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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2019.4">
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3 <description> - Linear mixed effects modeling</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime longitudinal linear-mixed-effects
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9
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10
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11 #if $input_files_mmetadatafile:
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12 #def list_dict_to_string(list_dict):
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13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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14 #for d in list_dict[1:]:
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15 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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16 #end for
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17 #return $file_list
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18 #end def
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19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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20 #end if
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21
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22
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23 --p-state-column="$pstatecolumn"
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24 --p-individual-id-column="$pindividualidcolumn"
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25
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26 #if str($itable) != 'None':
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27 --i-table=$itable
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28 #end if
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29
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30 #if str($pmetric):
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31 --p-metric="$pmetric"
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32 #end if
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33
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34 #if str($pgroupcolumns):
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35 --p-group-columns="$pgroupcolumns"
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36 #end if
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37
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38 #if str($prandomeffects):
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39 --p-random-effects="$prandomeffects"
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40 #end if
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41
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42 #if str($ppalette) != 'None':
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43 --p-palette=$ppalette
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44 #end if
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45
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46 #if $plowess:
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47 --p-lowess
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48 #end if
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49
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4
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50 #if str($pci):
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2
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51 --p-ci=$pci
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52 #end if
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53
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54 #if str($pformula):
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55 --p-formula="$pformula"
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56 #end if
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57
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58 --o-visualization=ovisualization
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59 ;
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60 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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61 && cp -r out/* '$ovisualization.files_path'
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62 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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63 ]]></command>
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64 <inputs>
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65 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
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66 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
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67 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric. [optional]" name="itable" optional="True" type="data"/>
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68 <param label="--p-metric: TEXT Dependent variable column name. Must be a column name located in the metadata or feature table files. [optional]" name="pmetric" optional="True" type="text"/>
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69 <param label="--p-group-columns: TEXT Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of 'metric'. [optional]" name="pgroupcolumns" optional="True" type="text"/>
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70 <param label="--p-random-effects: TEXT Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of 'metric'. To add a random slope, the same value passed to 'state-column' should be passed here. A random intercept for each individual is set by default and does not need to be passed here. [optional]" name="prandomeffects" optional="True" type="text"/>
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71 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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72 <option selected="True" value="None">Selection is Optional</option>
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73 <option value="Set1">Set1</option>
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74 <option value="Set2">Set2</option>
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75 <option value="Set3">Set3</option>
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76 <option value="Pastel1">Pastel1</option>
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77 <option value="Pastel2">Pastel2</option>
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78 <option value="Paired">Paired</option>
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79 <option value="Accent">Accent</option>
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80 <option value="Dark2">Dark2</option>
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81 <option value="tab10">tab10</option>
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82 <option value="tab20">tab20</option>
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83 <option value="tab20b">tab20b</option>
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84 <option value="tab20c">tab20c</option>
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85 <option value="viridis">viridis</option>
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86 <option value="plasma">plasma</option>
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87 <option value="inferno">inferno</option>
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88 <option value="magma">magma</option>
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89 <option value="terrain">terrain</option>
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90 <option value="rainbow">rainbow</option>
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91 </param>
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92 <param label="--p-lowess: --p-no-lowess Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting. [default: False]" name="plowess" selected="False" type="boolean"/>
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93 <param label="--p-ci: NUMBER Size of the confidence interval for the regression Range(0, 100) estimate. [default: 95]" name="pci" optional="True" type="float" min="0" max="100" value="95"/>
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94 <param label="--p-formula: TEXT R-style formula to use for model specification. A formula must be used if the 'metric' parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format 'a ~ b + c', where 'a' is the metric (dependent variable) and 'b' and 'c' are independent covariates. Use '+' to add a variable; '+ a:b' to add an interaction between variables a and b; '*' to include a variable and all interactions; and '-' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [optional]" name="pformula" optional="True" type="text"/>
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95
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4
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96 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
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2
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97 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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98 </repeat>
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99
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100 </inputs>
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101 <outputs>
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102 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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103 </outputs>
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104 <help><![CDATA[
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105 Linear mixed effects modeling
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106 #############################
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107
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108 Linear mixed effects models evaluate the contribution of exogenous
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109 covariates "group_columns" and "random_effects" to a single dependent
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110 variable, "metric". Perform LME and plot line plots of each group column. A
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111 feature table artifact is required input, though whether "metric" is
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112 derived from the feature table or metadata is optional.
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113
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114 Parameters
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115 ----------
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116 metadata : Metadata
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117 Sample metadata file containing individual_id_column.
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118 state_column : Str
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119 Metadata column containing state (time) variable information.
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120 individual_id_column : Str
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121 Metadata column containing IDs for individual subjects.
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122 metric : Str, optional
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123 Dependent variable column name. Must be a column name located in the
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124 metadata or feature table files.
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125 group_columns : Str, optional
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126 Comma-separated list (without spaces) of metadata columns to use as
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127 independent covariates used to determine mean structure of "metric".
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128 random_effects : Str, optional
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129 Comma-separated list (without spaces) of metadata columns to use as
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130 independent covariates used to determine the variance and covariance
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131 structure (random effects) of "metric". To add a random slope, the same
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132 value passed to "state_column" should be passed here. A random
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133 intercept for each individual is set by default and does not need to be
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134 passed here.
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135 table : FeatureTable[RelativeFrequency], optional
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136 Feature table containing metric.
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137 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
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138 Color palette to use for generating boxplots.
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139 lowess : Bool, optional
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140 Estimate locally weighted scatterplot smoothing. Note that this will
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141 eliminate confidence interval plotting.
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142 ci : Float % Range(0, 100), optional
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143 Size of the confidence interval for the regression estimate.
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144 formula : Str, optional
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145 R-style formula to use for model specification. A formula must be used
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146 if the "metric" parameter is None. Note that the metric and group
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147 columns specified in the formula will override metric and group columns
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148 that are passed separately as parameters to this method. Formulae will
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149 be in the format "a ~ b + c", where "a" is the metric (dependent
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150 variable) and "b" and "c" are independent covariates. Use "+" to add a
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151 variable; "+ a:b" to add an interaction between variables a and b; "*"
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152 to include a variable and all interactions; and "-" to subtract a
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153 particular term (e.g., an interaction term). See
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154 https://patsy.readthedocs.io/en/latest/formulas.html for full
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155 documentation of valid formula operators. Always enclose formulae in
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156 quotes to avoid unpleasant surprises.
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157
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158 Returns
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159 -------
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160 visualization : Visualization
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161 ]]></help>
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162 <macros>
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163 <import>qiime_citation.xml</import>
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164 </macros>
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165 <expand macro="qiime_citation"/>
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166 </tool>
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