Mercurial > repos > q2d2 > qiime2__longitudinal__volatility

annotate qiime2__longitudinal__volatility.xml @ 3:085340f69dfe draft

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author q2d2
date Thu, 25 Apr 2024 21:15:59 +0000
parents 0e3d1b6523e2
children 7c4629181605
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
3
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9 q2galaxy (version: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 longitudinal volatility" id="qiime2__longitudinal__volatility" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Generate interactive volatility plot</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
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17 </requirements>
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18 <version_command>q2galaxy version longitudinal</version_command>
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19 <command detect_errors="exit_code">q2galaxy run longitudinal volatility '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
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25 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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26 <param name="type" type="select" label="metadata: Metadata">
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27 <option value="tsv" selected="true">Metadata from TSV</option>
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28 <option value="qza">Metadata from Artifact</option>
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29 </param>
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30 <when value="tsv">
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31 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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32 </when>
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33 <when value="qza">
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34 <param name="source" type="data" format="qza" label="Metadata Source"/>
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35 </when>
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36 </conditional>
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37 </repeat>
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38 <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (time) variable information.">
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39 <sanitizer>
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40 <valid initial="string.printable"/>
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41 </sanitizer>
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42 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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43 </param>
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44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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45 <param name="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional] Feature table containing metrics.">
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46 <options options_filter_attribute="metadata.semantic_type">
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47 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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48 </options>
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49 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
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50 </param>
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51 <conditional name="__q2galaxy__GUI__conditional__individual_id_column__" label="individual_id_column: Str">
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52 <param name="__q2galaxy__GUI__select__" type="select" label="individual_id_column: Str" help="[optional] Metadata column containing IDs for individual subjects.">
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53 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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54 <option value="__q2galaxy__::control::provide">Provide a value</option>
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55 </param>
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56 <when value="__q2galaxy__::control::default">
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57 <param name="individual_id_column" type="hidden" value="__q2galaxy__::literal::None"/>
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58 </when>
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59 <when value="__q2galaxy__::control::provide">
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60 <param name="individual_id_column" type="text">
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61 <sanitizer>
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62 <valid initial="string.printable"/>
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63 </sanitizer>
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64 </param>
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65 </when>
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66 </conditional>
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67 <conditional name="__q2galaxy__GUI__conditional__default_group_column__" label="default_group_column: Str">
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68 <param name="__q2galaxy__GUI__select__" type="select" label="default_group_column: Str" help="[optional] The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization).">
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69 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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70 <option value="__q2galaxy__::control::provide">Provide a value</option>
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71 </param>
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72 <when value="__q2galaxy__::control::default">
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73 <param name="default_group_column" type="hidden" value="__q2galaxy__::literal::None"/>
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74 </when>
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75 <when value="__q2galaxy__::control::provide">
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76 <param name="default_group_column" type="text">
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77 <sanitizer>
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78 <valid initial="string.printable"/>
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79 </sanitizer>
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80 </param>
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81 </when>
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82 </conditional>
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83 <conditional name="__q2galaxy__GUI__conditional__default_metric__" label="default_metric: Str">
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84 <param name="__q2galaxy__GUI__select__" type="select" label="default_metric: Str" help="[optional] Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization).">
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85 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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86 <option value="__q2galaxy__::control::provide">Provide a value</option>
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87 </param>
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88 <when value="__q2galaxy__::control::default">
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89 <param name="default_metric" type="hidden" value="__q2galaxy__::literal::None"/>
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90 </when>
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91 <when value="__q2galaxy__::control::provide">
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92 <param name="default_metric" type="text">
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93 <sanitizer>
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94 <valid initial="string.printable"/>
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95 </sanitizer>
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96 </param>
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97 </when>
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98 </conditional>
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99 <param name="yscale" type="select" label="yscale: Str % Choices('linear', 'pow', 'sqrt', 'log')" display="radio">
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100 <option value="linear" selected="true">linear</option>
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101 <option value="pow">pow</option>
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102 <option value="sqrt">sqrt</option>
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103 <option value="log">log</option>
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104 </param>
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105 </section>
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106 </inputs>
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107 <outputs>
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108 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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109 </outputs>
2
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110 <tests>
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111 <test>
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112 <repeat name="metadata">
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113 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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114 <param name="type" value="tsv"/>
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115 <param name="source" value="volatility.test0.metadata.tsv" ftype="qiime2.tabular"/>
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116 </conditional>
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117 </repeat>
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118 <param name="state_column" value="month"/>
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119 <output name="visualization" ftype="qzv">
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120 <assert_contents>
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121 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/data\/index.html">
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122 <has_line_matching expression="^\s*&quot;month&quot;: null,$"/>
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123 </has_archive_member>
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124 </assert_contents>
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125 </output>
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126 </test>
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127 </tests>
0
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128 <help>
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129 QIIME 2: longitudinal volatility
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130 ================================
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131 Generate interactive volatility plot
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132
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133
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134 Outputs:
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135 --------
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136 :visualization.qzv: &lt;no description&gt;
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137
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138 |
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139
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140 Description:
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141 ------------
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142 Generate an interactive control chart depicting the longitudinal volatility of sample metadata and/or feature frequencies across time (as set using the "state_column" parameter). Any numeric metadata column (and metadata-transformable artifacts, e.g., alpha diversity results) can be plotted on the y-axis, and are selectable using the "metric_column" selector. Metric values are averaged to compare across any categorical metadata column using the "group_column" selector. Longitudinal volatility for individual subjects sampled over time is co-plotted as "spaghetti" plots if the "individual_id_column" parameter is used. state_column will typically be a measure of time, but any numeric metadata column can be used.
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143
2
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144 Examples:
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145 ---------
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146
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147 longitudinal_volatility
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148 ***********************
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149 Using the ``qiime2 longitudinal volatility`` tool:
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150 #. For *"metadata"*:
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151
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152 - Perform the following steps.
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153
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154 #. Leave as ``Metadata from TSV``
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155 #. Set *"Metadata Source"* to ``metadata.tsv``
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156
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157
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158 #. Set *"state_column"* to ``month``
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159 #. Press the ``Execute`` button.
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160
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161 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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162 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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163
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164 .. list-table::
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165 :align: left
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166 :header-rows: 1
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167
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168 * - History Name
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169 - *"Name"* to set (be sure to press ``Save``)
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170 * - ``#: qiime2 longitudinal volatility [...] : visualization.qzv``
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171 - ``volatility-plot.qzv``
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172
0
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173
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174 |
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175
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176 </help>
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177 <citations>
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178 <citation type="doi">10.1128/mSystems.00219-18</citation>
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179 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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180 </citations>
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181 </tool>