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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:46:45 +0000
parents da97d578001c
children 38a55b074008
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, 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:
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9 q2galaxy (version: 2022.11.1)
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10 for:
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11 qiime2 (version: 2022.11.1)
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12 -->
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13 <tool name="qiime2 diversity-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Beta Passthrough (non-phylogenetic)</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.11</container>
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17 </requirements>
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18 <version_command>q2galaxy version diversity_lib</version_command>
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19 <command detect_errors="exit_code">q2galaxy run diversity_lib beta_passthrough '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples over which beta diversity should be computed.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[Frequency]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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29 </param>
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30 <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'kulsinski', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')">
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31 <option value="__q2galaxy__::literal::None">Selection required</option>
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32 <option value="aitchison">aitchison</option>
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33 <option value="canberra">canberra</option>
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34 <option value="canberra_adkins">canberra_adkins</option>
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35 <option value="chebyshev">chebyshev</option>
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36 <option value="cityblock">cityblock</option>
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37 <option value="correlation">correlation</option>
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38 <option value="cosine">cosine</option>
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39 <option value="dice">dice</option>
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40 <option value="euclidean">euclidean</option>
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41 <option value="hamming">hamming</option>
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42 <option value="jensenshannon">jensenshannon</option>
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43 <option value="kulsinski">kulsinski</option>
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44 <option value="matching">matching</option>
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45 <option value="minkowski">minkowski</option>
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46 <option value="rogerstanimoto">rogerstanimoto</option>
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47 <option value="russellrao">russellrao</option>
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48 <option value="seuclidean">seuclidean</option>
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49 <option value="sokalmichener">sokalmichener</option>
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50 <option value="sokalsneath">sokalsneath</option>
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51 <option value="sqeuclidean">sqeuclidean</option>
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52 <option value="yule">yule</option>
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53 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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54 </param>
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55 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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56 <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1] A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics."/>
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57 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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58 <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.">
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59 <option value="auto">auto (Str)</option>
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60 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
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61 </param>
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62 <when value="auto">
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63 <param name="n_jobs" type="hidden" value="auto"/>
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64 </when>
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65 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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66 <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1] The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."/>
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67 </when>
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68 </conditional>
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69 </section>
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70 </inputs>
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71 <outputs>
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72 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="table" value="beta_passthrough.test0.feature-table.qza" ftype="qza"/>
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77 <param name="metric" value="euclidean"/>
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78 <output name="distance_matrix" ftype="qza">
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79 <assert_contents>
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80 <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}\/metadata.yaml">
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81 <has_line_matching expression="type: DistanceMatrix"/>
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82 </has_archive_member>
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83 </assert_contents>
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84 </output>
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85 </test>
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86 <test>
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87 <param name="table" value="beta_passthrough.test1.feature-table.qza" ftype="qza"/>
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88 <param name="metric" value="kulsinski"/>
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89 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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90 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
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91 <param name="n_jobs" value="1"/>
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92 </conditional>
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93 <output name="distance_matrix" ftype="qza">
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94 <assert_contents>
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95 <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}\/metadata.yaml">
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96 <has_line_matching expression="type: DistanceMatrix"/>
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97 </has_archive_member>
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98 </assert_contents>
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99 </output>
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100 </test>
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101 <test>
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102 <param name="table" value="beta_passthrough.test2.feature-table.qza" ftype="qza"/>
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103 <param name="metric" value="aitchison"/>
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104 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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105 <param name="__q2galaxy__GUI__select__" value="auto"/>
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106 <param name="n_jobs" value="auto"/>
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107 </conditional>
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108 <output name="distance_matrix" ftype="qza">
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109 <assert_contents>
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110 <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}\/metadata.yaml">
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111 <has_line_matching expression="type: DistanceMatrix"/>
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112 </has_archive_member>
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113 </assert_contents>
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114 </output>
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115 </test>
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116 <test>
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117 <param name="table" value="beta_passthrough.test3.feature-table.qza" ftype="qza"/>
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118 <param name="metric" value="aitchison"/>
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119 <param name="pseudocount" value="5"/>
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120 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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121 <param name="__q2galaxy__GUI__select__" value="auto"/>
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122 <param name="n_jobs" value="auto"/>
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123 </conditional>
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124 <output name="distance_matrix" ftype="qza">
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125 <assert_contents>
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126 <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}\/metadata.yaml">
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127 <has_line_matching expression="type: DistanceMatrix"/>
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128 </has_archive_member>
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129 </assert_contents>
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130 </output>
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131 </test>
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132 </tests>
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133 <help>
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134 QIIME 2: diversity-lib beta-passthrough
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135 =======================================
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136 Beta Passthrough (non-phylogenetic)
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137
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138
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139 Outputs:
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140 --------
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141 :distance_matrix.qza: The resulting distance matrix.
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142
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143 |
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144
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145 Description:
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146 ------------
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147 Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.
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148
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149 Examples:
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150 ---------
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151
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152 run on one core (by default)
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153 ****************************
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154 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
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155 #. Set *"table"* to ``#: feature-table.qza``
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156 #. Set *"metric"* to ``euclidean``
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157 #. Press the ``Execute`` button.
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158
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159 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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160 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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161
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162 .. list-table::
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163 :align: left
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164 :header-rows: 1
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165
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166 * - History Name
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167 - *"Name"* to set (be sure to press ``Save``)
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168 * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``
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169 - ``euclidean-dm.qza``
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170
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171 to run on n cores, replace 1 here with your preferred integer
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172 *************************************************************
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173 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
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174 #. Set *"table"* to ``#: feature-table.qza``
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175 #. Set *"metric"* to ``kulsinski``
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176 #. Expand the ``additional options`` section
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177
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178 - Leave *"n_jobs"* as its default value of ``1``
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179
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180 #. Press the ``Execute`` button.
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181
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182 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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183 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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184
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185 .. list-table::
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186 :align: left
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187 :header-rows: 1
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188
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189 * - History Name
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190 - *"Name"* to set (be sure to press ``Save``)
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191 * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``
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192 - ``kulsinski-dm.qza``
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193
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194 use 'auto' to run on all of host system's available CPU cores
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195 *************************************************************
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196 | A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
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197 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
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198 #. Set *"table"* to ``#: feature-table.qza``
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199 #. Set *"metric"* to ``aitchison``
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200 #. Expand the ``additional options`` section
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201
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202 - Set *"n_jobs"* to ``auto``
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203
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204 #. Press the ``Execute`` button.
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205
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206 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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207 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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208
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209 .. list-table::
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210 :align: left
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211 :header-rows: 1
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212
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213 * - History Name
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214 - *"Name"* to set (be sure to press ``Save``)
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215 * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``
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216 - ``aitchison-dm.qza``
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217
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218 use 'pseudocount' to manually set a pseudocount for compositional metrics
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219 *************************************************************************
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220 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
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221 #. Set *"table"* to ``#: feature-table.qza``
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222 #. Set *"metric"* to ``aitchison``
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223 #. Expand the ``additional options`` section
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224
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225 #. Set *"pseudocount"* to ``5``
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226 #. Set *"n_jobs"* to ``auto``
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227
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228 #. Press the ``Execute`` button.
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229
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230 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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231 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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232
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233 .. list-table::
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234 :align: left
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235 :header-rows: 1
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236
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237 * - History Name
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238 - *"Name"* to set (be sure to press ``Save``)
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239 * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza``
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240 - ``aitchison-dm.qza``
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241
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242
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243 |
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244
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245 </help>
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246 <citations>
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247 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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248 </citations>
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249 </tool>