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<tool id="muscle" name="Muscle" version="1.0.0">
<description>Multiple sequence alignment</description>
<command>muscle
-quiet
#if $input.select == '1':
-in $input.file
#else:
-profile
-in1 $input.file1
-in2 $input.file2
#end if
#if $usetree.select == 'yes':
-usetree_nowarn $usetree.file
#end if
$refine
-out $output
$diags
-maxiters $maxiters
-maxhours $maxhours
#if $advanced.select == 'yes':
-maxtrees $advanced.maxtrees
-anchorspacing $advanced.anchorspacing
-diagbreak $advanced.diagbreak
-diaglength $advanced.diaglength
-diagmargin $advanced.diagmargin
-smoothwindow $advanced.smoothwindow
$advanced.brenner
$advanced.dimer
#end if
</command>
<inputs>
<conditional name="input">
    <param name="select" type="select" label="Mode">
        <option value="1" selected="true">Single file</option>
        <option value="2">Profile-profile alignment</option>
    </param>
    <when value="1">
        <param name="file" type="data" format="fasta" label="Unaligned sequences" />
    </when>
    <when value="2">
        <param name="file1" type="data" format="fasta" label="Aligned sequences #1" />
        <param name="file2" type="data" format="fasta" label="Aligned sequences #2" />
    </when>
</conditional>
<conditional name="usetree">
    <param name="select" type="select" label="Use guide tree" help="NB: The best guide tree for multiple alignment is not in general the correct evolutionary tree">
      <option value="no" selected="True">No</option>
      <option value="yes">Yes</option>
    </param>
    <when value="no">
        <param name="file" type="hidden" value="" /> 
    </when>
    <when value="yes">
        <param name="file" type="data" format="phylip" label="Guide tree in Newick/Phylip format" />
    </when>
</conditional>
<param name="refine" type="boolean" truevalue="-refine" falsevalue="" label="Refine an existing alignment" />
<param name="diags" type="boolean" truevalue="-diags" falsevalue="" label="Find diagonals" help="Faster for similar sequences" />
<param name="maxiters" label="Maximum number of iterations" type="integer" value="16" help="Use small number for very large files (as low as 1 or 2)." />
<param name="maxhours" label="Maximum hours" type="float" value="24.0" help="If this time is exceeded, muscle will write out current alignment and stop." />
<conditional name="advanced">
    <param name="select" type="select" label="Show advanced options">
      <option value="no" selected="True">No</option>
      <option value="yes">Yes</option>
    </param>
    <when value="no">
    </when>
    <when value="yes">
        <param name="maxtrees" label="Maximum number of new trees to create in iteration 2" type="integer" value="1" />
        <param name="anchorspacing" label="Minimum spacing between anchor columns" type="integer" value="32" />
        <param name="diagbreak" label="Maximum distance between two diagonals that allows them to merge into one diagonal" type="integer" value="1" />
        <param name="diaglength" label="Minimum length of diagonal" type="integer" value="24" />
        <param name="diagmargin" label="Discard this many positions at ends of diagonal" type="integer" value="5" />
        <param name="smoothwindow" label="Window used for anchor column smoothing" type="integer" value="7" />
        <!-- flags -->
        <param name="brenner" label="Use Steven Brenner's method for computing the root alignment" type="boolean" truevalue="-brenner" falsevalue="" selected="false" />
        <param name="dimer" label="Use dimer approximation for the SP score" help="Faster, slightly less accurate" type="boolean" truevalue="-dimer" falsevalue="" selected="false" />
    </when>
</conditional>
</inputs>
<outputs>
<data format="fasta" name="output" />
</outputs>
<help>
**What it does**

Perform multiple sequence alignment.

**Documentation**

http://www.drive5.com/muscle/muscle_userguide3.8.pdf

**Author**

Robert C. Edgar

**Citation**

Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

</help>
</tool>