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1 <tool id="muscle" name="Muscle" version="1.0.0">
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2 <description>Multiple sequence alignment</description>
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3 <command>muscle
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4 -quiet
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5 #if $input.select == '1':
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6 -in $input.file
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7 #else:
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8 -profile
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9 -in1 $input.file1
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10 -in2 $input.file2
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11 #end if
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12 #if $usetree.select == 'yes':
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13 -usetree_nowarn $usetree.file
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14 #end if
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15 $refine
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16 -out $output
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17 $diags
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18 -maxiters $maxiters
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19 -maxhours $maxhours
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20 #if $advanced.select == 'yes':
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21 -maxtrees $advanced.maxtrees
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22 -anchorspacing $advanced.anchorspacing
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23 -diagbreak $advanced.diagbreak
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24 -diaglength $advanced.diaglength
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25 -diagmargin $advanced.diagmargin
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26 -smoothwindow $advanced.smoothwindow
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27 $advanced.brenner
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28 $advanced.dimer
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29 #end if
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30 </command>
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31 <inputs>
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32 <conditional name="input">
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33 <param name="select" type="select" label="Mode">
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34 <option value="1" selected="true">Single file</option>
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35 <option value="2">Profile-profile alignment</option>
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36 </param>
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37 <when value="1">
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38 <param name="file" type="data" format="fasta" label="Unaligned sequences" />
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39 </when>
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40 <when value="2">
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41 <param name="file1" type="data" format="fasta" label="Aligned sequences #1" />
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42 <param name="file2" type="data" format="fasta" label="Aligned sequences #2" />
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43 </when>
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44 </conditional>
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45 <conditional name="usetree">
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46 <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">
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47 <option value="no" selected="True">No</option>
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48 <option value="yes">Yes</option>
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49 </param>
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50 <when value="no">
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51 <param name="file" type="hidden" value="" />
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52 </when>
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53 <when value="yes">
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54 <param name="file" type="data" format="phylip" label="Guide tree in Newick/Phylip format" />
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55 </when>
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56 </conditional>
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57 <param name="refine" type="boolean" truevalue="-refine" falsevalue="" label="Refine an existing alignment" />
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58 <param name="diags" type="boolean" truevalue="-diags" falsevalue="" label="Find diagonals" help="Faster for similar sequences" />
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59 <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)." />
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60 <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." />
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61 <conditional name="advanced">
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62 <param name="select" type="select" label="Show advanced options">
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63 <option value="no" selected="True">No</option>
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64 <option value="yes">Yes</option>
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65 </param>
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66 <when value="no">
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67 </when>
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68 <when value="yes">
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69 <param name="maxtrees" label="Maximum number of new trees to create in iteration 2" type="integer" value="1" />
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70 <param name="anchorspacing" label="Minimum spacing between anchor columns" type="integer" value="32" />
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71 <param name="diagbreak" label="Maximum distance between two diagonals that allows them to merge into one diagonal" type="integer" value="1" />
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72 <param name="diaglength" label="Minimum length of diagonal" type="integer" value="24" />
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73 <param name="diagmargin" label="Discard this many positions at ends of diagonal" type="integer" value="5" />
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74 <param name="smoothwindow" label="Window used for anchor column smoothing" type="integer" value="7" />
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75 <!-- flags -->
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76 <param name="brenner" label="Use Steven Brenner's method for computing the root alignment" type="boolean" truevalue="-brenner" falsevalue="" selected="false" />
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77 <param name="dimer" label="Use dimer approximation for the SP score" help="Faster, slightly less accurate" type="boolean" truevalue="-dimer" falsevalue="" selected="false" />
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78 </when>
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79 </conditional>
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80 </inputs>
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81 <outputs>
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82 <data format="fasta" name="output" />
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83 </outputs>
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84 <help>
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85 **What it does**
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86
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87 Perform multiple sequence alignment.
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88
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89 **Documentation**
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90
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91 http://www.drive5.com/muscle/muscle_userguide3.8.pdf
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92
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93 **Author**
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94
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95 Robert C. Edgar
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96
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97 **Citation**
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98
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99 Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
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100
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101 </help>
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102 </tool>
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