annotate raxml.xml @ 1:e45298aa1eb3 draft default tip

planemo upload commit 2c71c5e5604b9c05648b883fddbb163a8e03c807-dirty
author tiagoantao
date Tue, 03 Nov 2015 16:29:54 -0500
parents 66bcdd1ac9ca
children
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1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
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2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
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3 <requirements>
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4 <requirement type='package' version="8.2.4">raxml</requirement>
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5 </requirements>
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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:-1}
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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 $search_model_selector.aa_model_empirical_base_frequencies
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20 #if $search_model_selector.aa_search_matrix:
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21 --aa_search_matrix $search_model_selector.aa_search_matrix
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22 #end if
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23 #end if
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24 ## (-p)
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25 #if $random_seed:
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26 --random_seed $random_seed
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27 #else
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28 --random_seed 1234567890
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29 #end if
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30
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31 ## Optional parameters
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32
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33 #if str( $selExtraOpts.extraOptions ) == 'full':
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34 ## (-N/#)
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35 #if $selExtraOpts.number_of_runs:
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36 --number_of_runs $selExtraOpts.number_of_runs
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37 #end if
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38 #if $selExtraOpts.number_of_runs_bootstop:
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39 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop
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40 #end if
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41 ## (-a)
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42 #if $selExtraOpts.weightfile:
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43 --weightfile $selExtraOpts.weightfile
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44 #end if
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45 ## (-b)
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46 #if str ($selExtraOpts.secondary_structure_model) != "":
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47 --secondary_structure_model $selExtraOpts.secondary_structure_model
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48 #end if
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49 ## (-b)
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50 #if $selExtraOpts.bootseed:
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51 --bootseed $selExtraOpts.bootseed
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52 #end if
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53 ## (-c)
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54 #if $selExtraOpts.numofcats:
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55 --numofcats $selExtraOpts.numofcats
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56 #end if
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57 ## (-d)
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58 $selExtraOpts.search_complete_random_tree
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59 ## (-D)
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60 $selExtraOpts.ml_search_convergence
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61 ## (-e)
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62 #if $selExtraOpts.model_opt_precision:
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63 --model_opt_precision $selExtraOpts.model_opt_precision
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64 #end if
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65 ## (-E)
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66 #if $selExtraOpts.excludefile:
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67 --excludefile $selExtraOpts.excludefile
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68 #end if
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69 ## (-f)
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70 #if $selExtraOpts.search_algorithm:
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71 --search_algorithm $selExtraOpts.search_algorithm
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72 #end if
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73 ## (-F)
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74 $selExtraOpts.save_memory_cat_model
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75 ## (-g)
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76 #if $selExtraOpts.groupingfile:
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77 --groupingfile $selExtraOpts.groupingfile
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78 #end if
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79 ## (-G)
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80 #if $selExtraOpts.enable_evol_heuristics:
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81 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics
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82 #end if
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83 ## (-i)
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84 #if $selExtraOpts.initial_rearrangement_setting:
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85 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting
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86 #end if
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87 ## (-I)
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88 #if $selExtraOpts.posterior_bootstopping_analysis:
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89 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis
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90 #end if
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91 ## (-J)
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92 #if $selExtraOpts.majority_rule_consensus:
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93 --majority_rule_consensus $selExtraOpts.majority_rule_consensus
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94 #end if
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95 ## (-k)
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96 $selExtraOpts.print_branch_lengths
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97 ## (-K)
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98 #if str ($selExtraOpts.multistate_sub_model) != "":
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99 --multistate_sub_model $selExtraOpts.multistate_sub_model
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100 #end if
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101 ## (-m) - see elsewhere
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102 ## (-M)
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103 $selExtraOpts.estimate_individual_branch_lengths
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104 ## (-n) - see elsewhere
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105 ## (-o)
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106 #if $selExtraOpts.outgroup_name:
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107 --outgroup_name $selExtraOpts.outgroup_name
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108 #end if
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109 ## (-O)
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110 $selExtraOpts.disable_undetermined_seq_check
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111 ## (-P)
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112 #if $selExtraOpts.external_protein_model:
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113 --external_protein_model $selExtraOpts.external_protein_model
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114 #end if
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115 ## (-q)
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116 #if $selExtraOpts.multiple_model:
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117 --multiple_model $selExtraOpts.multiple_model
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118 #end if
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119 ## (-r)
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120 #if $selExtraOpts.constraint_file:
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121 --constraint_file $selExtraOpts.constraint_file
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122 #end if
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123 ## (-R)
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124 #if $selExtraOpts.bin_model_parameter_file:
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125 --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file
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126 #end if
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127 ## (-S)
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128 #if $selExtraOpts.secondary_structure_file:
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129 --secondary_structure_file $selExtraOpts.secondary_structure_file
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130 #end if
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131 ## (-t)
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132 #if $selExtraOpts.start_tree_file:
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133 --starting_tree $selExtraOpts.start_tree_file
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134 #end if
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135 ## (-T) see elsewhere
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136 ## (-u)
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137 $selExtraOpts.use_median_approximation
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138 ## (-U)
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139 $selExtraOpts.save_memory_gappy_alignments
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140 ## (-V)
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141 $selExtraOpts.disable_rate_heterogeneity
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142 ## (-W)
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143 #if $selExtraOpts.sliding_window_size:
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144 --sliding_window_size $selExtraOpts.sliding_window_size
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145 #end if
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146 ## (-x)
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147 #if $selExtraOpts.rapid_bootstrap_random_seed:
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148 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
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149 #end if
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150 ## (-y)
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151 $selExtraOpts.parsimony_starting_tree_only
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152 ## (-z)
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153 #if $selExtraOpts.file_multiple_trees:
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154 --file_multiple_trees $selExtraOpts.file_multiple_trees
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155 #end if
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156 #end if
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157
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158 </command>
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159 <inputs>
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160 ## (-s)
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161 <param type="data" format="fasta,phylip" name="infile" label="Source file"/>
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162 ## (-m)
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163 <conditional name="search_model_selector">
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164 <param name="model_type" type="select" label="Model Type">
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165 <option value="nucleotide" selected="true">Nucleotide</option>
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166 <option value="aminoacid">Amino Acid</option>
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167 <option value="binary">Binary</option>
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168 <option value="multistate">Multistate</option>
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169 </param>
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170 <when value="nucleotide">
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171 ## Nucleotide substitution models
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172 <param name="base_model" type="select" label="Substitution Model">
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173 <option value="GTRCAT">GTRCAT</option>
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174 <option value="GTRCATI">GTRCATI</option>
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175 <option value="GTRGAMMA" select="true">GTRGAMMA</option>
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176 <option value="GTRGAMMAI">GTRGAMMAI</option>
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177 </param>
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178 </when>
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179 ## Aminoacid substitution models
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180 <when value="aminoacid">
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181 <param name="aa_model_empirical_base_frequencies"
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182 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" />
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183 <param name="base_model" type="select" label="Substitution Model (-m)">
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184 <option value="PROTCAT" select="true">PROTCAT</option>
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185 <option value="PROTCATI">PROTCATI</option>
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186 <option value="PROTGAMMA">PROTGAMMA</option>
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187 <option value="PROTGAMMAI">PROTGAMMAI</option>
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188 </param>
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189 <param name="aa_search_matrix" type="select" label="Matrix">
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190 <option value="DAYHOFF" select="true">DAYHOFF</option>
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191 <option value="DCMUT">DCMUT</option>
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192 <option value="JTT">JTT</option>
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193 <option value="MTREV">MTREV</option>
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194 <option value="WAG">WAG</option>
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195 <option value="RTREV">RTREV</option>
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196 <option value="CPREV">CPREV</option>
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197 <option value="VT">VT</option>
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198 <option value="BLOSUM62">BLOSUM62</option>
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199 <option value="MTMAM">MTMAM</option>
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200 <option value="LG">LG</option>
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201 <option value="MTART">MTART</option>
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202 <option value="MTZOA">MTZOA</option>
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203 <option value="PMB">PMB</option>
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204 <option value="HIVB">HIVB</option>
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205 <option value="HIVW">HIVW</option>
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206 <option value="JTTDCMUT">JTTDCMUT</option>
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207 <option value="FLU">FLU</option>
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208 <option value="DUMMY">DUMMY</option>
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209 <option value="DUMMY2">DUMMY2</option>
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210 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
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211 <option value="GTR">GTR</option>
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212 </param>
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213 </when>
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214 ## Binary substitution models
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215 <when value="binary">
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216 <param name="base_model" type="select" label="Substitution Model">
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217 <option value="BINCAT">BINCAT</option>
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218 <option value="BINCATI">BINCATI</option>
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219 <option value="BINGAMMA">BINGAMMA</option>
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220 <option value="BINGAMMAI">BINGAMMAI</option>
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221 </param>
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222 </when>
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223 ## Multi-state substitution models
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224 <when value="multistate">
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225 <param name="base_model" type="select" label="Substitution Model">
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226 <option value="MULTICAT">MULTICAT</option>
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227 <option value="MULTICATI">MULTICATI</option>
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228 <option value="MULTIGAMMA">MULTIGAMMA</option>
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229 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
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230 </param>
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231 </when>
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232 </conditional>
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233 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random
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234 seed used for the parsimony inferences" />
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235 <conditional name="selExtraOpts">
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236 <param name="extraOptions" type="select" label="RAxML options to use"
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237 help="The required minimal settings are the input file and the
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238 substitution model. To specify extra options select the 'Full option list'">
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239 <option value="required">Required options only</option>
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240 <option value="full">Full option list</option>
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241 </param>
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242 <when value="full">
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243 ## (-N/#)
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244 <param name="number_of_runs" type="integer" size="8" value=""
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245 label="Number of runs" help="Specify the number of
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246 alternative runs (-N|#) on distinct starting trees In combination
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247 with the '-b' option will invoke a multiple boostrap analysis.
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248 You can add the bootstopping criteria by choosing the autoMR,
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249 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
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250 providing a number here. Bootstopping will only work in
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251 combination with '-x' or '-b'."
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252 optional="True" />
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253 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True">
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254 <option value="" selected="yes"></option>
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255 <option value="autoMR">autoMR</option>
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256 <option value="autoMRE">autoMRE</option>
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257 <option value="autoMRE_IGN">autoMRE_IGN</option>
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258 <option value="autoFC">autoFC</option>
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259 </param>
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260 ## Alphabetical Listing of Advanced Options
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261 ## (-a)
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262 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" />
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263 ## (-A)
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264 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True">
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265 <option value="" selected="yes"></option>
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266 <option value="S6A">S6A</option>
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267 <option value="S6B">S6B</option>
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268 <option value="S6C">S6C</option>
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269 <option value="S6D">S6D</option>
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270 <option value="S6E">S6E</option>
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271 <option value="S7A">S7A</option>
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272 <option value="S7B">S7B</option>
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273 <option value="S7C">S7C</option>
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274 <option value="S7D">S7D</option>
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275 <option value="S7E">S7E</option>
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276 <option value="S7F">S7F</option>
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277 <option value="S16">S16</option>
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278 <option value="S16A">S16A</option>
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279 <option value="S16B">S16B</option>
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280 </param>
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281 ## (-b)
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282 <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true' optional="True" />
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283 ## (-x)
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284 <param name="rapid_bootstrap_random_seed" type="integer" value='' size="7" label="Rapid bootstrapping random seed" 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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285 ## (-B)
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286 <param name="cutoff_threshold" type="float" size="8" label="MR Cutoff threshold" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" />
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287 ## (-c)
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288 <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" />
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289 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now.
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290 ## (-d)
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291 <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="--search_complete_random_tree" falsevalue="" display="checkboxes" label="Start ML optimization from a complete random starting tree" />
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292 ## (-D)
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293 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" />
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294 ## (-e)
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295 <param name="model_opt_precision" type="float" size="8" label="Model optimization precision" 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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296 ## (-E)
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297 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" />
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298 ## (-f)
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299 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True">
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300 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
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301 <option value="A">Compute marginal ancestral states (A)</option>
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302 <option value="b">Draw bipartition information (b)</option>
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303 <option value="c">Check if the alignment can be read (c)</option>
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304 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option>
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305 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
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306 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
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307 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
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308 <option value="j">Generate bootstrapped alignment files (j)</option>
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309 <option value="J">Compute SH-like support values for the -t tree (J)</option>
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310 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
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311 <option value="n">Compute log likelihood score for -z trees (n)</option>
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312 <option value="o">Use old slower search algorithm (o)</option>
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313 <option value="p">Stepwise MP addition of new sequences (p)</option>
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314 <option value="q">Fast quartet calculator (q)</option>
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315 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
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316 <option value="s">Split a multi-gene alignment (s)</option>
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317 <option value="S">Compute site-specific placement bias (S)</option>
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318 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
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319 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
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320 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
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321 <option value="v">Classify environmental sequences (v)</option>
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322 <option value="w">Compute ELW-test on -z trees (w)</option>
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323 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
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324 <option value="y">Classify environmental sequences into a reference tree (y)</option>
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325 </param>
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326 ## (-F)
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327 <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="--save_memory_cat_model" falsevalue="" display="checkboxes" label="ML tree searches under CAT model" 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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328 ## (-g)
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329 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" />
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330 ## (-G)
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331 <param name="enable_evol_heuristics" type="float" size="8" label="Enable the ML-based evolutionary placement algorithm heuristics" 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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332 <validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/>
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333 </param>
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334 ## (-i)
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335 <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting" optional="True" />
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336 ## (-I)
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337 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True">
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338 <option value="" selected="True"></option>
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339 <option value="autoFC">Frequency-based criterion (autoFC)</option>
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340 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
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341 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
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342 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
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343 </param>
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344 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy
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345 ## (-J)
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346 <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True">
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347 <option value="" selected="True"></option>
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348 <option value="MR">Majority-rule consensus tree (MR)</option>
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349 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
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350 <option value="STRICT">Strict consensus tree (STRICT)</option>
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351 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
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352 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
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353 </param>
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354 ## (-k)
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355 <param name="print_branch_lengths" type="boolean" checked="no" truevalue="--print_branch_lengths" falsevalue="" display="checkboxes" label="Print bootstrapped trees with branch lengths" 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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356 ## (-K)
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357 <param name="multistate_sub_model" type="select" label="Specify a
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358 multi-state substitution model" optional="True">
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359 <option value="" selected="true"></option>
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360 <option value="GTR">GTR</option>
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361 <option value="ORDERED">ORDERED</option>
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362 <option value="MK">MK</option>
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363 </param>
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364 ## (-M)
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365 <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes" label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-q)." optional="True" />
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366 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files
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367 ## (-o)
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368 <param name="outgroup_name" type="text" size="40" value="" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" />
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369 ## (-O)
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370 <param name="disable_undetermined_seq_check" type="boolean" checked="no" truevalue="--disable_undertermined_seq_check" falsevalue="" display="checkboxes" label="Disable check for completely undetermined sequence in alignment" 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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371 <param name="external_protein_model" format="txt" type="data" label="External AA substitution model" 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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372 ## (-q)
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373 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" 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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374 ## (-r)
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375 <param name="constraint_file" format="txt" type="data" label="Binary constraint tree" 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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376 ## (-R)
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377 <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" 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." />
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378 ## (-s) source file option is in the required options section
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379 ## (-S)
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380 <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" 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 '()&lt;&gt;[]{}' to define stem regions and pseudoknots."/>
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381 ## (-t)
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382 <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True" help="Specify a user starting tree file name in Newick format." />
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383 ## (-T) is hard-coded in the required options section
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384 <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" />
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385 ## (-U)
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386 <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="--save_memory_gappy_alignments" falsevalue="" display="checkboxes" label="Save memory on large gappy alignments" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" />
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387 ## (-V)
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388 <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="--disable_raite_heterogeneity" falsevalue="" display="checkboxes" label="Disable rate heterogeneity" 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" />
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389 ## (-W)
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390 <param name="sliding_window_size" type="integer" size="5" value="" label="Sliding window size" 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'" />
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391 ## (-x) - see it by the (-b)
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392 ## (-y)
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393 <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes" label="Compute a randomized parsimony starting tree only" 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." />
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394 ## (-z)
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395 <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file" 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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396 </when> ## full option list
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397 </conditional> ## END $selExtraOpts
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398 </inputs>
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399 <outputs>
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400 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
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401 ## REQUIRED
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402 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
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403 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
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404 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
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405 </data>
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406 <data format="txt" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
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407 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
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408 </data>
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409 <data format="txt" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
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410 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
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411 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
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412 </data>
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413 <data format="txt" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
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414 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
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415 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
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416 </data>
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417 ## ADVANCED
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418 <data format="txt" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
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419 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
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420 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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421 </data>
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422 <data format="txt" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
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423 <filter>(selExtraOpts['extraOptions'] == 'full')</filter>
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424 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '' or selExtraOpts['bootseed'] == '') and (selExtraOpts['search_algorithm'] == 'a')</filter>
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425 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
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426 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter>
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427 </data>
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428 <data format="txt" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
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429 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
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430 <filter>(selExtraOpts['multiple_model'] != '')</filter>
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431 </data>
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432 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
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433 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
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434 <filter>selExtraOpts['multiple_model'] is not None </filter>
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435 </data>
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436 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
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437 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
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438 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
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439 <filter>(selExtraOpts['bootseed'] == '')</filter>
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440 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
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441 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
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442 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
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443 </data>
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444 <data format="txt" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
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445 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
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446 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
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447 <filter>selExtraOpts['bootseed'] == ''</filter>
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448 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
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449 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
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450 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
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451 </data>
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452 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
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453 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
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454 <filter>(selExtraOpts['multiple_model'] is not None)</filter>
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455 </data>
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456 <data format="txt" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
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457 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
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458 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
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459 <filter>(selExtraOpts['bootseed'] == '')</filter>
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460 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
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461 <filter>(selExtraOpts['constraint_file'] is None)</filter>
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462 <filter>(selExtraOpts['groupingfile'] is None)</filter>
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463 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter>
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464 <filter>(selExtraOpts['start_tree_file'] is None)</filter>
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465 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
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466 </data>
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467 <data format="txt" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
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468 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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469 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
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470 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
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471 </data>
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472 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
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473 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
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474 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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475 </data>
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476 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
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477 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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478 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
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479 </data>
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480 <data format="txt" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
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481 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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482 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter>
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483 </data>
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484 <data format="txt" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
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485 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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486 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter>
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487 </data>
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488 <data format="txt" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
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489 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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490 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter>
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491 </data>
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492 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
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493 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
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494 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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495 </data>
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496 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
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497 <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
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498 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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499 </data>
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500 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
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501 <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
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502 <filter>selExtraOpts['extraOptions'] == "full"</filter>
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503 </data>
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504 </outputs>
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505 <tests>
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506 <test>
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507 <param name="extraOptions" value="required"/>
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508 <param name="infile" value="dna.phy"/>
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509 <param name="model_type" value="nucleotide"/>
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510 <param name="base_model" value="GTRCAT"/>
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511 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy">
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512 <output name="bestTreeReq"/>
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513 <assert_contents>
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514 <has_text_matching expression="Frog" />
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515 </assert_contents>
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516 </output>
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517 </test>
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518 </tests>
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519 <help>
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520 Title:
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521 ______
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522 Randomized Axelerated Maximum Likelihood
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523
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524 Author:
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525 _______
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526 Alexandros Stamatakis
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527
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528 Description:
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529 ____________
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530
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531 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic
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532 trees. The program is explicitly being developed to efficiently infer trees for
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533 extremely large datasets, either in terms of the number of taxa and/or the
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534 sequence length.
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535
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536 This wrapper works with the RAxML version 8.2.4.
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537
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538 URL:
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539 ____
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540 Author's page: http://www.exelixis-lab.org/
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541
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542 Help: http://groups.google.com/group/raxml
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543
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544
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545 Tool development:
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546 -----------------
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547 Oleksandr Moskalenko with adaptations from Tiago Antao.
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548
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549 </help>
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550 <citations>
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551 <citation type="doi">10.1093/bioinformatics/btu033</citation>
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552 <citation type="bibtex">
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553 @article{stamatakis2014raxml,
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554 title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
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555 author={Stamatakis, Alexandros},
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556 journal={Bioinformatics},
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557 volume={30},
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558 number={9},
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559 pages={1312--1313},
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560 year={2014},
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561 publisher={Oxford Univ Press}}
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562 </citation>
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563 </citations>
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564 </tool>