annotate qiime2-2020.8/qiime_phylogeny_align-to-tree-mafft-iqtree.xml @ 22:292c84bd5ab6 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:55:05 +0000
parents d93d8888f0b0
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1 <?xml version="1.0" ?>
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2 <tool id="qiime_phylogeny_align-to-tree-mafft-iqtree" name="qiime phylogeny align-to-tree-mafft-iqtree"
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3 version="2020.8">
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4 <description>Build a phylogenetic tree using iqtree and mafft alignment.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime phylogeny align-to-tree-mafft-iqtree
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10
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11 --i-sequences=$isequences
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12
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13 #if str($pnthreads) != 'None':
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14 --p-n-threads=$pnthreads
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15 #end if
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16
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17 --p-mask-max-gap-frequency=$pmaskmaxgapfrequency
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18
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19 --p-mask-min-conservation=$pmaskminconservation
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20
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21 #if str($psubstitutionmodel) != 'None':
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22 --p-substitution-model=$psubstitutionmodel
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23 #end if
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24
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25 #if $pfast:
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26 --p-fast
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27 #end if
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28
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29 #if str($palrt):
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30 --p-alrt=$palrt
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31 #end if
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32 #if str($pseed):
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33 --p-seed=$pseed
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34 #end if
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35 #if str($pstopiter):
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36 --p-stop-iter=$pstopiter
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37 #end if
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38 #if str($pperturbnnistrength):
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39 --p-perturb-nni-strength=$pperturbnnistrength
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40 #end if
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41 --o-alignment=oalignment
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42
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43 --o-masked-alignment=omaskedalignment
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44
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45 --o-tree=otree
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46
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47 --o-rooted-tree=orootedtree
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48
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49 #if str($examples) != 'None':
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50 --examples=$examples
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51 #end if
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52
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53 ;
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54 cp orootedtree.qza $orootedtree
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55
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56 ]]></command>
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57 <inputs>
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58 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data" />
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59 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
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60 <option selected="True" value="None">Selection is Optional</option>
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61 <option value="Int % Range(1">Int % Range(1</option>
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62 <option value="None">None</option>
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63 </param>
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64 <param exclude_max="False" label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" />
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65 <param exclude_max="False" label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" />
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66 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
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67 <option selected="True" value="None">Selection is Optional</option>
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68 <option value="JC">JC</option>
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69 <option value="JC+I">JC+I</option>
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70 <option value="JC+G">JC+G</option>
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71 <option value="JC+I+G">JC+I+G</option>
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72 <option value="JC+R2">JC+R2</option>
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73 <option value="JC+R3">JC+R3</option>
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74 <option value="JC+R4">JC+R4</option>
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75 <option value="JC+R5">JC+R5</option>
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76 <option value="JC+R6">JC+R6</option>
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77 <option value="JC+R7">JC+R7</option>
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78 <option value="JC+R8">JC+R8</option>
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79 <option value="JC+R9">JC+R9</option>
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80 <option value="JC+R10">JC+R10</option>
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81 <option value="F81">F81</option>
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82 <option value="F81+I">F81+I</option>
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83 <option value="F81+G">F81+G</option>
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84 <option value="F81+I+G">F81+I+G</option>
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85 <option value="F81+R2">F81+R2</option>
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86 <option value="F81+R3">F81+R3</option>
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87 <option value="F81+R4">F81+R4</option>
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88 <option value="F81+R5">F81+R5</option>
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89 <option value="F81+R6">F81+R6</option>
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90 <option value="F81+R7">F81+R7</option>
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91 <option value="F81+R8">F81+R8</option>
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92 <option value="F81+R9">F81+R9</option>
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93 <option value="F81+R10">F81+R10</option>
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94 <option value="K80">K80</option>
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95 <option value="K80+I">K80+I</option>
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96 <option value="K80+G">K80+G</option>
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97 <option value="K80+I+G">K80+I+G</option>
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98 <option value="K80+R2">K80+R2</option>
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99 <option value="K80+R3">K80+R3</option>
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100 <option value="K80+R4">K80+R4</option>
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101 <option value="K80+R5">K80+R5</option>
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102 <option value="K80+R6">K80+R6</option>
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103 <option value="K80+R7">K80+R7</option>
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104 <option value="K80+R8">K80+R8</option>
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105 <option value="K80+R9">K80+R9</option>
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106 <option value="K80+R10">K80+R10</option>
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107 <option value="HKY">HKY</option>
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108 <option value="HKY+I">HKY+I</option>
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109 <option value="HKY+G">HKY+G</option>
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110 <option value="HKY+I+G">HKY+I+G</option>
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111 <option value="HKY+R2">HKY+R2</option>
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112 <option value="HKY+R3">HKY+R3</option>
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113 <option value="HKY+R4">HKY+R4</option>
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114 <option value="HKY+R5">HKY+R5</option>
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115 <option value="HKY+R6">HKY+R6</option>
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116 <option value="HKY+R7">HKY+R7</option>
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117 <option value="HKY+R8">HKY+R8</option>
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118 <option value="HKY+R9">HKY+R9</option>
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119 <option value="HKY+R10">HKY+R10</option>
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120 <option value="TNe">TNe</option>
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121 <option value="TNe+I">TNe+I</option>
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122 <option value="TNe+G">TNe+G</option>
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123 <option value="TNe+I+G">TNe+I+G</option>
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124 <option value="TNe+R2">TNe+R2</option>
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125 <option value="TNe+R3">TNe+R3</option>
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126 <option value="TNe+R4">TNe+R4</option>
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127 <option value="TNe+R5">TNe+R5</option>
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128 <option value="TNe+R6">TNe+R6</option>
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129 <option value="TNe+R7">TNe+R7</option>
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130 <option value="TNe+R8">TNe+R8</option>
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131 <option value="TNe+R9">TNe+R9</option>
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132 <option value="TNe+R10">TNe+R10</option>
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133 <option value="TN">TN</option>
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134 <option value="TN+I">TN+I</option>
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135 <option value="TN+G">TN+G</option>
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136 <option value="TN+I+G">TN+I+G</option>
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137 <option value="TN+R2">TN+R2</option>
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138 <option value="TN+R3">TN+R3</option>
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139 <option value="TN+R4">TN+R4</option>
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140 <option value="TN+R5">TN+R5</option>
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141 <option value="TN+R6">TN+R6</option>
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142 <option value="TN+R7">TN+R7</option>
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143 <option value="TN+R8">TN+R8</option>
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144 <option value="TN+R9">TN+R9</option>
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145 <option value="TN+R10">TN+R10</option>
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146 <option value="K81">K81</option>
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147 <option value="K81+I">K81+I</option>
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148 <option value="K81+G">K81+G</option>
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149 <option value="K81+I+G">K81+I+G</option>
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150 <option value="K81+R2">K81+R2</option>
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151 <option value="K81+R3">K81+R3</option>
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152 <option value="K81+R4">K81+R4</option>
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153 <option value="K81+R5">K81+R5</option>
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154 <option value="K81+R6">K81+R6</option>
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155 <option value="K81+R7">K81+R7</option>
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156 <option value="K81+R8">K81+R8</option>
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157 <option value="K81+R9">K81+R9</option>
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158 <option value="K81+R10">K81+R10</option>
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159 <option value="K81u">K81u</option>
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160 <option value="K81u+I">K81u+I</option>
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161 <option value="K81u+G">K81u+G</option>
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162 <option value="K81u+I+G">K81u+I+G</option>
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163 <option value="K81u+R2">K81u+R2</option>
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164 <option value="K81u+R3">K81u+R3</option>
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165 <option value="K81u+R4">K81u+R4</option>
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166 <option value="K81u+R5">K81u+R5</option>
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parents:
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167 <option value="K81u+R6">K81u+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
168 <option value="K81u+R7">K81u+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
169 <option value="K81u+R8">K81u+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
170 <option value="K81u+R9">K81u+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
171 <option value="K81u+R10">K81u+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
172 <option value="TPM2">TPM2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
173 <option value="TPM2+I">TPM2+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
174 <option value="TPM2+G">TPM2+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
175 <option value="TPM2+I+G">TPM2+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
176 <option value="TPM2+R2">TPM2+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
177 <option value="TPM2+R3">TPM2+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
178 <option value="TPM2+R4">TPM2+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
179 <option value="TPM2+R5">TPM2+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
180 <option value="TPM2+R6">TPM2+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
181 <option value="TPM2+R7">TPM2+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
182 <option value="TPM2+R8">TPM2+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
183 <option value="TPM2+R9">TPM2+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
184 <option value="TPM2+R10">TPM2+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
185 <option value="TPM2u">TPM2u</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
186 <option value="TPM2u+I">TPM2u+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
187 <option value="TPM2u+G">TPM2u+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
188 <option value="TPM2u+I+G">TPM2u+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
189 <option value="TPM2u+R2">TPM2u+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
190 <option value="TPM2u+R3">TPM2u+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
191 <option value="TPM2u+R4">TPM2u+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
192 <option value="TPM2u+R5">TPM2u+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
193 <option value="TPM2u+R6">TPM2u+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
194 <option value="TPM2u+R7">TPM2u+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
195 <option value="TPM2u+R8">TPM2u+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
196 <option value="TPM2u+R9">TPM2u+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
197 <option value="TPM2u+R10">TPM2u+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
198 <option value="TPM3">TPM3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
199 <option value="TPM3+I">TPM3+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
200 <option value="TPM3+G">TPM3+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
201 <option value="TPM3+I+G">TPM3+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
202 <option value="TPM3+R2">TPM3+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
203 <option value="TPM3+R3">TPM3+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
204 <option value="TPM3+R4">TPM3+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
205 <option value="TPM3+R5">TPM3+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
206 <option value="TPM3+R6">TPM3+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
207 <option value="TPM3+R7">TPM3+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
208 <option value="TPM3+R8">TPM3+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
209 <option value="TPM3+R9">TPM3+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
210 <option value="TPM3+R10">TPM3+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
211 <option value="TPM3u">TPM3u</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
212 <option value="TPM3u+I">TPM3u+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
213 <option value="TPM3u+G">TPM3u+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
214 <option value="TPM3u+I+G">TPM3u+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
215 <option value="TPM3u+R2">TPM3u+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
216 <option value="TPM3u+R3">TPM3u+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
217 <option value="TPM3u+R4">TPM3u+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
218 <option value="TPM3u+R5">TPM3u+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
219 <option value="TPM3u+R6">TPM3u+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
220 <option value="TPM3u+R7">TPM3u+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
221 <option value="TPM3u+R8">TPM3u+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
222 <option value="TPM3u+R9">TPM3u+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
223 <option value="TPM3u+R10">TPM3u+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
224 <option value="TIMe">TIMe</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
225 <option value="TIMe+I">TIMe+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
226 <option value="TIMe+G">TIMe+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
227 <option value="TIMe+I+G">TIMe+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
228 <option value="TIMe+R2">TIMe+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
229 <option value="TIMe+R3">TIMe+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
230 <option value="TIMe+R4">TIMe+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
231 <option value="TIMe+R5">TIMe+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
232 <option value="TIMe+R6">TIMe+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
233 <option value="TIMe+R7">TIMe+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
234 <option value="TIMe+R8">TIMe+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
235 <option value="TIMe+R9">TIMe+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
236 <option value="TIMe+R10">TIMe+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
237 <option value="TIM">TIM</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
238 <option value="TIM+I">TIM+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
239 <option value="TIM+G">TIM+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
240 <option value="TIM+I+G">TIM+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
241 <option value="TIM+R2">TIM+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
242 <option value="TIM+R3">TIM+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
243 <option value="TIM+R4">TIM+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
244 <option value="TIM+R5">TIM+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
245 <option value="TIM+R6">TIM+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
246 <option value="TIM+R7">TIM+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
247 <option value="TIM+R8">TIM+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
248 <option value="TIM+R9">TIM+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
249 <option value="TIM+R10">TIM+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
250 <option value="TIM2e">TIM2e</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
251 <option value="TIM2e+I">TIM2e+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
252 <option value="TIM2e+G">TIM2e+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
253 <option value="TIM2e+I+G">TIM2e+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
254 <option value="TIM2e+R2">TIM2e+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
255 <option value="TIM2e+R3">TIM2e+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
256 <option value="TIM2e+R4">TIM2e+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
257 <option value="TIM2e+R5">TIM2e+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
258 <option value="TIM2e+R6">TIM2e+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
259 <option value="TIM2e+R7">TIM2e+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
260 <option value="TIM2e+R8">TIM2e+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
261 <option value="TIM2e+R9">TIM2e+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
262 <option value="TIM2e+R10">TIM2e+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
263 <option value="TIM2">TIM2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
264 <option value="TIM2+I">TIM2+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
265 <option value="TIM2+G">TIM2+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
266 <option value="TIM2+I+G">TIM2+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
267 <option value="TIM2+R2">TIM2+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
268 <option value="TIM2+R3">TIM2+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
269 <option value="TIM2+R4">TIM2+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
270 <option value="TIM2+R5">TIM2+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
271 <option value="TIM2+R6">TIM2+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
272 <option value="TIM2+R7">TIM2+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
273 <option value="TIM2+R8">TIM2+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
274 <option value="TIM2+R9">TIM2+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
275 <option value="TIM2+R10">TIM2+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
276 <option value="TIM3e">TIM3e</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
277 <option value="TIM3e+I">TIM3e+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
278 <option value="TIM3e+G">TIM3e+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
279 <option value="TIM3e+I+G">TIM3e+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
280 <option value="TIM3e+R2">TIM3e+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
281 <option value="TIM3e+R3">TIM3e+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
282 <option value="TIM3e+R4">TIM3e+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
283 <option value="TIM3e+R5">TIM3e+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
284 <option value="TIM3e+R6">TIM3e+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
285 <option value="TIM3e+R7">TIM3e+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
286 <option value="TIM3e+R8">TIM3e+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
287 <option value="TIM3e+R9">TIM3e+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
288 <option value="TIM3e+R10">TIM3e+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
289 <option value="TIM3">TIM3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
290 <option value="TIM3+I">TIM3+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
291 <option value="TIM3+G">TIM3+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
292 <option value="TIM3+I+G">TIM3+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
293 <option value="TIM3+R2">TIM3+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
294 <option value="TIM3+R3">TIM3+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
295 <option value="TIM3+R4">TIM3+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
296 <option value="TIM3+R5">TIM3+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
297 <option value="TIM3+R6">TIM3+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
298 <option value="TIM3+R7">TIM3+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
299 <option value="TIM3+R8">TIM3+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
300 <option value="TIM3+R9">TIM3+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
301 <option value="TIM3+R10">TIM3+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
302 <option value="TVMe">TVMe</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
303 <option value="TVMe+I">TVMe+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
304 <option value="TVMe+G">TVMe+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
305 <option value="TVMe+I+G">TVMe+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
306 <option value="TVMe+R2">TVMe+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
307 <option value="TVMe+R3">TVMe+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
308 <option value="TVMe+R4">TVMe+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
309 <option value="TVMe+R5">TVMe+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
310 <option value="TVMe+R6">TVMe+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
311 <option value="TVMe+R7">TVMe+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
312 <option value="TVMe+R8">TVMe+R8</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
313 <option value="TVMe+R9">TVMe+R9</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
314 <option value="TVMe+R10">TVMe+R10</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
315 <option value="TVM">TVM</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
316 <option value="TVM+I">TVM+I</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
317 <option value="TVM+G">TVM+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
318 <option value="TVM+I+G">TVM+I+G</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
319 <option value="TVM+R2">TVM+R2</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
320 <option value="TVM+R3">TVM+R3</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
321 <option value="TVM+R4">TVM+R4</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
322 <option value="TVM+R5">TVM+R5</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
323 <option value="TVM+R6">TVM+R6</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
324 <option value="TVM+R7">TVM+R7</option>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
325 <option value="TVM+R8">TVM+R8</option>
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326 <option value="TVM+R9">TVM+R9</option>
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327 <option value="TVM+R10">TVM+R10</option>
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328 <option value="SYM">SYM</option>
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329 <option value="SYM+I">SYM+I</option>
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330 <option value="SYM+G">SYM+G</option>
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331 <option value="SYM+I+G">SYM+I+G</option>
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332 <option value="SYM+R2">SYM+R2</option>
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333 <option value="SYM+R3">SYM+R3</option>
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334 <option value="SYM+R4">SYM+R4</option>
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335 <option value="SYM+R5">SYM+R5</option>
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336 <option value="SYM+R6">SYM+R6</option>
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337 <option value="SYM+R7">SYM+R7</option>
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338 <option value="SYM+R8">SYM+R8</option>
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339 <option value="SYM+R9">SYM+R9</option>
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340 <option value="SYM+R10">SYM+R10</option>
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341 <option value="GTR">GTR</option>
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342 <option value="GTR+I">GTR+I</option>
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343 <option value="GTR+G">GTR+G</option>
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344 <option value="GTR+I+G">GTR+I+G</option>
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345 <option value="GTR+R2">GTR+R2</option>
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346 <option value="GTR+R3">GTR+R3</option>
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347 <option value="GTR+R4">GTR+R4</option>
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348 <option value="GTR+R5">GTR+R5</option>
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349 <option value="GTR+R6">GTR+R6</option>
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350 <option value="GTR+R7">GTR+R7</option>
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351 <option value="GTR+R8">GTR+R8</option>
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352 <option value="GTR+R9">GTR+R9</option>
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353 <option value="GTR+R10">GTR+R10</option>
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354 <option value="MFP">MFP</option>
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355 <option value="TEST">TEST</option>
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356 </param>
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357 <param label="--p-fast: --p-fast: / --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean" />
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358 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. [optional]" name="palrt" optional="False" type="text" />
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359 <param label="--p-seed: INTEGER Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
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360 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="False" type="text" />
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361 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 1.0) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="False" type="text" />
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362 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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363
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364 </inputs>
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365
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366 <outputs>
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367 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
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368 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
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369 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
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370 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
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371
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372 </outputs>
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373
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374 <help><![CDATA[
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375 Build a phylogenetic tree using iqtree and mafft alignment.
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376 ###############################################################
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377
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378 This pipeline will start by creating a sequence alignment using MAFFT,
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florianbegusch
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diff changeset
379 after which any alignment columns that are phylogenetically uninformative
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380 or ambiguously aligned will be removed (masked). The resulting masked
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381 alignment will be used to infer a phylogenetic tree using IQ-TREE. By
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382 default the best fit substitution model will be determined by ModelFinder
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383 prior to phylogenetic inference. The resulting tree will be subsequently
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384 rooted at its midpoint. Output files from each step of the pipeline will be
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385 saved. This includes both the unmasked and masked MAFFT alignment from
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386 q2-alignment methods, and both the rooted and unrooted phylogenies from
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florianbegusch
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387 q2-phylogeny methods.
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388
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389 Parameters
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390 ----------
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391 sequences : FeatureData[Sequence]
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florianbegusch
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392 The sequences to be used for creating a iqtree based rooted
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florianbegusch
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393 phylogenetic tree.
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394 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
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diff changeset
395 The number of threads. (Use 0 to automatically use all available cores
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florianbegusch
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396 This value is used when aligning the sequences and creating the tree
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397 with iqtree.
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398 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
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399 The maximum relative frequency of gap characters in a column for the
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400 column to be retained. This relative frequency must be a number between
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401 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
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florianbegusch
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402 gap characters, and 1.0 retains all columns regardless of gap
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florianbegusch
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403 character frequency. This value is used when masking the aligned
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florianbegusch
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404 sequences.
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405 mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
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florianbegusch
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406 The minimum relative frequency of at least one non-gap character in a
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florianbegusch
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407 column for that column to be retained. This relative frequency must be
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408 a number between 0.0 and 1.0 (inclusive). For example, if a value of
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409 0.4 is provided, a column will only be retained if it contains at
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410 least one character that is present in at least 40% of the sequences.
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411 This value is used when masking the aligned sequences.
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412 substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional
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413 Model of Nucleotide Substitution. If not provided, IQ-TREE will
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414 determine the best fit substitution model automatically.
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415 fast : Bool, optional
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416 Fast search to resemble FastTree.
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417 alrt : Int % Range(1000, None), optional
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418 Single branch test method. Number of bootstrap replicates to perform an
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419 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
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florianbegusch
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420 replicates is recomended.
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421 seed : Int, optional
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florianbegusch
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422 Random number seed for the iqtree parsimony starting tree. This allows
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423 you to reproduce tree results. If not supplied then one will be
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424 randomly chosen.
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425 stop_iter : Int % Range(1, None), optional
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426 Number of unsuccessful iterations to stop. If not set, program defaults
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427 will be used. See IQ-TREE manual for details.
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428 perturb_nni_strength : Float % Range(0.01, 1.0), optional
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429 Perturbation strength for randomized NNI. If not set, program defaults
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florianbegusch
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430 will be used. See IQ-TREE manual for details.
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florianbegusch
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diff changeset
431
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432 Returns
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433 -------
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434 alignment : FeatureData[AlignedSequence]
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florianbegusch
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435 The aligned sequences.
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florianbegusch
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436 masked_alignment : FeatureData[AlignedSequence]
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florianbegusch
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437 The masked alignment.
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438 tree : Phylogeny[Unrooted]
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florianbegusch
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439 The unrooted phylogenetic tree.
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florianbegusch
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440 rooted_tree : Phylogeny[Rooted]
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florianbegusch
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441 The rooted phylogenetic tree.
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442 ]]></help>
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florianbegusch
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443 <macros>
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444 <import>qiime_citation.xml</import>
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florianbegusch
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445 </macros>
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florianbegusch
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446 <expand macro="qiime_citation"/>
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447 </tool>