$distance_method --op $op --ep $ep $input > $output</command>
	<inputs>
		<param format="txt" name="input" type="data" label="Source file"/>
		<conditional name="datatype_condition">
			<param type="select" name="type" label="Data type">
				<option value="auto">Automatic detection</option>
				<option value="nt">Nucleic acids</option>
				<option value="aa">Amino acids</option>
			</param>   
			<when value="aa">
				<conditional name="PAM_value_condition">
					<param type="select" name="matrix" label="Matrix" help="Usefull only for amino acids">
						<option value="bl62">BLOSUM 62</option>
						<option value="bl30">BLOSUM 30</option>
						<option value="bl45">BLOSUM 45</option>
						<option value="bl80">BLOSUM 80</option>
						<option value="PAM">PAM</option>
					</param>
					<when value="bl30"></when>
					<when value="bl45"></when>
					<when value="bl62"></when>
					<when value="bl80"></when>
					<when value="PAM">
						<param type="text" name="PAM_value" help="Must be greater than 0" value="80" label="Coefficient of the PAM matrix" />						
					</when>
				</conditional>
			</when>
			<when value="auto">
				<conditional name="PAM_value_condition">
					<param type="select" name="matrix" label="Matrix" help="Usefull only for amino acids">
						<option value="bl62">BLOSUM 62</option>
						<option value="bl30">BLOSUM 30</option>
						<option value="bl45">BLOSUM 45</option>
						<option value="bl80">BLOSUM 80</option>
						<option value="PAM">PAM</option>
					</param>
					<when value="bl30"></when>
					<when value="bl45"></when>
					<when value="bl62"></when>
					<when value="bl80"></when>
					<when value="PAM">
						<param type="text" name="PAM_value" help="Must be greater than 0" value="80" label="Coefficient of the PAM matrix" />						
					</when>
				</conditional>
			</when>	
			<when value="nt">
			</when>			
		</conditional>
		<param type="text" name="iterations" help="1000 for maximum quality" value="1000" label="Maximum number of iterations" />	
		<param type="text" name="op" help="1.53 default value" value="1.53" label="Gap opening penalty" />	
		<param type="text" name="ep" help="0.0 default value" value="0.0" label="Gap extension penalty" />	
		<param type="select" name="distance_method" label="Distance method" help="Distance method must be chosen regarding your data">
			<option value="6merpair">Shared 6mers distance (fastest)</option>
			<option value="globalpair">Global alignment (NW)</option>
			<option value="localpair">Local alignment (SW)</option>
			<option value="genafpair">Local, affine gap cost</option>
			<option value="fastapair">FASTA distance</option>		
		</param>		
	</inputs>
	<outputs>
		<data format="fasta" name="output" />
	</outputs>
	<help>

.. class:: infomark

**Program encapsulated in Galaxy by Southgreen**


.. class:: infomark

**MAFFT version 6.717b, 2009**

-----
	
==============
 Please cite: 
==============

"Parallelization of the MAFFT multiple sequence alignment program.", **Katoh, Toh**, Bioinformatics 26:1899-1900, 2010. (describes the multithread version; Linux only)

"Multiple Alignment of DNA Sequences with MAFFT.", **Katoh, Asimenos, Toh**, Methods in Molecular Biology 537:39-64, 2009. (outlines DNA alignment methods and several tips including group-to-group alignment and rough clustering of a large number of sequences)

"Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.", **Katoh, Toh**, BMC Bioinformatics 9:212, 2008. (describes RNA structural alignment methods)

"Recent developments in the MAFFT multiple sequence alignment program.", **Katoh, Toh**, Briefings in Bioinformatics 9:286-298, 2008. (outlines version 6; Fast Breaking Paper in Thomson Reuters' ScienceWatch)

"PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences." **Katoh, Toh**, Bioinformatics 23:372-374, Errata, 2007. (describes the PartTree algorithm)

"MAFFT version 5: improvement in accuracy of multiple sequence alignment.", **Katoh, Kuma, Toh, Miyata**, Nucleic Acids Res. 33:511-518, 2005. (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)

"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.", **Katoh, Misawa, Kuma, Miyata**, Nucleic Acids Res. 30:3059-3066, 2002.
 

-----	
	
==========
 Overview
==========	

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i wich is accurate for alignment with less than 200 sequences, FFT-NS-2 which is fast for alignment with less than 10000 sequences. 

-----

For further informations, please visite the MAFFT_ website.

.. _MAFFT: http://mafft.cbrc.jp/alignment/software/

	</help>

</tool>