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1 <tool id="sniplay_fastme" name="FastME" version="1.0.2">
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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</requirement>
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10 </requirements>
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11
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12 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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13 <version_command>
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14 <!--
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15 tool_binary -v
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16 -->
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17 </version_command>
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18
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19 <!-- [REQUIRED] The command to execute -->
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20 <command>
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21 fastme --input_data=$input_data --dna=$model --output_tree=$fileout
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22 #if str( $distance ) == "SPR":
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23 --spr
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24 #elif str( $distance )[:3] == "NNI" :
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25 #if str( $distance ) == "NNI_B" :
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26 --nni=B
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27 #else :
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28 --nni=O
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29 #end if
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30
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31 #else :
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32 --method=$distance
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33 #end if
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34 > $fileout_log
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35 </command>
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36
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37 <!-- [REQUIRED] Input files and tool parameters -->
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38 <inputs>
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39 <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
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40 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
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41 <param name="model" type="select" label="Evolutionary model" >
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42 <option value="p">p-distance</option>
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43 <option value="Y">RY symetric</option>
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44 <option value="R">RY</option>
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45 <option value="J">JC69</option>
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46 <option value="K">K2P</option>
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47 <option value="1">F81</option>
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48 <option value="4" selected="true">F84</option>
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49 <option value="T">TN93</option>
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50 <option value="L">LogDet</option>
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51 </param>
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52 <param name="distance" type="select" label="Distance methode" >
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53 <option value="B">TaxAdd_BalME</option>
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54 <option value="O">TaxAdd_OLSME</option>
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55 <option value="I" selected="true">BIONJ</option>
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56 <option value="N">NJ</option>
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57 <option value="U">UNJ</option>
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58 <option value="NNI_B">NNI_BalME</option>
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59 <option value="NNI_O">NNI_OLS</option>
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60 <option value="SPR">SPR</option>
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61 </param>
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62 </inputs>
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63
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64 <!-- [REQUIRED] Output files -->
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65 <outputs>
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66 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
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67 <data name="fileout" type="data" format="txt" label="${fileout_label}" />
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68 </outputs>
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69
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70 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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71 <stdio>
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72 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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73 <exit_code range="1:" level="fatal" />
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74 </stdio>
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75
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76 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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77 <tests>
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78 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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79
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80 <test>
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81 <param name="filein" value="phylip" />
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82 <param name="model" value="4"/>
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83 <param name="distance" value="I"/>
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84 <output name="fileout" file="newick" />
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85 <output name="fileout_log" file="newick.log" />
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86 </test>
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87
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88 <!-- [HELP] Multiple tests can be defined with different parameters -->
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89 <!--
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90 <test>
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91 </test>
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92 -->
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93 </tests>
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94
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95 <!-- [OPTIONAL] Help displayed in Galaxy -->
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96 <help>
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97
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98 .. class:: infomark
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99
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100 **Authors**
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101
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102 | Richard Desper and Olivier Gascuel,
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103 | Journal of Computational Biology 19(5), 687-705, 2002.
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104 | Molecular Biology and Evolution 21(3), 587-598, 2004.
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105 | Please cite these papers if you use this software in your publications.
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106
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107
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108 .. class:: infomark
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109
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110 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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111
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112 .. class:: infomark
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113
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114 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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115
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116 ---------------------------------------------------
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117
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118
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119 ======
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120 FastMe
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121 ======
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122
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123 -----------
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124 Description
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125 -----------
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126
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127 FastME - A distance based phylogeny reconstruction algorithm.
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128
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129 FastME showed better topological accuracy than NJ,
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130 BIONJ, WEIGHBOR and FITCH, in all evolutionary
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131 conditions we tested, which include large range
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132 deviations from molecular clock and substitution rates.
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133
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134
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135
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136 -----------------
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137 Workflow position
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138 -----------------
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139
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140 **Upstream tools**
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141
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142 =========== ========================== =======
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143 Name output file(s) format
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144 =========== ========================== =======
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145 Readseq phylip conversion phylip
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146 =========== ========================== =======
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147
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148
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149 **Downstream tools**
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150
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151 =========== ========================== =======
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152 Name output file(s) format
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153 =========== ========================== =======
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154 Rooting out tree Newick
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155 =========== ========================== =======
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156
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157
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158 ----------
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159 Input file
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160 ----------
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161
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162 Phylip file
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163 Phylip file with sequence alignments
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164
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165
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166 ----------
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167 Parameters
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168 ----------
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169
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170 Output name
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171 Output base name for the ouput files
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172
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173 Evolutionary model
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174 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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175
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176 Distance methode
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177 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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178
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179 ------------
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180 Output files
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181 ------------
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182
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183 Output_name
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184 Resulting tree at Newick format
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185
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186 Output_name.log
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187 Log file
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188
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189 ------------
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190 Dependencies
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191 ------------
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192 FastME
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193 http://www.atgc-montpellier.fr/fastme
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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 ---------------
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200 Working example
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201 ---------------
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202
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203 Input files
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204 ===========
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205
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206 Philip file
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207 -----------
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208
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209 ::
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210
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211 168 5125
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212 IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
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213 KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT
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214
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215 Parameters
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216 ==========
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217
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218 Output name -> Newick tree
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219
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220 Evolutionary model -> F84
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221
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222 Distance methode -> BIONJ
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223
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224 Output files
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225 ============
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226
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227 Newick tree
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228 -----------
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229
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230 ::
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231
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232 (((((((((((((((((((((((((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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233
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234
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235 </help>
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236
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237 </tool>
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