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1 <tool id="sniplay_fastme" name="FastME" version="1.1.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Calculate distance tree for an alignment file</description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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9 <requirement type="package" version="2.1.4">fastme
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10 </requirement>
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11 </requirements>
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12
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13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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14 <stdio>
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15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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16 <exit_code range="1:" level="fatal" />
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17 </stdio>
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18
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19
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20 <!-- [REQUIRED] The command to execute -->
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21 <command>
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22 fastme --input_data=$input_data --dna=$model --output_tree=$fileout
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23 #if str( $distance ) == "SPR":
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24 --spr
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25 #elif str( $distance )[:3] == "NNI" :
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26 #if str( $distance ) == "NNI_B" :
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27 --nni=B
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28 #else :
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29 --nni=O
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30 #end if
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31
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32 #else :
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33 --method=$distance
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34 #end if
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35 > $fileout_log
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36 </command>
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37
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38
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39
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40 <!-- [REQUIRED] Input files and tool parameters -->
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41 <inputs>
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42 <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
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43 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
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44 <param name="fileout_label2" type="text" value="Unused" label="none" help="Output name for files" />
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45 <param name="model" type="select" label="Evolutionary model" >
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46 <option value="p">p-distance</option>
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47 <option value="Y">RY symetric</option>
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48 <option value="R">RY</option>
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49 <option value="J">JC69</option>
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50 <option value="K">K2P</option>
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51 <option value="1">F81</option>
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52 <option value="4" selected="true">F84</option>
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53 <option value="T">TN93</option>
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54 <option value="L">LogDet</option>
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55 </param>
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56 <param name="distance" type="select" label="Distance methode" >
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57 <option value="B">TaxAdd_BalME</option>
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58 <option value="O">TaxAdd_OLSME</option>
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59 <option value="I" selected="true">BIONJ</option>
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60 <option value="N">NJ</option>
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61 <option value="U">UNJ</option>
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62 <option value="NNI_B">NNI_BalME</option>
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63 <option value="NNI_O">NNI_OLS</option>
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64 <option value="SPR">SPR</option>
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65 </param>
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66 </inputs>
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67
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68 <!-- [REQUIRED] Output files -->
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69 <outputs>
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70 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
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71 <data name="fileout" type="data" format="txt" label="${fileout_label}" />
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72 </outputs>
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73
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74 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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75 <tests>
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76 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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77
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78 <test>
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79 <param name="filein" value="phylip" />
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80 <param name="model" value="4"/>
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81 <param name="distance" value="I"/>
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82 <output name="fileout" file="newick" />
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83 <output name="fileout_log" file="newick.log" />
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84 </test>
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85
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86 <!-- [HELP] Multiple tests can be defined with different parameters -->
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87 <!--
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88 <test>
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89 </test>
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90 -->
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91 </tests>
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92
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93 <!-- [OPTIONAL] Help displayed in Galaxy -->
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94 <help>
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95
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96 .. class:: infomark
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97
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98 **Authors**
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99
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100 | Richard Desper and Olivier Gascuel,
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101 | Journal of Computational Biology 19(5), 687-705, 2002.
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102 | Molecular Biology and Evolution 21(3), 587-598, 2004.
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103 | Please cite these papers if you use this software in your publications.
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104
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105
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106 .. class:: infomark
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107
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108 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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109
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110 .. class:: infomark
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111
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112 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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113
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114 ---------------------------------------------------
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115
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116
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117 ======
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118 FastMe
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119 ======
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120
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121 -----------
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122 Description
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123 -----------
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124
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125
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126 FastME - A distance based phylogeny reconstruction algorithm.
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127
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128 FastME showed better topological accuracy than NJ,
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129 BIONJ, WEIGHBOR and FITCH, in all evolutionary
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130 conditions we tested, which include large range
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131 deviations from molecular clock and substitution rates.
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132
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133
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134
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135 -----------------
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136 Workflow position
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137 -----------------
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138
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139 **Upstream tools**
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140
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141 =========== ========================== =======
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142 Name output file(s) format
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143 =========== ========================== =======
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144 Readseq phylip conversion phylip
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145 =========== ========================== =======
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146
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147
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148 **Downstream tools**
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149
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150 =========== ========================== =======
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151 Name output file(s) format
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152 =========== ========================== =======
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153 Rooting out tree Newick
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154 =========== ========================== =======
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155
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156
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157 ----------
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158 Input file
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159 ----------
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160
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161 Phylip file
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162 Phylip file with sequence alignments
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163
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164
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165 ----------
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166 Parameters
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167 ----------
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168
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169 Output name
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170 Output base name for the ouput files
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171
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172 Evolutionary model
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173 Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet.
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174
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175 Distance methode
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176 FastME computes a tree using a distance algorithm. You may choose this method/topologie from: TaxAdd_BalME, TaxAdd_OLSME, BIONJ (default), NJ, UNJ, NNI_BalME, NNI_OLS or SPR
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177
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178 ------------
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179 Output files
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180 ------------
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181
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182 Output_name
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183 Resulting tree at Newick format
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184
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185 Output_name.log
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186 Log file
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187
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188 ------------
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189 Dependencies
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190 ------------
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191 FastME
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192 http://www.atgc-montpellier.fr/fastme
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193
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194
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195
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196 ---------------------------------------------------
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197
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198 ---------------
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199 Working example
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200 ---------------
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201
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202 Input files
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203 ===========
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204
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205 Philip file
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206 -----------
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207
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208 ::
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209
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210 168 5125
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211 IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
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212 KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT
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213
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214 Parameters
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215 ==========
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216
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217 Output name -> Newick tree
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218
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219 Evolutionary model -> F84
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220
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221 Distance methode -> BIONJ
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222
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223 Output files
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224 ============
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225
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226 Newick tree
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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 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
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232
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233
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234 </help>
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235
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236 <citations>
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237 <!-- [HELP] As DOI or BibTex entry -->
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238 <citation type="bibtex">
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239 @article{Lefort30062015,
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240 author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier},
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241 title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program},
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242 year = {2015},
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243 doi = {10.1093/molbev/msv150},
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244 abstract ={FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, 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. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).},
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245 URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract},
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246 eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html},
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247 journal = {Molecular Biology and Evolution}
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248 }
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249
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250 </citation>
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251
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252 </citations>
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253
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254
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255 </tool>
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