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1 <tool id="fastme" name="FastME" version="2.1.4.2">
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2 <description>Distance-based inference of phylogenetic trees</description>
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3 <requirements>
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4
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4 <requirement type="package" version="2.1.4">fastme</requirement>
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5 </requirements>
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6 <version_command>
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7 <![CDATA[ fastme --version ]]>
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8 </version_command>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12 <command>fastme --input_data=$input
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13 --output_tree=$outputTree
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14 --output_matrix=$outputMatrix
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15 --output_info=$outputLog
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16 --nb_threads=\${GALAXY_SLOTS:-1}
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17
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18 #if $typeChoice.datatype =="d"
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19 --dna=$typeChoice.modeldna
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20
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21 #else if $typeChoice.datatype =="p"
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22 --protein=$typeChoice.modelprot
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23
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24 #else if $typeChoice.datatype =="cfg":
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25 ## Read information of sequence type
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26 ## read an info file to choose which option set and set a model by default
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27 #set $info = open( str($input_info) ).read()
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28 #if 'dna' in $info:
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29 --dna=T
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30 #else if 'protein' in $info:
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31 --protein=L
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32 #end if
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33 #end if
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34
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35 #if $gammaChoice.gamma == "true"
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36 --gamma=$gammaChoice.rate
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37 #end if
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38
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39 $distance
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40 $equilibrium
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41 $removeGap
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42 $treeRefinement
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43
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44 #if $bootChoice.boot == "true"
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45 --output_boot=$outputBoostrap
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46 --bootstrap=$bootChoice.replicates
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47 #end if
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48
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49 >> tmp_stdout;
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50 cat tmp_stdout > $outputLog;
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51
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52 </command>
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53 <inputs>
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54 <param name="input" type="data" format="phylip, phy" label="Fastme input" help="Phylip Alignment or Matrix file"/>
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55 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
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56 <conditional name="typeChoice">
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57 <param name="datatype" type="select" display="radio" label="Data type" >
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58 <option value="d">DNA</option>
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59 <option value="p">Protein</option>
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60 <option value="m">Matrix</option>
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61 <option value="cfg">Config file</option>
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62 </param>
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63 <when value="d">
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64 <param name="modeldna" type="select" label="Evolutionary model">
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65 <option value="4">F84</option>
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66 <option value="R">RY</option>
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67 <option value="1">F81</option>
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68 <option value="J">JC69</option>
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69 <option value="K">K2P</option>
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70 <option value="T" selected="true">TN93</option>
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71 <option value="p">p-distance</option>
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72 </param>
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73 </when>
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74 <when value="p">
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75 <param name="modelprot" type="select" label="Evolutionary model">
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76 <option value="L">LG</option>
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77 <option value="W">WAG</option>
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78 <option value="J">JTT</option>
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79 <option value="h">Day off</option>
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80 <option value="C">CpRev</option>
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81 <option value="D">DCMut</option>
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82 <option value="b">HIVb</option>
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83 <option value="I">HIVw</option>
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84 <option value="M">MtREV</option>
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85 <option value="R">RtREV</option>
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86 <option value="p">p-distance</option>
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87 </param>
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88 </when>
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89 <when value="m"/>
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90 <when value="cfg">
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91 <param name="input_info" format="txt" type="data" multiple="false" label="Config file" help="Precompute file containning sequence description (dna or protein)"/>
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92 </when>
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93 </conditional>
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94 <param name="equilibrium" type="boolean" label="Equilibrium frequencies" truevalue="--equilibrium" falsevalue="" help="By default, frequencies are globally counted from the nucleotides alignment or defined by the proteic substitution model. By checking the box, frequencies are pairwise estimated by counting the nucleotides or estimated by counting the amino-acids in the alignment."/>
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95 <conditional name="gammaChoice">
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96 <param name="gamma" type="select" label="Gamma distributed rates across sites">
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97 <option value="true">Yes</option>
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98 <option value="false">No</option>
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99 </param>
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100 <when value="true">
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101 <param name="rate" type="float" label="Gamma distribution parameter" value="1" min="0"/>
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102 </when>
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103 <when value="false" />
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104 </conditional>
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105 <param name="removeGap" type="select" display="radio" label="Remove gap strategy">
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106 <option value="">Pairwise deletion of gaps</option>
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107 <option value="--remove_gap">Remove all sites with gap</option>
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108 </param>
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109 <param name="distance" type="select" label="Distance algorithm">
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110 <option value="--method=I">BIONJ</option>
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111 <option value="--method=B --branch_length=B">TaxAdd BalME</option>
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112 <option value="--method=O --branch_length=O">TaxAdd OLSME</option>
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113 <option value="--method=N">NJ</option>
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114 <option value="--method=U">UNJ</option>
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115 </param>
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116 <param name="treeRefinement" type="select" display="radio" label="Tree Refinement" help='(NNI) Nearest Neighbor Interchanges,(SPR) Subtree Pruning and Regrafting '>
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117 <option value="">None</option>
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118 <option value="--nni=O">OLS NNI</option>
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119 <option value="--nni=B">BalME NNI</option>
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120 <option value="--spr" selected="true">BalME SPR</option>
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121 <option value="--nni=B --spr">BalME NNI + SPR</option>
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122 </param>
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123 <conditional name="bootChoice">
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124 <param name="boot" type="select" label="Bootstrap">
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125 <option value="false">No</option>
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126 <option value="true">Yes</option>
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127 </param>
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128 <when value="false"/>
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129 <when value="true">
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130 <param name="replicates" type="integer" value="1000" label="Number of replicates"/>
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131 </when>
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132 </conditional>
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133 </inputs>
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134 <outputs>
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135 <data name="outputTree" format="nwk" label="${fileout_label}"/>
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136 <data name="outputLog" format="txt" label="FastME Information"/>
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137 <data name="outputBoostrap" format="nwk" label="FastME Bootstrap trees">
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138 <filter>bootChoice['boot'] == "true"</filter>
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139 </data>
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140 <data name="outputMatrix" format="txt" label="FastME Distance matrix"/>
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141 </outputs>
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142 <tests>
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143 <test>
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144 <param name="input" value="phylip" />
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145 <param name="modeldna" value="4"/>
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146 <param name="gamma" value="false"/>
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147 <param name="treeRefinement" value=""/>
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148 <param name="distance" value="--method=I"/>
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149 <output name="outputTree" file="newick" />
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150 </test>
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151 <test>
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152 <param name="input" value="phylip" />
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153 <param name="modeldna" value="T"/>
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154 <param name="distance" value="--method=I"/>
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155 <param name="treeRefinement" value="--nni=B --spr"/>
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156 <param name="fileout_label" value="TreeTn93BionjSpr.nwk" />
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157 <output name="outputTree" file="TreeTn93BionjSpr.nwk" />
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158 </test>
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159 </tests>
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160 <help>
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161
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162 .. class:: infomark
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163
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164
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165 **FastME version 2.1.4**
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166
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167
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168 .. class:: infomark
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169
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170
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171 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. Correia Damien, CNRS.
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172 **Support** For any questions about Galaxy integration, please send an e-mail to vincent.lefort@lirmm.fr
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173
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174
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175 -----
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176
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177
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178 ############
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179 FastME 2.0
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180 ############
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181
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182 Comprehensive, accurate and fast distance-based phylogeny inference program
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183
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184
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185 -----------
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186 Description
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187 -----------
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188
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189 FastME provides distance algorithms to infer phylogenies. It's based on balanced minimum evolution, which is the very principle of NJ.
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190
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191 FastME included Nearest Neighbor Interchange (NNI) and also Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.
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192
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193 ------------
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194 Dependencies
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195 ------------
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196 FastME
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197 http://www.atgc-montpellier.fr/fastme
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198
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199
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200
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201 ---------------------------------------------------
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202
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203 ---------------
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204 Working example
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205 ---------------
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206
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207 Input files
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208 ===========
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209
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210 **Phylip file**::
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211
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212
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213 4 120
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214 Orangutan CCAAACGACA TTTCATATGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTGTCCGGAA
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215 Gorilla CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTCTCCGAAA
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216 Human CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATAAGA GACAAGTGAG CTCTCCGAAA
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217 Chimp CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTCTCCGAAA
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218
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219 CCAACATATC AGACATATGT GAATTTCAAT TATTGTACGG GCATCCTGGG CTCTCAAAGT
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220 CCAAGATATC AGACATTTAT GAATTTCAAT TATTGTACGG GCATCCTGGG CTCTCAAAGT
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221 CCAAGATACC AGACATTTGT GAATTTCAAT TATTGTACTG GCATCCTGGG CTCTCAAAGT
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222 CCAAGATATC AGACATTTAT GAATTTCAAT TATTGTACTG GCATCCTGGG CTCTCAAAGT
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223
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224
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225
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226 Parameters
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227 ==========
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228
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229 ::
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230
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231 Output name: Newick tree
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232 Evolutionary model : TN93
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233 Distance method : BIONJ
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234
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235
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236 Output files
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237 ============
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238
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239 **Newick tree**::
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240
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241 ((Gorilla:0.005755,Orangutan:0.020680):0.001063,Human:0.006655,Chimp:0.002132);
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242
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243 -----
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244
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245 OPTIONS
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246 =======
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247
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248
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249 -i file, --input_data=file
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250 The input data file contains sequence alignment(s) or a distance matrix(ces).
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251
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252 -u input_tree_file, --user_tree=input_tree_file
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253 FastME may use an existing topology available in the input user tree file which corresponds to the input dataset.
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254
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255 -o output_tree_file, --output_tree=output_tree_file
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256 FastME will write the infered tree into the output tree file.
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257
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258 -O output_matrix_file, --output_matrix=output_matrix_file
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259 Use output matrix file option if you want FastME to write the distances
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260 matrix computed from the input alignment in the output matrix file.
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261
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262 -I output_information_file, --output_info=output_information_file
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263 Use this option if you want FastME to write information
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264 about its execution in the output information file.
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265
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266 -B output_bootstrap_trees_file, --output_boot=output_bootstrap_trees_file
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267 Use this option if you want FastME to write bootstrap trees
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268 in the bootstrap trees file.
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269
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270 -a, --append
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271 Use this option to append results to existing output files (if any).
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272 By default output files will be overwritten.
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273
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274 -m method, --method=method
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275 FastME computes a tree using a distance algorithm.
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276 You may choose this method from:
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277 TaxAdd_(B)alME, TaxAdd_(O)LSME, B(I)ONJ (default),
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278 (N)J or (U)NJ.
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279
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280 -d model, --dna=model
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281 Use this option if your input data file contains DNA sequences alignment(s).
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282 You may also indicate the evolutionary [model] which can be choosen from:
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283 (p)-distance, R(Y) symmetric, (R)Y, (J)C69, (K)2P, F8(1), F8(4) (default), (T)N93, (L)ogDet.
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284
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285 -p model, --protein=model
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286 Use this option if your input data file contains protein sequences alignment(s).
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287 You may also indicate the evolutionary [model] which can be choosen from:
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288 (p)-distance, (F)81 like, (L)G (default), (W)AG, (J)TT, Day(h)off, (D)CMut, (C)pRev,
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289 (M)tREV, (R)tREV, HIV(b), H(I)Vw or FL(U).
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290
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291 -r, --remove_gap
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292 Use this option to completely remove any site which has a gap in
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293 any sequence. By default, FastME is doing pairwise deletion of gaps.
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294
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295 -e, --equilibrium
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296 The equilibrium frequencies for DNA are always estimated by counting
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297 the occurence of the nucleotides in the input alignment.
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298 For amino-acid sequences, the equilibrium frequencies are estimated
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299 using the frequencies defined by the substitution model.
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300 Use this option if you whish to estimate the amino-acid frequencies
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301 by counting their occurence in the input alignment.
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302
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303 -g alpha, --gamma=alpha
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304 Use this option if you wish to have gamma distributed rates across sites.
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305 By default, FastME runs with no gamma variation.
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306 If running FastME with gamma distributed rates across sites, the [alpha] default value is 1.0.
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307 Only helpful when the input data file contains sequences alignment(s).
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308
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309 -n NNI, --nni=NNI
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310 Use this option to do [NNI] tree topology improvement.
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311 You may choose the [NNI] type from:
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312 NNI_(B)alME (default) or NNI_(O)LS.
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313
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314 -s, --spr
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315 Use this option to do SPR tree topology improvement.
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316
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317 -w branch, --branch_length=branch
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318 Use this option to indicate the branch length to assign to the tree.
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319 Only helpful when not improving the tree topology (no NNI nor SPR).
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320 You may choose the branch length from:
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321 (B)alLS (default), (O)LS or (n)one. (n)one is only available with BIONJ, NJ or UNJ.
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322
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323 -D datasets, --datasets=datasets
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324 Use this option to indicate the number of datasets in your input
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325 data file. Default value is 1.
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326
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327 -b replicates, --bootstrap=replicates
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328 Use this option to indicate the number of replicates FastME will
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329 do for bootstrapping. Default value is 0.
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330 Only helpful when the input data file contains sequences alignment(s).
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331
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332 -z seed, --seed=seed
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333 Use this option to initialize randomization with seed value. Only helpful when bootstrapping.
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334
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335 -c Use this option if you want FastME only to compute distance matrix.
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336 Only helpful when the input data file contains sequences alignment(s).
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337
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338 -T number_of_threads, --nb_threads=number_of_threads
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339 Use this option to set the number of threads to use.
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340 Default number of threads is 4.
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341
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342 -v value, --verbose=value
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343 Sets the verbose level to value [0-3]. Default value is 0
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344
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345 -V, --version
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346 Prints the FastME version.
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347
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348 -h, --help Display this usage.
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349
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350
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351 For further informations, please visite FastME_
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352
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353 .. _FastME: http://www.atgc-montpellier.fr/fastme/usersguide.php
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354
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355 </help>
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356 <citations>
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357 <citation type="doi">10.1093/molbev/msv150</citation>
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358 <citation type="doi">10.1089/106652702761034136</citation>
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359 </citations>
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360 </tool> |
