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1 <tool id="Arpa" name="Arpa">
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2
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3 <description>Arpa</description>
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4 <requirements>
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5 <requirement type="package" version="1.0.0">arpa_package</requirement>
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6 </requirements>
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7 <command interpreter="ruby">
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8 wrapper_arpa.rb $output $input
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9 "$tipo_script.data_type $aligner $trimmer $tipo_script.type_statistic_method.type_tree.program
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10 #if $tipo_script.type_statistic_method.tree_select != "bayesian":
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11 --bp $tipo_script.type_statistic_method.type_tree.bootstrap
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12 #end if
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13 #if $tipo_script.type_statistic_method.tree_select != "neighbor" and $tipo_script.type_statistic_method.tree_select != "maxparsi" and $tipo_script.type_statistic_method.type_tree.program != "-p phylip_ml":
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14 $tipo_script.type_statistic_method.type_tree.evolut_model --nb $tipo_script.type_statistic_method.type_tree.nb_categ
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15 #end if
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16 #if $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
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17 --a $tipo_script.type_statistic_method.type_tree.gam_distribution
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18 #end if
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19 #if $tipo_script.data_type == "-t aa" and $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
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20 --in $tipo_script.type_statistic_method.type_tree.proportion
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21 #end if
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22 #if $tipo_script.type_statistic_method.tree_select == "bayesian":
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23 --ngen $tipo_script.type_statistic_method.type_tree.ngeneration $tipo_script.type_statistic_method.type_tree.chains_run $tipo_script.type_statistic_method.type_tree.independent_analyses $tipo_script.type_statistic_method.type_tree.variation_model --printfreq $tipo_script.type_statistic_method.type_tree.chain_printed --samplefreq $tipo_script.type_statistic_method.type_tree.markov_chain --burnin $tipo_script.type_statistic_method.type_tree.samples_discarded
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24 #end if
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25 #if $tipo_script.type_statistic_method.type_tree.program == "-p raxml":
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26 $tipo_script.type_statistic_method.type_tree.subst_rates
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27 #end if
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28 #if $tipo_script.data_type == "-t aa" and $tipo_script.type_statistic_method.type_tree.program == "-p raxml":
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29 $tipo_script.type_statistic_method.type_tree.freq_raxml_aa
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30 #end if
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31 #if $tipo_script.data_type == "-t nucl" and $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
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32 --kappa $tipo_script.type_statistic_method.type_tree.trans_ratio
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33 #end if
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34 "
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35 </command>
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36
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37 <inputs>
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38
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39 <param name="input" type="data" format="fasta" label="Fasta file"/>
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40
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41 <param name="aligner" type="select" label="Multiple Alignment">
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42 <option value="-a alignm">Align-m</option>
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43 <option selected="True" value="-a clustalw">Clustalw</option>
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44 <option value="-a mafft">Mafft</option>
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45 <option value="-a muscle">Muscle</option>
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46 <option value="-a probcons">Probcons</option>
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47 <option value="-a tcoffee">T-Coffee</option>
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48 </param>
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49
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50 <param name="trimmer" type="select" label="Alignment trimming">
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51 <option value="-c gblocks">G Blocks</option>
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52 <option selected="True" value="-c total">Total</option>
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53 <option value="-c trimal">TrimAl</option>
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54 </param>
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55
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56 <conditional name="tipo_script">
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57
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58 <param name="data_type" type="select" label="Select Search">
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59 <option value="">Select</option>
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60 <option value="-t aa">Amino acid sequences</option>
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61 <option value="-t nucl">DNA sequences</option>
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62 </param>
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63
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64 <when value="-t aa">
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65
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66 <conditional name="type_statistic_method">
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67
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68 <param name="tree_select" type="select" label="Phylogenetic tree">
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69 <option value="">Select</option>
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70 <option value="maxlike">Maximum Likelihood</option>
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71 <option value="neighbor">Neighbor-joining</option>
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72 <option value="maxparsi">Maximum Parsimony</option>
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73 <option value="bayesian">Bayesian Inference</option>
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74 </param>
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75
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76 <when value="maxlike">
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77 <conditional name="type_tree">
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78 <param name="program" type="select" label="Maximum Likelihood">
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79 <option value="">Select</option>
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80 <option value="-p phyml">PhyML</option>
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81 <option value="-p raxml">RAxML</option>
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82 <option value="-p garli">GARLI</option>
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83 <option value="-p phylip_ml">PHYLIP_ML</option>
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84 <option value="-p weighbor">WEIGHBOR</option>
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85 </param>
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86
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87 <when value="-p phyml">
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88 <param name="evolut_model" type="select" label="Evolutionary model">
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89 <option value="--mg BLOSUM62">BLOSUM62</option>
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90 <option value="--mg CPREV">CPREV</option>
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91 <option value="--mg Dayhoff">Dayhoff</option>
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92 <option value="--mg DCMut">DCMut</option>
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93 <option value="--mg GTR">GTR</option>
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94 <option selected="True" value="--mg JTT">JTT</option>
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95 <option value="--mg MtMam">MtMam</option>
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96 <option value="--mg MtREV">MtREV</option>
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97 <option value="--mg RtREV">RtREV</option>
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98 <option value="--mg VT">VT</option>
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99 <option value="--mg WAG">WAG</option>
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100 </param>
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101
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102 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
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103
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104 <param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>
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105
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106 <param name="gam_distribution" label="Gamma Distribution [1 - 20]" type="integer" value="1"/>
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107
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108 <param name="proportion" label="proportion of invariable sites [0 - 20]" type="integer" value="0"/>
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109
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110 </when>
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111
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112 <when value="-p raxml">
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113 <param name="evolut_model" type="select" label="Evolutionary model">
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114 <option value="--mg BLOSUM62">BLOSUM62</option>
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115 <option value="--mg CPREV">CPREV</option>
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116 <option selected="True" value="--mg Dayhoff">Dayhoff</option>
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117 <option value="--mg DCMut">DCMut</option>
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118 <option value="--mg GTR">GTR</option>
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119 <option value="--mg JTT">JTT</option>
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120 <option value="--mg MtMam">MtMam</option>
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121 <option value="--mg MtREV">MtREV</option>
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122 <option value="--mg RtREV">RtREV</option>
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123 <option value="--mg VT">VT</option>
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124 <option value="--mg WAG">WAG</option>
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125 </param>
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126
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127 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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128
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129 <param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>
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130
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131 <param name="subst_rates" type="select" label="Substitution Rates">
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132 <option value="--rates_raxml_aa PROTGAMMA">PROTGAMMA</option>
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133 </param>
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134
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135 <param name="freq_raxml_aa" type="select" label="Empirical Base Frequencies">
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136 <option value="--freq_raxml_aa F">F</option>
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137 </param>
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138
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139 </when>
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140
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141
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142 <when value="-p garli">
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143 <param name="evolut_model" type="select" label="Evolutionary model">
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144 <option value="--mg Dayhoff">Dayhoff</option>
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145 <option value="--mg jones">jones</option>
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146 <option value="--mg MtMam">MtMam</option>
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147 <option value="--mg MtREV">MtREV</option>
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148 <option selected="True" value="--mg poisson">poisson</option>
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149 <option value="--mg WAG">WAG</option>
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150 </param>
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151
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152 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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153
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154 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
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155
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156 </when>
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157
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158 <when value="-p phylip_ml">
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159 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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160 </when>
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161
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162
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163 <when value="-p weighbor">
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164 <param name="evolut_model" type="select" label="Evolutionary model">
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165 <option value="--mg BLOSUM62">BLOSUM62</option>
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166 <option value="--mg Dayhoff">Dayhoff</option>
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167 <option value="--mg JTT">JTT</option>
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168 <option value="--mg MTREV24">MTREV24</option>
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169 <option value="--mg VT">VT</option>
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170 <option selected="True" value="--mg WAG">WAG</option>
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171 </param>
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172
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173 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
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174
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175 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="6"/>
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176
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177 </when>
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178
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179 </conditional>
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180
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181 </when>
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182
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183
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184 <when value="neighbor">
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185 <conditional name="type_tree">
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186 <param name="program" type="select" label="Neighbor-joining">
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187 <option selected="True" value="-p phylip_nj">PHYLIP_NJ</option>
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188 </param>
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189
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190 <when value="-p phylip_nj">
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191 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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192 </when>
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193
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194 </conditional>
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195 </when>
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196
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197 <when value="maxparsi">
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198 <conditional name="type_tree">
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199 <param name="program" type="select" label="Maximum Parsimony">
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200 <option selected="True" value="-p phylip_mp">PHYLIP_MP</option>
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201 </param>
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202
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203 <when value="-p phylip_mp">
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204 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="500"/>
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205 </when>
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206
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207 </conditional>
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208 </when>
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209
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210 <when value="bayesian">
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211 <conditional name="type_tree">
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212 <param name="program" type="select" label="Bayesian Inference">
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213 <option value="-p mrbayes">MrBayes</option>
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214 </param>
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215
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216 <when value="-p mrbayes">
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217 <param name="evolut_model" type="select" label="Evolutionary model">
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218 <option value="--mg BLOSUM">BLOSUM</option>
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219 <option value="--mg CPREV">CPREV</option>
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220 <option value="--mg Dayhoff">Dayhoff</option>
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221 <option value="--mg equalin">equalin</option>
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222 <option value="--mg GTR">GTR</option>
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223 <option value="--mg jones">jones</option>
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224 <option value="--mg MtMam">MtMam</option>
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225 <option value="--mg MtREV">MtREV</option>
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226 <option selected="True" value="--mg poisson">poisson</option>
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227 <option value="--mg RtREV">RtREV</option>
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228 <option value="--mg VT">VT</option>
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229 <option value="--mg WAG">WAG</option>
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230 </param>
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231
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232 <param name="ngeneration" label="Generation Number[10 - 1000000]" type="integer" value="1000"/>
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233
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234 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
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235
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236 <param name="chain_printed" label="Chain Printed[1 - 1000]" type="integer" value="100"/>
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237
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238 <param name="markov_chain" label="Markov Chain Sampled[1 - 1000]" type="integer" value="100"/>
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239
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240 <param name="chains_run" type="select" label="Chains Run">
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241 <option value="--nchains 0">0</option>
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242 <option value="--nchains 1">1</option>
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243 <option value="--nchains 2">2</option>
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244 <option value="--nchains 3">3</option>
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245 <option selected="True" value="--nchains 4">4</option>
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246 </param>
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247
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248 <param name="samples_discarded" label="Number of Samples Discarded[10 - 1000]" type="integer" value="10"/>
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249
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250 <param name="independent_analyses" type="select" label="Number of independent Analyses">
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251 <option selected="True" value="--nruns 2">2</option>
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252 </param>
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253
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254 <param name="variation_model" type="select" label="Rate Variation Model">
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255 <option selected="True" value="--rates_mrbayes Equal">Equal</option>
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256 </param>
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257 </when>
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258 </conditional>
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259 </when>
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260 </conditional>
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261 </when>
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262
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263
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264
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265 <when value="-t nucl">
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266
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267 <conditional name="type_statistic_method">
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268 <param name="tree_select" type="select" label="Phylogenetic tree">
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269 <option value="">Select</option>
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270 <option value="maxlike">Maximum Likelihood</option>
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271 <option value="neighbor">Neighbor-joining</option>
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272 <option value="maxparsi">Maximum Parsimony</option>
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273 <option value="bayesian">Bayesian Inference</option>
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274 </param>
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275 <when value="maxlike">
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276 <conditional name="type_tree">
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277
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278 <param name="program" type="select" label="Maximum Likelihood">
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279 <option value="">Select</option>
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280 <option value="-p phyml">PhyML</option>
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281 <option value="-p raxml">RAxML</option>
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282 <option value="-p garli">GARLI</option>
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283 <option value="-p phylip_ml">PHYLIP_ML</option>
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284 <option value="-p weighbor">WEIGHBOR</option>
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285 </param>
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286
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287 <when value="-p phyml">
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288 <param name="evolut_model" type="select" label="Evolutionary model">
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289 <option value="--mg Custom">Custom</option>
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290 <option value="--mg F81">F81</option>
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291 <option value="--mg F84">F84</option>
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292 <option value="--mg GTR">GTR</option>
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293 <option selected="True" value="--mg HKY">HKY</option>
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294 <option value="--mg JC69">JC69</option>
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295 <option value="--mg K2P">K2P</option>
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296 <option value="--mg TN93">TN93</option>
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297 </param>
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298
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299 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
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300
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301 <param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>
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302
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303 <param name="gam_distribution" label="Gamma Distribution [1 - 20]" type="integer" value="1"/>
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304
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305 <param name="trans_ratio" label="Transition / transversion ratio [0 - 20]" type="integer" value="4"/>
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306
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307 </when>
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308
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309 <when value="-p raxml">
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310 <param name="evolut_model" type="select" label="Evolutionary model">
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311 <option selected="True" value="--mg GTR">GTR</option>
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312 </param>
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313
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314 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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315
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316 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
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317
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318 <param name="subst_rates" type="select" label="Substitution Rates">
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319 <option selected="True" value="--rates_raxml_nucl GAMMA">GAMMA</option>
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320 </param>
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321
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322 </when>
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323
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324
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325 <when value="-p garli">
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326 <param name="evolut_model" type="select" label="Evolutionary model">
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327 <option value="--mg F81">F81</option>
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328 <option value="--mg GTR">GTR</option>
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329 <option value="--mg HKY">HKY</option>
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330 <option selected="True" value="--mg JC">JC</option>
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331 <option value="--mg K3P">K3P</option>
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332 <option value="--mg K80">K80</option>
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333 <option value="--mg SYM">SYM</option>
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334 <option value="--mg TIM">TIM</option>
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335 <option value="--mg TrN">TrN</option>
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336 <option value="--mg TVM">TVM</option>
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337 </param>
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338
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339 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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340
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341 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
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342
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343 </when>
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344
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345 <when value="-p phylip_ml">
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346 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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347 </when>
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348
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349
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350 <when value="-p weighbor">
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351 <param name="evolut_model" type="select" label="Evolutionary model">
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352 <option value="--mg GTR">GTR</option>
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353 <option selected="True" value="--mg HKY">HKY</option>
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354 <option value="--mg TN">TN</option>
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355 </param>
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356
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357 <param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>
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358
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359 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
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360
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361 </when>
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362
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363 </conditional>
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364 </when>
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365
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366
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367 <when value="neighbor">
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368 <conditional name="type_tree">
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369 <param name="program" type="select" label="Neighbor-joining">
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370 <option selected="True" value="-p phylip_nj">PHYLIP_NJ</option>
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371 </param>
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372
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373 <when value="-p phylip_nj">
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374 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
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375 </when>
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376
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377 </conditional>
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378 </when>
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379
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380 <when value="maxparsi">
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381 <conditional name="type_tree">
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382 <param name="program" type="select" label="Maximum Parsimony">
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383 <option selected="True" value="-p phylip_mp">PHYLIP_MP</option>
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384 </param>
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385
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386 <when value="-p phylip_mp">
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387 <param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="500"/>
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388 </when>
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389
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390 </conditional>
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391 </when>
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392
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393 <when value="bayesian">
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394 <conditional name="type_tree">
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395 <param name="program" type="select" label="Bayesian Inference">
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396 <option selected="True" value="-p mrbayes">MrBayes</option>
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397 </param>
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398
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399 <when value="-p mrbayes">
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400 <param name="evolut_model" type="select" label="Evolutionary model">
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401 <option value="--mg F81">F81</option>
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402 <option value="--mg GTR">GTR</option>
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403 <option value="--mg HKY">HKY</option>
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404 <option value="--mg HKY85">HKY85</option>
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405 <option selected="--mg True" value="JC">JC</option>
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406 <option value="--mg JC69">JC69</option>
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407 <option value="--mg K3P">K3P</option>
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408 <option value="--mg K80">K80</option>
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409 <option value="--mg SYM">SYM</option>
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410 <option value="--mg TIM">TIM</option>
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411 <option value="--mg TrN">TrN</option>
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412 <option value="--mg TVM">TVM</option>
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413 </param>
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414
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415 <param name="ngeneration" label="Generation Number[10 - 1000000]" type="integer" value="1000"/>
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416
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417 <param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>
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418
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419 <param name="chain_printed" label="Chain Printed[1 - 1000]" type="integer" value="100"/>
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420
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421 <param name="markov_chain" label="Markov Chain Sampled[1 - 1000]" type="integer" value="100"/>
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422
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423 <param name="chains_run" type="select" label="Chains Run:">
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424 <option selected="True" value="--nchains 4">4</option>
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425 </param>
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426
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427 <param name="samples_discarded" label="Number of Samples Discarded[0 - 20]" type="integer" value="10"/>
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428
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429 <param name="independent_analyses" type="select" label="Number of independent Analyses">
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430 <option selected="True" value="--nruns 2">2</option>
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431 </param>
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432
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433 <param name="variation_model" type="select" label="Rate Variation Model">
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434 <option selected="True" value="--rates_mrbayes Equal">Equal</option>
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435 </param>
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436 </when>
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437 </conditional>
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438 </when>
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439 </conditional>
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440
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441 </when>
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442
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443 </conditional>
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444 </inputs>
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445
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446 <outputs>
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447 <data format="txt" name="output" />
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448 </outputs>
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449
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450 <tests>
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451 <test>
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452 <param name="input" value=""/>
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453 <output name="out_file1" file=""/>
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454 </test>
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455 </tests>
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456
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457 <help>
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458 </help>
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459
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460 </tool>
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