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1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
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2 <requirements>
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3 <requirement type='package' version="8.2.3">raxml</requirement>
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4 </requirements>
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5 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
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6 <command interpreter="python">raxml.py
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7 ## Required parameters
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8 ## Program name and threads are hard-coded as they are dependent on the binary and threads are specified in the Galaxy's tool configuration
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9 ## binary is hard-coded to the pthreads enabled raxml executable
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10 --binary "raxmlHPC-PTHREADS"
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11 ## (-T)
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12 --threads \${GALAXY_SLOTS:-4}
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13 ## (-s)
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14 --source $infile
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15 ## (-m)
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16 --model_type $search_model_selector.model_type
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17 --base_model $search_model_selector.base_model
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18 #if str( $search_model_selector.model_type ) == 'aminoacid':
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19 #if str( $search_model_selector.aa_model_empirical_base_frequences) == 'true':
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20 --aa_empirical_freq
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21 #end if
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22 #if $search_model_selector.aa_search_matrix:
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23 --aa_search_matrix $search_model_selector.aa_search_matrix
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24 #end if
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25 #end if
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26 ## (-p)
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27 #if $random_seed:
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28 --random_seed $random_seed
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29 #else
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30 --random_seed 1234567890
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31 #end if
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32
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33 ## Optional parameters
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34
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35 #if str( $selExtraOpts.extraOptions ) == 'full':
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36 ## (-N/#)
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37 #if $selExtraOpts.number_of_runs:
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38 --number_of_runs $selExtraOpts.number_of_runs
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39 #end if
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40 #if $selExtraOpts.number_of_runs_bootstop:
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41 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop
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42 #end if
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43 ## (-a)
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44 #if $selExtraOpts.weightfile:
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45 --weightfile $selExtraOpts.weightfile
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46 #end if
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47 ## (-b)
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48 #if str ($selExtraOpts.secondary_structure_model) != "":
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49 --secondary_structure_model $selExtraOpts.secondary_structure_model
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50 #end if
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51 ## (-b)
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52 #if $selExtraOpts.bootseed:
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53 --bootseed $selExtraOpts.bootseed
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54 #end if
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55 ## (-c)
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56 #if $selExtraOpts.numofcats:
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57 --numofcats $selExtraOpts.numofcats
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58 #end if
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59 ## (-d)
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60 #if str ($selExtraOpts.search_complete_random_tree) == "true":
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61 --search_complete_random_tree
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62 #end if
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63 ## (-D)
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64 #if str ($selExtraOpts.ml_search_convergence) == "true":
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65 --ml_search_convergence
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66 #end if
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67 ## (-e)
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68 #if $selExtraOpts.model_opt_precision:
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69 --model_opt_precision $selExtraOpts.model_opt_precision
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70 #end if
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71 ## (-E)
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72 #if $selExtraOpts.excludefile:
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73 --excludefile $selExtraOpts.excludefile
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74 #end if
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75 ## (-f)
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76 #if $selExtraOpts.search_algorithm:
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77 --search_algorithm $selExtraOpts.search_algorithm
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78 #end if
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79 ## (-F)
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80 #if str ($selExtraOpts.save_memory_cat_model) == "true":
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81 --save_memory_cat_model
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82 #end if
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83 ## (-g)
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84 #if $selExtraOpts.groupingfile:
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85 --groupingfile $selExtraOpts.groupingfile
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86 #end if
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87 ## (-G)
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88 #if $selExtraOpts.enable_evol_heuristics:
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89 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics
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90 #end if
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91 ## (-i)
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92 #if $selExtraOpts.initial_rearrangement_setting:
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93 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting
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94 #end if
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95 ## (-I)
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96 #if $selExtraOpts.posterior_bootstopping_analysis:
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97 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis
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98 #end if
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99 ## (-J)
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100 #if $selExtraOpts.majority_rule_consensus:
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101 --majority_rule_consensus $selExtraOpts.majority_rule_consensus
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102 #end if
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103 ## (-k)
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104 #if str ($selExtraOpts.print_branch_lengths) == "true":
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105 --print_branch_lengths
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106 #end if
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107 ## (-K)
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108 #if str ($selExtraOpts.multistate_sub_model) != "":
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109 --multistate_sub_model $selExtraOpts.multistate_sub_model
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110 #end if
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111 ## (-m) - see elsewhere
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112 ## (-M)
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113 #if str ($selExtraOpts.estimate_individual_branch_lengths) == "true":
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114 --estimate_individual_branch_lengths
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115 #end if
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116 ## (-n) - see elsewhere
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117 ## (-o)
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118 #if $selExtraOpts.outgroup_name:
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119 --outgroup_name $selExtraOpts.outgroup_name
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120 #end if
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121 ## (-O)
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122 #if str ($selExtraOpts.disable_undetermined_seq_check) == "true":
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123 --disable_undetermined_seq_check
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124 #end if
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125 ## (-P)
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126 #if $selExtraOpts.external_protein_model:
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127 --external_protein_model $selExtraOpts.external_protein_model
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128 #end if
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129 ## (-q)
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130 #if $selExtraOpts.multiple_model:
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131 --multiple_model $selExtraOpts.multiple_model
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132 #end if
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133 ## (-r)
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134 #if $selExtraOpts.constraint_file:
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135 --constraint_file $selExtraOpts.constraint_file
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136 #end if
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137 ## (-R)
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138 #if $selExtraOpts.bin_model_parameter_file:
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139 --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file
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140 #end if
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141 ## (-S)
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142 #if $selExtraOpts.secondary_structure_file:
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143 --secondary_structure_file $selExtraOpts.secondary_structure_file
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144 #end if
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145 ## (-t)
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146 #if $selExtraOpts.start_tree_file:
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147 --starting_tree $selExtraOpts.start_tree_file
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148 #end if
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149 ## (-T) see elsewhere
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150 ## (-u)
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151 #if str ($selExtraOpts.use_median_approximation) == "true":
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152 --use_median_approximation
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153 #end if
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154 ## (-U)
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155 #if str ($selExtraOpts.save_memory_gappy_alignments) == "true":
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156 --save_memory_gappy_alignments
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157 #end if
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158 ## (-V)
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159 #if str ($selExtraOpts.disable_rate_heterogeneity) == "true":
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160 --disable_rate_heterogeneity
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161 #end if
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162 ## (-W)
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163 #if $selExtraOpts.sliding_window_size:
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164 --sliding_window_size $selExtraOpts.sliding_window_size
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165 #end if
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166 ## (-x)
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167 #if $selExtraOpts.rapid_bootstrap_random_seed:
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168 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
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169 #end if
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170 ## (-y)
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171 #if str ($selExtraOpts.parsimony_starting_tree_only) == "true":
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172 --parsimony_starting_tree_only
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173 #end if
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174 ## (-z)
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175 #if $selExtraOpts.file_multiple_trees:
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176 --file_multiple_trees $selExtraOpts.file_multiple_trees
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177 #end if
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178 #end if
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179
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180 ##silent sys.stderr.write("DEBUG1 START\n")
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181 ##silent sys.stderr.write($selExtraOpts.extraOptions)
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182 ##silent sys.stderr.write("\nDEBUG1 END\n")
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183
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184 </command>
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185 <inputs>
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186 <conditional name="choose_input_type">
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187 <param name="input_type" type="select" label="Input type">
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188 <option value="fasta">Fasta</option>
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189 <option value="phylip">Phylip</option>
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190 </param>
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191 ## (-s)
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192 <when value="fasta">
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193 <param type="data" format="fasta" name="infile" label="Source file"/>
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194 </when>
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195 <when value="phylip">
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196 <param type="data" format="phylip" name="infile" label="Source file"/>
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197 </when>
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198 </conditional>
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199 ## (-m)
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200 <conditional name="search_model_selector">
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201 <param name="model_type" type="select" label="Model Type">
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202 <option value="nucleotide" selected="true">Nucleotide</option>
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203 <option value="aminoacid">Amino Acid</option>
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204 <option value="binary">Binary</option>
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205 <option value="multistate">Multistate</option>
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206 </param>
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207 <when value="nucleotide">
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208 ## Nucleotide substitution models
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209 <param name="base_model" type="select" label="Substitution Model (-m)">
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210 <option value="GTRCAT">GTRCAT</option>
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211 <option value="GTRCATI">GTRCATI</option>
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212 <option value="GTRGAMMA" select="true">GTRGAMMA</option>
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213 <option value="GTRGAMMAI">GTRGAMMAI</option>
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214 </param>
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215 </when>
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216 ## Aminoacid substitution models
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217 <when value="aminoacid">
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218 <param name="aa_model_empirical_base_frequences"
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219 type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use empirical base frequencies in AA models" />
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220 <param name="base_model" type="select" label="Substitution Model (-m)">
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221 <option value="PROTCAT" select="true">PROTCAT</option>
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222 <option value="PROTCATI">PROTCATI</option>
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223 <option value="PROTGAMMA">PROTGAMMA</option>
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224 <option value="PROTGAMMAI">PROTGAMMAI</option>
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225 </param>
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226 <param name="aa_search_matrix" type="select" label="Matrix">
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227 <option value="DAYHOFF" select="true">DAYHOFF</option>
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228 <option value="DCMUT">DCMUT</option>
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229 <option value="JTT">JTT</option>
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230 <option value="MTREV">MTREV</option>
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231 <option value="WAG">WAG</option>
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232 <option value="RTREV">RTREV</option>
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233 <option value="CPREV">CPREV</option>
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234 <option value="VT">VT</option>
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235 <option value="BLOSUM62">BLOSUM62</option>
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236 <option value="MTMAM">MTMAM</option>
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237 <option value="LG">LG</option>
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238 <option value="MTART">MTART</option>
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239 <option value="MTZOA">MTZOA</option>
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240 <option value="PMB">PMB</option>
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241 <option value="HIVB">HIVB</option>
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242 <option value="HIVW">HIVW</option>
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243 <option value="JTTDCMUT">JTTDCMUT</option>
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244 <option value="FLU">FLU</option>
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245 <option value="DUMMY">DUMMY</option>
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246 <option value="DUMMY2">DUMMY2</option>
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247 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
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248 <option value="GTR">GTR</option>
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249 </param>
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250 </when>
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251 ## Binary substitution models
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252 <when value="binary">
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253 <param name="base_model" type="select" label="Substitution Model (-m)">
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254 <option value="BINCAT">BINCAT</option>
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255 <option value="BINCATI">BINCATI</option>
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256 <option value="BINGAMMA">BINGAMMA</option>
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257 <option value="BINGAMMAI">BINGAMMAI</option>
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258 </param>
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259 </when>
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260 ## Multi-state substitution models
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261 <when value="multistate">
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262 <param name="base_model" type="select" label="Substitution Model (-m)">
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263 <option value="MULTICAT">MULTICAT</option>
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264 <option value="MULTICATI">MULTICATI</option>
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265 <option value="MULTIGAMMA">MULTIGAMMA</option>
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266 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
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267 </param>
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268 </when>
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269 </conditional>
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270 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random
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271 seed used for the parsimony inferences (-p)" />
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272 <conditional name="selExtraOpts">
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273 <param name="extraOptions" type="select" label="RAxML options to use"
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274 help="The required minimal settings are the input file and the
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275 substitution model. To specify extra options select the 'Full option list'">
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276 <option value="required">Required options only</option>
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277 <option value="full">Full option list</option>
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278 </param>
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279 <when value="full">
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280 ## (-N/#)
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281 <param name="number_of_runs" type="integer" size="8" value=""
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282 label="Number of runs (-N|#)" help="Specify the number of
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283 alternative runs on distinct starting trees In combination
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284 with the '-b' option will invoke a multiple boostrap analysis.
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285 You can add the bootstopping criteria by choosing the autoMR,
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286 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
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287 providing a number here. Bootstopping will only work in
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288 combination with '-x' or '-b'."
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289 optional="True" />
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290 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs (-N/#)" optional="True">
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291 <option value="" selected="yes"></option>
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292 <option value="autoMR">autoMR</option>
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293 <option value="autoMRE">autoMRE</option>
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294 <option value="autoMRE_IGN">autoMRE_IGN</option>
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295 <option value="autoFC">autoFC</option>
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296 </param>
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297 ## Alphabetical Listing of Advanced Options
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298 ## (-a)
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299 <param format="txt" name="weightfile" type="data" label="Column weight file (-a)" optional="True" />
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300 ## (-A)
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301 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model (-A)" optional="True">
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302 <option value="" selected="yes"></option>
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303 <option value="S6A">S6A</option>
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304 <option value="S6B">S6B</option>
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305 <option value="S6C">S6C</option>
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306 <option value="S6D">S6D</option>
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307 <option value="S6E">S6E</option>
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308 <option value="S7A">S7A</option>
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309 <option value="S7B">S7B</option>
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310 <option value="S7C">S7C</option>
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311 <option value="S7D">S7D</option>
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312 <option value="S7E">S7E</option>
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313 <option value="S7F">S7F</option>
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314 <option value="S16">S16</option>
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315 <option value="S16A">S16A</option>
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316 <option value="S16B">S16B</option>
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317 </param>
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318 ## (-b)
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319 <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping (-b)" refresh_on_change='true' optional="True" />
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320 ## (-x)
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321 <param name="rapid_bootstrap_random_seed" type="integer" value='' size="7" label="Rapid bootstrapping random seed (-x)" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." />
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322 ## (-B)
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323 <param name="cutoff_threshold" type="float" size="8" label="MR Cutoff threshold (-B)" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" />
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324 ## (-c)
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325 <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX (-c)" optional="True" />
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326 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now.
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327 ## (-d)
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328 <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="true" falsevalue="false" display="checkboxes" label="Start ML optimization from a complete random starting tree (-d)" />
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329 ## (-D)
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330 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="true" falsevalue="false" label="ML search convergence criterion (-D)" />
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331 ## (-e)
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332 <param name="model_opt_precision" type="float" size="8" label="Model optimization precision (-e)" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" />
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333 ## (-E)
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334 <param format="txt" name="excludefile" type="data" label="Exclude file (-E)" optional="True" />
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335 ## (-f)
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336 <param name="search_algorithm" type="select" label="Algorithm to execute (-f)" optional="True">
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337 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
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338 <option value="A">Compute marginal ancestral states (A)</option>
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339 <option value="b">Draw bipartition information (b)</option>
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340 <option value="c">Check if the alignment can be read (c)</option>
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341 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option>
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342 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
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343 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
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344 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
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345 <option value="j">Generate bootstrapped alignment files (j)</option>
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346 <option value="J">Compute SH-like support values for the -t tree (J)</option>
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347 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
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348 <option value="n">Compute log likelihood score for -z trees (n)</option>
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349 <option value="o">Use old slower search algorithm (o)</option>
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350 <option value="p">Stepwise MP addition of new sequences (p)</option>
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351 <option value="q">Fast quartet calculator (q)</option>
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352 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
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353 <option value="s">Split a multi-gene alignment (s)</option>
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354 <option value="S">Compute site-specific placement bias (S)</option>
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355 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
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356 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
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357 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
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358 <option value="v">Classify environmental sequences (v)</option>
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359 <option value="w">Compute ELW-test on -z trees (w)</option>
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360 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
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361 <option value="y">Classify environmental sequences into a reference tree (y)</option>
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362 </param>
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363 ## (-F)
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364 <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="ML tree searches under CAT model (-F)" optional="True" help="ML tree searches under CAT model for very large trees without switching to GAMMA in the end (saves memory) and no thorough optimization under GAMMA" />
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365 ## (-g)
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366 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree (-g)" optional="True" />
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367 ## (-G)
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368 <param name="enable_evol_heuristics" type="float" size="8" label="Enable the ML-based evolutionary placement algorithm heuristics (-G)" help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)." optional="True" >
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369 <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/>
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370 </param>
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371 ## (-i)
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372 <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting (-i)" optional="True" />
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373 ## (-I)
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374 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis (-I)" optional="True">
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375 <option value="" selected="True"></option>
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376 <option value="autoFC">Frequency-based criterion (autoFC)</option>
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377 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
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378 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
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379 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
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380 </param>
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381 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy
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382 ## (-J)
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383 <param name="majority_rule_consensus" type="select" label="Compute consensus tree (-J)" optional="True">
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384 <option value="" selected="True"></option>
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385 <option value="MR">Majority-rule consensus tree (MR)</option>
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386 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
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387 <option value="STRICT">Strict consensus tree (STRICT)</option>
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388 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
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389 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
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390 </param>
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391 ## (-k)
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392 <param name="print_branch_lengths" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Print bootstrapped trees with branch lengths (-k)" help="Specifies that bootstrapped trees should be printed with branch lengths. The bootstraps will run a bit longer, because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively." optional="True" />
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393 ## (-K)
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394 <param name="multistate_sub_model" type="select" label="Specify a
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395 multi-state substitution model (-K)" optional="True">
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396 <option value="" selected="true"></option>
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397 <option value="GTR">GTR</option>
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398 <option value="ORDERED">ORDERED</option>
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399 <option value="MK">MK</option>
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400 </param>
|
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401 ## (-M)
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402 <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Estimate individual per-partition branch lengths (-M)" help="Only has effect with a partition file (-q)." optional="True" />
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403 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files
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404 ## (-o)
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405 <param name="outgroup_name" type="text" size="40" value="" label="Outgroup name (-o)" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" />
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406 ## (-O)
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407 <param name="disable_undetermined_seq_check" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Disable check for completely undetermined sequence in alignment (-O)" optional="True" help="Disable the check for completely undetermined sequence in alignment. The program will not exit with an error message when '-O' is specified." />
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408 <param name="external_protein_model" format="txt" type="data" label="External AA substitution model (-P)" help="Specify the file name of a user-defined AA (Protein) substitution model. This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies." optional="True" />
|
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409 ## (-q)
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410 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions (-q)" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." />
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411 ## (-r)
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412 <param name="constraint_file" format="txt" type="data" label="Binary constraint tree (-r)" optional="True" help="Specify the file name of a binary constraint tree. This tree does not need to be comprehensive, i.e. must not contain all taxa." />
|
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413 ## (-R)
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414 <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file (-R)" optional="True" help="Specify the file name of a binary model parameter file that has previously been generated with RAxML using the '-f e' tree evaluation option." />
|
|
|
415 ## (-s) source file option is in the required options section
|
|
|
416 ## (-S)
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|
417 <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file (-S)" optional="True" help="Specify the name of a secondary structure file. The file can contain '.' for alignment columns that do not form part of a stem and characters '()<>[]{}' to define stem regions and pseudoknots."/>
|
|
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418 ## (-t)
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419 <param name="start_tree_file" format="txt" type="data" label="Starting tree file (-t)" optional="True" help="Specify a user starting tree file name in Newick format." />
|
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420 ## (-T) is hard-coded in the required options section
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|
421 <param name="use_median_approximation" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use the median for the discrete approximation (-u)" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" />
|
|
|
422 ## (-U)
|
|
|
423 <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Save memory on large gappy alignments (-U)" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" />
|
|
|
424 ## (-V)
|
|
|
425 <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Disable rate heterogeneity (-V)" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity." optional="True" />
|
|
|
426 ## (-W)
|
|
|
427 <param name="sliding_window_size" type="integer" size="5" value="" label="Sliding window size (-W)" optional="True" help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites'" />
|
|
|
428 ## (-x) - see it by the (-b)
|
|
|
429 ## (-y)
|
|
|
430 <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Compute a randomized parsimony starting tree only (-y)" optional="True" help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." />
|
|
|
431 ## (-z)
|
|
|
432 <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file (-z)" help="Specify the file name of a file containing multiple trees e.g. from a bootstrap that shall be used to draw bipartition values onto a tree provided with '-t', It can also be used to compute per site log likelihoods in combination with '-f g' and to read a bunch of trees for '-f h', '-f m' and '-f n'." optional="True" />
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|
433 </when> ## full option list
|
|
|
434 </conditional> ## END $selExtraOpts
|
|
|
435 </inputs>
|
|
|
436 <outputs>
|
|
|
437 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
|
|
|
438 ## REQUIRED
|
|
|
439 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
|
|
|
440 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
|
|
|
441 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
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|
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442 </data>
|
|
|
443 <data format="txt" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
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|
444 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
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|
|
445 </data>
|
|
|
446 <data format="txt" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
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|
447 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
|
|
|
448 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
|
|
|
449 </data>
|
|
|
450 <data format="txt" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
|
|
|
451 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
|
|
|
452 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
|
|
|
453 </data>
|
|
|
454 ## ADVANCED
|
|
|
455 <data format="txt" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
|
|
|
456 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
|
|
|
457 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
458 </data>
|
|
|
459 <data format="txt" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
|
|
|
460 <filter>(selExtraOpts['extraOptions'] == 'full')</filter>
|
|
|
461 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '' or selExtraOpts['bootseed'] == '') and (selExtraOpts['search_algorithm'] == 'a')</filter>
|
|
|
462 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
|
|
|
463 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter>
|
|
|
464 </data>
|
|
|
465 <data format="txt" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
|
|
|
466 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
467 <filter>(selExtraOpts['multiple_model'] != '')</filter>
|
|
|
468 </data>
|
|
|
469 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
|
|
|
470 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
471 <filter>selExtraOpts['multiple_model'] is not None </filter>
|
|
|
472 </data>
|
|
|
473 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
|
|
|
474 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
475 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
|
|
|
476 <filter>(selExtraOpts['bootseed'] == '')</filter>
|
|
|
477 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
|
|
|
478 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
|
|
|
479 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
|
|
|
480 </data>
|
|
|
481 <data format="txt" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
|
|
|
482 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
483 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
|
|
|
484 <filter>selExtraOpts['bootseed'] == ''</filter>
|
|
|
485 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
|
|
|
486 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
|
|
|
487 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
|
|
|
488 </data>
|
|
|
489 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
|
|
|
490 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
491 <filter>(selExtraOpts['multiple_model'] is not None)</filter>
|
|
|
492 </data>
|
|
|
493 <data format="txt" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
|
|
|
494 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
495 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
|
|
|
496 <filter>(selExtraOpts['bootseed'] == '')</filter>
|
|
|
497 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
|
|
|
498 <filter>(selExtraOpts['constraint_file'] is None)</filter>
|
|
|
499 <filter>(selExtraOpts['groupingfile'] is None)</filter>
|
|
|
500 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter>
|
|
|
501 <filter>(selExtraOpts['start_tree_file'] is None)</filter>
|
|
|
502 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
|
|
|
503 </data>
|
|
|
504 <data format="txt" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
|
|
|
505 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
506 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
|
|
|
507 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
|
|
|
508 </data>
|
|
|
509 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
|
|
|
510 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
|
|
|
511 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
512 </data>
|
|
|
513 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
|
|
|
514 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
515 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
|
|
|
516 </data>
|
|
|
517 <data format="txt" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
|
|
|
518 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
519 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter>
|
|
|
520 </data>
|
|
|
521 <data format="txt" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
|
|
|
522 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
523 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter>
|
|
|
524 </data>
|
|
|
525 <data format="txt" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
|
|
|
526 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
527 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter>
|
|
|
528 </data>
|
|
|
529 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
|
|
|
530 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
|
|
|
531 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
532 </data>
|
|
|
533 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
|
|
|
534 <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
|
|
|
535 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
536 </data>
|
|
|
537 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
|
|
|
538 <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
|
|
|
539 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
540 </data>
|
|
|
541 </outputs>
|
|
|
542 <tests>
|
|
|
543 <test>
|
|
|
544 <!-- test1 -->
|
|
|
545 <!-- raxmlHPC-PTHREADS-SSE3 -T 4 -s raxml_binary.phy -n galaxy -m BINCAT -p 12345 -->
|
|
|
546 <param name="extraOptions" value="required"/>
|
|
|
547 <param name="infile" value="raxml/inputs/raxml_binary.phy"/>
|
|
|
548 <param name="model_type" value="binary"/>
|
|
|
549 <param name="base_model" value="BINCAT"/>
|
|
|
550 <output name="bestTreeReq" file="raxml/test1/RAxML_bestTree.galaxy"/>
|
|
|
551 <output name="parsimonyTreeReq" file="raxml/test1/RAxML_parsimonyTree.galaxy"/>
|
|
|
552 <!-- <output name="info" file="raxml/test1/RAxML_info.galaxy"/> -->
|
|
|
553 <output name="logReq" file="raxml/test1/RAxML_log.galaxy">
|
|
|
554 <assert_contents>
|
|
|
555 <has_line_matching expression="^0\\..*" />
|
|
|
556 </assert_contents>
|
|
|
557 </output>
|
|
|
558 <output name="resultReq" file="raxml/test1/RAxML_result.galaxy">
|
|
|
559 <assert_contents>
|
|
|
560 <has_line_matching expression="Overall\sexecution\stime.*" />
|
|
|
561 </assert_contents>
|
|
|
562 </output>
|
|
|
563 </test>
|
|
|
564 <!--
|
|
|
565 <test>
|
|
|
566 -->
|
|
|
567 <!-- test2 -->
|
|
|
568 <!-- raxmlHPC-PTHREADS-SSE3 -T 4 -s raxml_binary.phy -n galaxy -m BINCAT -p 12345 -->
|
|
|
569 <!--
|
|
|
570 <param name="infile" value="raxml/inputs/raxml_binary.phy"/>
|
|
|
571 <param name="search_model_selector" value="binary"/>
|
|
|
572 <param name="base_model" value="BINCAT"/>
|
|
|
573 <output name="info" file="raxml/test1/RAxML_info.galaxy"/>
|
|
|
574 <output name="logReq" file="raxml/test1/RAxML_log.galaxy"/>
|
|
|
575 <output name="bestTreeReq" file="raxml/test1/RAxML_bestTree.galaxy"/>
|
|
|
576 <output name="parsimonyTreeReq" file="raxml/test1/RAxML_parsimonyTree.galaxy"/>
|
|
|
577 <output name="resultReq" file="raxml/test1/RAxML_result.galaxy"/>
|
|
|
578 -->
|
|
|
579 <!--
|
|
|
580 </test>
|
|
|
581 -->
|
|
|
582 </tests>
|
|
|
583 <help>
|
|
|
584 Title:
|
|
|
585 ______
|
|
|
586 Randomized Axelerated Maximum Likelihood
|
|
|
587
|
|
|
588 Author:
|
|
|
589 _______
|
|
|
590 Alexandros Stamatakis <alexandros.stamatakis@h-its.org>
|
|
|
591
|
|
|
592 Description:
|
|
|
593 ____________
|
|
|
594
|
|
|
595 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic
|
|
|
596 trees. The program is explicitly being developed to efficiently infer trees for
|
|
|
597 extremely large datasets, either in terms of the number of taxa and/or the
|
|
|
598 sequence length.
|
|
|
599
|
|
|
600 This wrapper works with the RAxML version 8.2.3.
|
|
|
601
|
|
|
602 URL:
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603 ____
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604 Author's page: http://www.exelixis-lab.org/
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605
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606 Help: http://groups.google.com/group/raxml
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607
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608
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609 Tool development:
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610 -----------------
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611 Oleksandr Moskalenko with adaptations from Tiago Antao.
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612
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613 </help>
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614 <citations>
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615 <citation type="doi">10.1093/bioinformatics/btu033</citation>
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616 <citation type="bibtex">
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617 @article{stamatakis2014raxml,
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618 title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
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619 author={Stamatakis, Alexandros},
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620 journal={Bioinformatics},
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621 volume={30},
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622 number={9},
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623 pages={1312--1313},
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624 year={2014},
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625 publisher={Oxford Univ Press}}
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626 </citation>
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627 </citations>
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628 </tool>
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