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1 <tool id="mafft1" name="MAFFT">
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2 <description>, a progressive multiple alignment builder</description>
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3 <command interpreter="bash">./mafft --quiet
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4 #if $datatype_condition.type == "nt":
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5 --nuc
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6 #end if
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7 #if $datatype_condition.type == "aa":
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8 --amino
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9 #end if
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10 #if $datatype_condition.type != "nt":
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11 #if $datatype_condition.PAM_value_condition.matrix == "bl30":
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12 --bl 30
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13 #end if
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14 #if $datatype_condition.PAM_value_condition.matrix == "bl45":
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15 --bl 45
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16 #end if
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17 #if $datatype_condition.PAM_value_condition.matrix == "bl62":
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18 --bl 62
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19 #end if
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20 #if $datatype_condition.PAM_value_condition.matrix == "bl80":
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21 --bl 80
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22 #end if
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23 #if $datatype_condition.PAM_value_condition.matrix == "PAM":
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24 --jtt $datatype_condition.PAM_value_condition.PAM_value
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25 #end if
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26 #end if
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27 --maxiterate $iterations --$distance_method --op $op --ep $ep $input > $output</command>
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28 <inputs>
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29 <param format="txt" name="input" type="data" label="Source file"/>
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30 <conditional name="datatype_condition">
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31 <param type="select" name="type" label="Data type">
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32 <option value="auto">Automatic detection</option>
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33 <option value="nt">Nucleic acids</option>
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34 <option value="aa">Amino acids</option>
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35 </param>
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36 <when value="aa">
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37 <conditional name="PAM_value_condition">
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38 <param type="select" name="matrix" label="Matrix" help="Usefull only for amino acids">
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39 <option value="bl62">BLOSUM 62</option>
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40 <option value="bl30">BLOSUM 30</option>
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41 <option value="bl45">BLOSUM 45</option>
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42 <option value="bl80">BLOSUM 80</option>
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43 <option value="PAM">PAM</option>
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44 </param>
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45 <when value="bl30"></when>
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46 <when value="bl45"></when>
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47 <when value="bl62"></when>
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48 <when value="bl80"></when>
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49 <when value="PAM">
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50 <param type="text" name="PAM_value" help="Must be greater than 0" value="80" label="Coefficient of the PAM matrix" />
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51 </when>
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52 </conditional>
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53 </when>
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54 <when value="auto">
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55 <conditional name="PAM_value_condition">
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56 <param type="select" name="matrix" label="Matrix" help="Usefull only for amino acids">
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57 <option value="bl62">BLOSUM 62</option>
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58 <option value="bl30">BLOSUM 30</option>
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59 <option value="bl45">BLOSUM 45</option>
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60 <option value="bl80">BLOSUM 80</option>
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61 <option value="PAM">PAM</option>
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62 </param>
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63 <when value="bl30"></when>
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64 <when value="bl45"></when>
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65 <when value="bl62"></when>
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66 <when value="bl80"></when>
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67 <when value="PAM">
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68 <param type="text" name="PAM_value" help="Must be greater than 0" value="80" label="Coefficient of the PAM matrix" />
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69 </when>
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70 </conditional>
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71 </when>
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72 <when value="nt">
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73 </when>
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74 </conditional>
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75 <param type="text" name="iterations" help="1000 for maximum quality" value="1000" label="Maximum number of iterations" />
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76 <param type="text" name="op" help="1.53 default value" value="1.53" label="Gap opening penalty" />
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77 <param type="text" name="ep" help="0.0 default value" value="0.0" label="Gap extension penalty" />
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78 <param type="select" name="distance_method" label="Distance method" help="Distance method must be chosen regarding your data">
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79 <option value="6merpair">Shared 6mers distance (fastest)</option>
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80 <option value="globalpair">Global alignment (NW)</option>
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81 <option value="localpair">Local alignment (SW)</option>
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82 <option value="genafpair">Local, affine gap cost</option>
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83 <option value="fastapair">FASTA distance</option>
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84 </param>
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85 </inputs>
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86 <outputs>
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87 <data format="fasta" name="output" />
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88 </outputs>
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89 <help>
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90
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91 .. class:: infomark
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92
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93 **Program encapsulated in Galaxy by Southgreen**
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94
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95
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96 .. class:: infomark
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97
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98 **MAFFT version 6.717b, 2009**
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99
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100 -----
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101
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102 ==============
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103 Please cite:
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104 ==============
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105
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106 "Parallelization of the MAFFT multiple sequence alignment program.", **Katoh, Toh**, Bioinformatics 26:1899-1900, 2010. (describes the multithread version; Linux only)
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107
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108 "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)
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109
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110 "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)
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111
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112 "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)
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113
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114 "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)
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115
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116 "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)
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117
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118 "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.
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119
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120
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121 -----
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122
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123 ==========
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124 Overview
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125 ==========
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126
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127 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.
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128
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129 -----
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130
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131 For further informations, please visite the MAFFT_ website.
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132
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133 .. _MAFFT: http://mafft.cbrc.jp/alignment/software/
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134
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135 </help>
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136
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137 </tool> |
