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1 <?xml version="1.0" ?>
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2 <tool id="qiime_phylogeny_align-to-tree-mafft-raxml" name="qiime phylogeny align-to-tree-mafft-raxml"
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3 version="2020.8">
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4 <description>Build a phylogenetic tree using raxml 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-raxml
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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 $pparttree:
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22 --p-parttree
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23 #end if
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24
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25 #if str($psubstitutionmodel) != 'None':
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26 --p-substitution-model=$psubstitutionmodel
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27 #end if
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28
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29 #if str($pseed):
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30 --p-seed=$pseed
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31 #end if
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32 #if str($praxmlversion) != 'None':
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33 --p-raxml-version=$praxmlversion
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34 #end if
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35
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36 --o-alignment=oalignment
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37
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38 --o-masked-alignment=omaskedalignment
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39
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40 --o-tree=otree
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41
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42 --o-rooted-tree=orootedtree
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43
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44 #if str($examples) != 'None':
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45 --examples=$examples
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46 #end if
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47
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48 ;
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49 cp orootedtree.qza $orootedtree
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50
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51 ]]></command>
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52 <inputs>
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53 <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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54 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
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55 <option selected="True" value="None">Selection is Optional</option>
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56 <option value="Int % Range(1">Int % Range(1</option>
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57 <option value="None">None</option>
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58 </param>
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59 <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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60 <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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61 <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline. [default: False]" name="pparttree" selected="False" type="boolean" />
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62 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
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63 <option selected="True" value="None">Selection is Optional</option>
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64 <option value="GTRGAMMA">GTRGAMMA</option>
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65 <option value="GTRGAMMAI">GTRGAMMAI</option>
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66 <option value="GTRCAT">GTRCAT</option>
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67 <option value="GTRCATI">GTRCATI</option>
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68 </param>
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69 <param label="--p-seed: INTEGER Random number seed for the 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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70 <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
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71 <option selected="True" value="None">Selection is Optional</option>
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72 <option value="Standard">Standard</option>
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73 <option value="SSE3">SSE3</option>
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74 <option value="AVX2">AVX2</option>
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75 </param>
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76 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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77
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78 </inputs>
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79
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80 <outputs>
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81 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
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82 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
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83 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
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84 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
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85
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86 </outputs>
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87
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88 <help><![CDATA[
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89 Build a phylogenetic tree using raxml and mafft alignment.
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90 ###############################################################
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91
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92 This pipeline will start by creating a sequence alignment using MAFFT,
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93 after which any alignment columns that are phylogenetically uninformative
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94 or ambiguously aligned will be removed (masked). The resulting masked
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95 alignment will be used to infer a phylogenetic tree using RAxML, under the
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96 specified substitution model, and then subsequently rooted at its midpoint.
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97 Output files from each step of the pipeline will be saved. This includes
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98 both the unmasked and masked MAFFT alignment from q2-alignment methods, and
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99 both the rooted and unrooted phylogenies from q2-phylogeny methods.
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100
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101 Parameters
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102 ----------
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103 sequences : FeatureData[Sequence]
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104 The sequences to be used for creating a iqtree based rooted
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105 phylogenetic tree.
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106 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
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107 The number of threads. (Use `all` to automatically use all available
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108 cores. This value is used when aligning the sequences and creating the
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109 tree with iqtree.
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110 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
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111 The maximum relative frequency of gap characters in a column for the
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112 column to be retained. This relative frequency must be a number between
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113 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
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114 gap characters, and 1.0 retains all columns regardless of gap
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115 character frequency. This value is used when masking the aligned
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116 sequences.
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117 mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
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118 The minimum relative frequency of at least one non-gap character in a
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119 column for that column to be retained. This relative frequency must be
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120 a number between 0.0 and 1.0 (inclusive). For example, if a value of
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121 0.4 is provided, a column will only be retained if it contains at
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122 least one character that is present in at least 40% of the sequences.
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123 This value is used when masking the aligned sequences.
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124 parttree : Bool, optional
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125 This flag is required if the number of sequences being aligned are
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126 larger than 1000000. Disabled by default. NOTE: if using this option,
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127 it is recomended that only the CAT-based substitution models of RAxML
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128 be considered for this pipeline.
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129 substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
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130 Model of Nucleotide Substitution.
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131 seed : Int, optional
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132 Random number seed for the parsimony starting tree. This allows you to
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133 reproduce tree results. If not supplied then one will be randomly
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134 chosen.
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135 raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
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136 Select a specific CPU optimization of RAxML to use. The SSE3 versions
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137 will run approximately 40% faster than the standard version. The AVX2
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138 version will run 10-30% faster than the SSE3 version.
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139
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140 Returns
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141 -------
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142 alignment : FeatureData[AlignedSequence]
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143 The aligned sequences.
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144 masked_alignment : FeatureData[AlignedSequence]
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145 The masked alignment.
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146 tree : Phylogeny[Unrooted]
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147 The unrooted phylogenetic tree.
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148 rooted_tree : Phylogeny[Rooted]
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149 The rooted phylogenetic tree.
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150 ]]></help>
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151 <macros>
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152 <import>qiime_citation.xml</import>
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153 </macros>
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154 <expand macro="qiime_citation"/>
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155 </tool> |
