--- a/mafft.xml	Sat Nov 11 15:06:34 2017 -0500
+++ b/mafft.xml	Wed Apr 15 15:33:37 2020 -0400
@@ -1,229 +1,294 @@
-<tool id="rbc_mafft" name="MAFFT" version="7.221.3">
-    <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
-            $cond_flavour.distance_method
-            --retree $cond_flavour.retree
-            --maxiterate $cond_flavour.iterations
-        #end if
-
-        ## specify threads to use
-        --thread \${GALAXY_SLOTS:-1}
-
-        $datatype
-        --ep $ep
-        --op $op
-        $adjustdirection
-        
-        #if $matrix_condition.matrix == "BLOSUM"
-          --bl ${matrix_condition.BLOSUM}
-        #elif $matrix_condition.matrix == "PAM"
-           --jtt ${matrix_condition.PAM}
-        #end if
-
-        $reorder
-        $getTree
-        $outputFormat
-        $inputSequences > $outputAlignment;
-
-        #if $getTree == "--treeout"
-            mv ${inputSequences}.tree $outputTree;
-        #end if
-    ]]>
-    </command>
-    <inputs>
-        <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
-        <param name="datatype" type="select" label="Data type">
-            <option value="">Auto detection</option>
-            <option value="--nuc">Nucleic acids</option>
-            <option value="--amino">Amino acids</option>
-        </param>
-        <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 --auto">auto</option>
-                <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>
-            </param>
-            <when value="mafft-fftns"/>
-            <when value="mafft --auto"/>
-            <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"/>
-            <when value="custom">
-                <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
-                    <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>
-                    <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>
-                    <option value="--localpair">Local alignment (Smith-Waterman)</option>
-                    <option value="--genafpair">Local, affine gap cost</option>
-                </param>
-                <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built this number of times in the progressive stage." help="Valid with 6mer distance" />
-                <param name="iterations" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
-            </when>
-        </conditional>
-        <param name="ep" type="float" value="0.123" label="Gap extend penalty" help="Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps" />
-        <param name="op" type="float" value="1.53" label="Gap opening penalty" help="1.53 default value" />
-        <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>
-        <conditional name="matrix_condition">
-            <param name="matrix" type="select" label="Matrix selection" display="radio" help="Usefull only for amino acids" >
-                <option value="">No matrix</option>
-                <option value="BLOSUM">BLOSUM</option>
-                <option value="PAM">PAM</option>
-            </param>
-            <when value=""/>
-            <when value="BLOSUM">
-                <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
-                    <option value="30">30</option>
-                    <option value="45">45</option>
-                    <option value="62" selected="true">62</option>
-                    <option value="80">80</option>
-                </param>
-            </when>
-            <when value="PAM">
-                <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the PAM matrix" />
-            </when>
-        </conditional>
-        <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" />
-        <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" />
-        <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
-            <option value="" selected="true">FASTA</option>
-            <option value="--clustalout">ClustalW</option>
-            <option value="--phylipout">Phylip</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="outputFormat" value="--clustalout" format="clustal"/>
-                <when input="outputFormat" value="--phylipout" format="phylip"/>
-            </change_format>
-        </data>
-        <data name="outputTree" format="txt" label="${tool.name} Guide Tree">
-            <filter>getTree == True</filter>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="inputSequences" value="sample.fa"/>
-            <param name="flavourType" value="mafft-fftns"/>
-            <param name="outputFormat" value=""/>
-            <output name="outputAlignment" 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="--clustalout"/>
-            <output name="outputAlignment" 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]
-
-**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)
---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.
---op
-    Gap opening penalty, default: 1.53
---ep
-    Offset (works like gap extension penalty), default: 0.0
---maxiterate
-    Maximum number of iterative refinement, default: 0
---clustalout
-    Output: clustal format, default: fasta
---thread
-    Number of threads (if unsure, --thread -1)
---retree number
-    Guide tree is built number times in the progressive stage.  Valid with 6mer distance.  Default: 2
-    ]]>
-    </help>
-    <citations>
-        <citation type="doi">10.1093/molbev/mst010</citation>
-    </citations>
-</tool>
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION@">
+  <description>Multiple alignment program for amino acid or nucleotide sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="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'
+        #if $cond_flavour.dist_flavour.distance_method == '--fastapair'
+          export FASTA_4_MAFFT=`which fasta36`;
+        #end if
+      #end if
+
+      #if $cond_flavour.flavourType != 'custom'
+        $cond_flavour.flavourType
+      #elif $cond_flavour.flavourType == 'custom'
+        ### full parameter options
+        mafft
+        $cond_flavour.dist_flavour.distance_method
+        #if $cond_flavour.dist_flavour.distance_method == '--6merpair'
+          --retree $cond_flavour.dist_flavour.retree
+          $cond_flavour.dist_flavour.distance_method.usetree.parttree
+
+          #if $cond_flavour.dist_flavour.distance_method.usetree.parttree==--parttree
+            $cond_flavour.dist_flavour.distance_method.usetree.treedistance
+            $cond_flavour.dist_flavour.distance_method.usetree.partsize
+            $cond_flavour.dist_flavour.distance_method.usetree.groupsize
+          #end if
+
+        #elif $cond_flavour.dist_flavour.distance_method == '--globalpair'
+          --weighti $cond_flavour.dist_flavour.weighti
+        #elif $cond_flavour.dist_flavour.distance_method == '--localpair'
+          --weighti $cond_flavour.dist_flavour.weighti
+          --lop $cond_flavour.dist_flavour.lop
+          --lep $cond_flavour.dist_flavour.lep
+          --lexp $cond_flavour.dist_flavour.lexp
+        #elif $cond_flavour.dist_flavour.distance_method == '--genafpair'
+          --weighti $cond_flavour.dist_flavour.weighti
+          --lop $cond_flavour.dist_flavour.lop
+          --lep $cond_flavour.dist_flavour.lep
+          --lexp $cond_flavour.dist_flavour.lexp
+          --LOP $cond_flavour.dist_flavour.skipLOP
+          --EXP $cond_flavour.dist_flavour.skipEXP 1
+        #elif $cond_flavour.dist_flavour.distance_method == '--fastapair'
+          --weighti $cond_flavour.dist_flavour.weighti
+        #end if
+        --maxiterate $cond_flavour.iterations
+        $cond_flavour.fft
+        $cond_flavour.score
+      #end if
+
+      ## specify threads to use
+      --thread \${GALAXY_SLOTS:-1}
+      $datatype
+      --ep $ep
+      --op $op
+
+      #if $matrix_condition.matrix == "BLOSUM"
+        --bl $matrix_condition.BLOSUM
+      #elif $matrix_condition.matrix == "PAM"
+        --jtt $matrix_condition.PAM
+        --tm $matrix_condition.tm
+      #elif $matrix_condition.matrix == "custom"
+        --aamatrix  '$matrix_condition.matrixfile'
+        --fmodel $matrix_condition.fmodel
+      #end if
+
+      $reorder
+      $getTree
+      $outputFormat
+      '$inputSequences' > '$outputAlignment';
+
+      #if $getTree == "--treeout"
+        mv '${inputSequences}.tree' '$outputTree';
+      #end if
+    ]]>
+  </command>
+  <inputs>
+    <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
+    <param name="datatype" type="select" label="Data type">
+      <option value="">Auto detection</option>
+      <option value="--nuc">Nucleic acids</option>
+      <option value="--amino">Amino acids</option>
+    </param>
+    <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 --auto">auto</option>
+        <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>
+      </param>
+      <when value="mafft-fftns"/>
+      <when value="mafft --auto"/>
+      <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"/>
+      <when value="custom">
+        <conditional name="dist_flavour">
+          <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
+            <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>
+            <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>
+            <option value="--localpair">Local alignment (Smith-Waterman)</option>
+            <option value="--genafpair">Local, affine gap cost</option>
+            <option value="--fastapair">All pairwise alignments are computed with FASTA</option>
+          </param>
+          <when value="--6merpair">
+            <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built this number of times in the progressive stage." help="Valid with 6mer distance" />
+            <conditional name="usetree">
+              <param name="parttree" type="select" label="Use a fast tree-building method?" help="Recommended for a large number (> ~10,000) of sequences are input" >
+                <option value="--parttree" selected="true">Yes</option>
+                <option value="">No</option>
+              </param>
+              <when value="--parttree">
+                <param name="treedistance" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
+                  <option value="--fastaparttree" selected="true">Distances based on FASTA</option>
+                  <option value="--dpparttree">Distances based on DP. (Needleman-Wunsch)</option>
+                </param>
+                <param name="partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm" />
+                <param name="groupsize" type="integer" value="" min="0" max="1000" label="Do not make alignment larger than ... sequences" />
+              </when>
+              <when value=""/>
+            </conditional>
+          </when>
+          <when value="--globalpair">
+            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
+          </when>
+          <when value="--localpair">
+            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
+            <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
+            <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
+            <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
+          </when>
+          <when value="--genafpair">
+            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
+            <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
+            <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
+            <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
+            <param name="skipLOP" type="float" value="-6.00" label="Gap opening penalty to skip the alignment" help="-6.00 default value" />
+            <param name="skipEXP" type="float" value="0.00" label="Gap extension penalty to skip the alignment" help="0 default value" />
+          </when>
+          <when value="--fastapair">
+            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
+          </when>
+        </conditional>
+        <param name="iterations" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
+        <param name="fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
+        <param name="score" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
+      </when>
+    </conditional>
+    <param name="ep" type="float" value="0.0" label="Gap extend penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps" />
+    <param name="op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value" />
+    <conditional name="matrix_condition">
+      <param name="matrix" type="select" label="Matrix selection" display="radio" help="Usefull only for amino acids" >
+        <option value="">No matrix</option>
+        <option value="BLOSUM" selected="true">BLOSUM</option>
+        <option value="PAM">PAM</option>
+        <option value="custom">Custom</option>
+      </param>
+      <when value=""/>
+      <when value="BLOSUM">
+        <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
+          <option value="30">30</option>
+          <option value="45">45</option>
+          <option value="62" selected="true">62</option>
+          <option value="80">80</option>
+        </param>
+      </when>
+      <when value="PAM">
+        <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the JTT PAM matrix" />
+        <param name="tm" type="integer" value="80" min="1" max="350" label="Coefficient of the  transmembrane PAM matrix" />
+      </when>
+      <when value="custom">
+        <param name="matrixfile" type="data" format="txt" label="User-defined AA scoring matrix" help="The format of matrixfile is the same to that of BLAST. Ignored when nucleotide sequences are input."/>
+        <param name="fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition information into the scoring matrix?" />
+      </when>
+    </conditional>
+    <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" />
+    <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" />
+    <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
+      <option value="" selected="true">FASTA</option>
+      <option value="--clustalout">ClustalW</option>
+      <option value="--phylipout">Phylip</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
+      <change_format>
+        <when input="outputFormat" value="--clustalout" format="clustal"/>
+        <when input="outputFormat" value="--phylipout" format="phylip"/>
+      </change_format>
+    </data>
+    <data name="outputTree" format="txt" label="${tool.name} Guide Tree">
+      <filter>getTree == True</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test expect_num_outputs="1" >
+      <param name="inputSequences" value="sample.fa"/>
+      <param name="flavourType" value="mafft-fftns"/>
+      <param name="outputFormat" value=""/>
+      <output name="outputAlignment" ftype="fasta" file="mafft_fftns_result.aln"/>
+    </test>
+    <test expect_num_outputs="1" >
+      <param name="inputSequences" value="sample.fa"/>
+      <param name="flavourType" value="mafft-nwns"/>
+      <param name="outputFormat" value="--clustalout"/>
+      <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln"/>
+    </test>
+    <test expect_num_outputs="1" >
+      <param name="inputSequences" value="sample.fa"/>
+      <param name="flavourType" value="custom"/>
+      <param name="matrix_condition" value="BLOSUM"/>
+      <param name="BLOSUM" value="62"/>
+      <param name="distance_method" value="--fastapair"/>
+      <param name="weighti" value="2.7"/>
+      <param name="iterations" value="1000"/>
+      <param name="outputFormat" value="--clustalout"/>
+      <output name="outputAlignment" ftype="clustal" file="mafft_custom_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]
+
+      **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)
+      --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.
+      --op
+      Gap opening penalty, default: 1.53
+      --ep
+      Offset (works like gap extension penalty), default: 0.0
+      --maxiterate
+      Maximum number of iterative refinement, default: 0
+      --clustalout
+      Output: clustal format, default: fasta
+      --thread
+      Number of threads (if unsure, --thread -1)
+      --retree number
+      Guide tree is built number times in the progressive stage.
+      Valid with 6mer distance.  Default: 2
+      ]]>
+    </help>
+  <expand macro="citations" />
+</tool>