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annotate qiime2__vizard__scatterplot_2d.xml @ 0:acada7129b61 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:59:12 +0000
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acada7129b61 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard commit 5f71b597c9495eae67a447744fded834f56ca1f7
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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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4
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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:
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 vizard scatterplot-2d" id="qiime2__vizard__scatterplot_2d" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>2D Scatterplot</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version vizard</version_command>
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22 <command detect_errors="exit_code">q2galaxy run vizard scatterplot_2d '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <repeat name="metadata" min="1" help="[required] Any metadata-like input with at least two numeric measures for visualizing." title="metadata: Metadata">
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28 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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29 <param name="type" type="select" label="metadata: Metadata">
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30 <option value="tsv" selected="true">Metadata from TSV</option>
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31 <option value="qza">Metadata from Artifact</option>
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32 </param>
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33 <when value="tsv">
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34 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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35 </when>
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36 <when value="qza">
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37 <param name="source" type="data" format="qza" label="Metadata Source"/>
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38 </when>
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39 </conditional>
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40 </repeat>
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41 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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42 <conditional name="__q2galaxy__GUI__conditional__x_measure__" label="x_measure: Str">
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43 <param name="__q2galaxy__GUI__select__" type="select" label="x_measure: Str" help="[optional] Numeric measure from the input Metadata that should be plotted on the x-axis.">
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44 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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45 <option value="__q2galaxy__::control::provide">Provide a value</option>
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46 </param>
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47 <when value="__q2galaxy__::control::default">
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48 <param name="x_measure" type="hidden" value="__q2galaxy__::literal::None"/>
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49 </when>
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50 <when value="__q2galaxy__::control::provide">
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51 <param name="x_measure" type="text">
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52 <sanitizer>
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53 <valid initial="string.printable"/>
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54 </sanitizer>
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55 </param>
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56 </when>
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57 </conditional>
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58 <conditional name="__q2galaxy__GUI__conditional__y_measure__" label="y_measure: Str">
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59 <param name="__q2galaxy__GUI__select__" type="select" label="y_measure: Str" help="[optional] Numeric measure from the input Metadata that should be plotted on the y-axis.">
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60 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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61 <option value="__q2galaxy__::control::provide">Provide a value</option>
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62 </param>
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63 <when value="__q2galaxy__::control::default">
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64 <param name="y_measure" type="hidden" value="__q2galaxy__::literal::None"/>
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65 </when>
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66 <when value="__q2galaxy__::control::provide">
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67 <param name="y_measure" type="text">
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68 <sanitizer>
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69 <valid initial="string.printable"/>
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70 </sanitizer>
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71 </param>
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72 </when>
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73 </conditional>
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74 <conditional name="__q2galaxy__GUI__conditional__color_by__" label="color_by: Str">
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75 <param name="__q2galaxy__GUI__select__" type="select" label="color_by: Str" help="[optional] Categorical measure from the input Metadata that should be used for color-coding the scatterplot.">
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76 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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77 <option value="__q2galaxy__::control::provide">Provide a value</option>
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78 </param>
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79 <when value="__q2galaxy__::control::default">
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80 <param name="color_by" type="hidden" value="__q2galaxy__::literal::None"/>
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81 </when>
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82 <when value="__q2galaxy__::control::provide">
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83 <param name="color_by" type="text">
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84 <sanitizer>
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85 <valid initial="string.printable"/>
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86 </sanitizer>
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87 </param>
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88 </when>
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89 </conditional>
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90 <conditional name="__q2galaxy__GUI__conditional__title__" label="title: Str">
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91 <param name="__q2galaxy__GUI__select__" type="select" label="title: Str" help="[optional] The title of the scatterplot.">
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92 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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93 <option value="__q2galaxy__::control::provide">Provide a value</option>
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94 </param>
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95 <when value="__q2galaxy__::control::default">
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96 <param name="title" type="hidden" value="__q2galaxy__::literal::None"/>
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97 </when>
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98 <when value="__q2galaxy__::control::provide">
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99 <param name="title" type="text">
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100 <sanitizer>
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101 <valid initial="string.printable"/>
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102 </sanitizer>
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103 </param>
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104 </when>
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105 </conditional>
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106 </section>
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107 </inputs>
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108 <outputs>
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109 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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110 </outputs>
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111 <tests>
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112 <test>
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113 <repeat name="metadata">
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114 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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115 <param name="type" value="tsv"/>
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116 <param name="source" value="scatterplot_2d.test0.metadata.tsv" ftype="qiime2.tabular"/>
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117 </conditional>
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118 </repeat>
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119 <output name="visualization" ftype="qzv"/>
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120 </test>
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121 <test>
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122 <repeat name="metadata">
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123 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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124 <param name="type" value="tsv"/>
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125 <param name="source" value="scatterplot_2d.test1.metadata.tsv" ftype="qiime2.tabular"/>
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126 </conditional>
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127 </repeat>
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128 <param name="x_measure" value="x"/>
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129 <param name="y_measure" value="y"/>
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130 <param name="color_by" value="group"/>
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131 <output name="visualization" ftype="qzv"/>
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132 </test>
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133 </tests>
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134 <help>
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135 QIIME 2: vizard scatterplot-2d
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136 ==============================
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137 2D Scatterplot
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138
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139
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140 Outputs:
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141 --------
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142 :visualization.qzv: &lt;no description&gt;
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143
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144 |
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145
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146 Description:
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147 ------------
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148 Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.
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149
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150 Examples:
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151 ---------
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152
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153 scatterplot_defaults
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154 ********************
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155 Using the ``qiime2 vizard scatterplot-2d`` tool:
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156 #. For *"metadata"*:
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157
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158 - Perform the following steps.
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159
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160 #. Leave as ``Metadata from TSV``
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161 #. Set *"Metadata Source"* to ``metadata.tsv``
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162
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163
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164 #. Press the ``Execute`` button.
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165
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166 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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167 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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168
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169 .. list-table::
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170 :align: left
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171 :header-rows: 1
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172
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173 * - History Name
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174 - *"Name"* to set (be sure to press ``Save``)
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175 * - ``#: qiime2 vizard scatterplot-2d [...] : visualization.qzv``
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176 - ``scatterplot.qzv``
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177
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178 scatterplot_all_measures
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179 ************************
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180 Using the ``qiime2 vizard scatterplot-2d`` tool:
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181 #. For *"metadata"*:
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182
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183 - Perform the following steps.
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184
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185 #. Leave as ``Metadata from TSV``
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186 #. Set *"Metadata Source"* to ``metadata.tsv``
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187
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188
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189 #. Expand the ``additional options`` section
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190
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191 #. Set *"x_measure"* to ``x``
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192 #. Set *"y_measure"* to ``y``
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193 #. Set *"color_by"* to ``group``
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194
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195 #. Press the ``Execute`` button.
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196
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197 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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198 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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199
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200 .. list-table::
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201 :align: left
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202 :header-rows: 1
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203
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204 * - History Name
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205 - *"Name"* to set (be sure to press ``Save``)
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206 * - ``#: qiime2 vizard scatterplot-2d [...] : visualization.qzv``
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207 - ``scatterplot.qzv``
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208
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209
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210 |
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211
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212 </help>
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213 <citations>
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214 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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215 </citations>
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216 </tool>