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annotate qiime2__diversity_lib__unweighted_unifrac.xml @ 4:7de32a239176 draft

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author q2d2
date Mon, 03 Jun 2024 23:21:02 +0000
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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:
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9 q2galaxy (version: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 diversity-lib unweighted-unifrac" id="qiime2__diversity_lib__unweighted_unifrac" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Unweighted Unifrac</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</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 unweighted_unifrac '$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 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which Unweighted Unifrac 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[RelativeFrequency]"/>
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27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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28 <filter type="add_value" value="FeatureTable[Frequency]"/>
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29 </options>
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30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
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31 </param>
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32 <param name="phylogeny" type="data" format="qza" label="phylogeny: Phylogeny[Rooted]" help="[required] Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.">
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33 <options options_filter_attribute="metadata.semantic_type">
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34 <filter type="add_value" value="Phylogeny[Rooted]"/>
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35 </options>
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36 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
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37 </param>
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38 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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39 <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/>
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40 </section>
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41 </inputs>
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42 <outputs>
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43 <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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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="table" value="unweighted_unifrac.test0.feature-table.qza" ftype="qza"/>
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48 <param name="phylogeny" value="unweighted_unifrac.test0.phylogeny.qza" ftype="qza"/>
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49 <output name="distance_matrix" ftype="qza">
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50 <assert_contents>
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51 <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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52 <has_line_matching expression="type: DistanceMatrix"/>
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53 </has_archive_member>
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54 </assert_contents>
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55 </output>
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56 </test>
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57 <test>
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58 <param name="table" value="unweighted_unifrac.test1.feature-table.qza" ftype="qza"/>
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59 <param name="phylogeny" value="unweighted_unifrac.test1.phylogeny.qza" ftype="qza"/>
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60 <output name="distance_matrix" ftype="qza">
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61 <assert_contents>
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62 <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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63 <has_line_matching expression="type: DistanceMatrix"/>
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64 </has_archive_member>
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65 </assert_contents>
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66 </output>
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67 </test>
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68 <test>
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69 <param name="table" value="unweighted_unifrac.test2.feature-table.qza" ftype="qza"/>
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70 <param name="phylogeny" value="unweighted_unifrac.test2.phylogeny.qza" ftype="qza"/>
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71 <output name="distance_matrix" ftype="qza">
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72 <assert_contents>
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73 <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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74 <has_line_matching expression="type: DistanceMatrix"/>
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75 </has_archive_member>
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76 </assert_contents>
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77 </output>
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78 </test>
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79 <test>
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80 <param name="table" value="unweighted_unifrac.test3.feature-table.qza" ftype="qza"/>
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81 <param name="phylogeny" value="unweighted_unifrac.test3.phylogeny.qza" ftype="qza"/>
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82 <param name="bypass_tips" value="__q2galaxy__::literal::True"/>
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83 <output name="distance_matrix" ftype="qza">
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84 <assert_contents>
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85 <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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86 <has_line_matching expression="type: DistanceMatrix"/>
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87 </has_archive_member>
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88 </assert_contents>
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89 </output>
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90 </test>
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91 </tests>
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92 <help>
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93 QIIME 2: diversity-lib unweighted-unifrac
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94 =========================================
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95 Unweighted Unifrac
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96
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97
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98 Outputs:
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99 --------
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100 :distance_matrix.qza: Distance matrix for Unweighted Unifrac.
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101
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102 |
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103
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104 Description:
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105 ------------
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106 Compute Unweighted Unifrac for each sample in a feature table
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107
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108 Examples:
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109 ---------
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110
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111 run on one core (by default)
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112 ****************************
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113 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool:
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114 #. Set *"table"* to ``#: feature-table.qza``
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115 #. Set *"phylogeny"* to ``#: phylogeny.qza``
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116 #. Press the ``Execute`` button.
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117
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118 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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119 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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120
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121 .. list-table::
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122 :align: left
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123 :header-rows: 1
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124
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125 * - History Name
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126 - *"Name"* to set (be sure to press ``Save``)
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127 * - ``#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza``
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128 - ``unweighted-unifrac-dm.qza``
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129
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130 to run on n cores, replace 1 here with your preferred integer
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131 *************************************************************
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132 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool:
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133 #. Set *"table"* to ``#: feature-table.qza``
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134 #. Set *"phylogeny"* to ``#: phylogeny.qza``
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135 #. Press the ``Execute`` button.
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136
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137 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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138 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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139
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140 .. list-table::
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141 :align: left
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142 :header-rows: 1
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143
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144 * - History Name
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145 - *"Name"* to set (be sure to press ``Save``)
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146 * - ``#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza``
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147 - ``unweighted-unifrac-dm.qza``
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148
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149 use 'auto' to run on all of host system's available CPU cores
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150 *************************************************************
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151 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool:
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152 #. Set *"table"* to ``#: feature-table.qza``
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153 #. Set *"phylogeny"* to ``#: phylogeny.qza``
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154 #. Press the ``Execute`` button.
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155
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156 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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157 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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158
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159 .. list-table::
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160 :align: left
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161 :header-rows: 1
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162
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163 * - History Name
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164 - *"Name"* to set (be sure to press ``Save``)
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165 * - ``#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza``
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166 - ``unweighted-unifrac-dm.qza``
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167
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168 use bypass_tips to trade specificity for reduced compute time
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169 *************************************************************
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170 | bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
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171 Using the ``qiime2 diversity-lib unweighted-unifrac`` tool:
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172 #. Set *"table"* to ``#: feature-table.qza``
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173 #. Set *"phylogeny"* to ``#: phylogeny.qza``
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174 #. Expand the ``additional options`` section
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175
3
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176 - Set *"bypass_tips"* to ``Yes``
0
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177
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178 #. Press the ``Execute`` button.
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179
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180 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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181 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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182
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183 .. list-table::
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184 :align: left
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185 :header-rows: 1
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186
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187 * - History Name
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188 - *"Name"* to set (be sure to press ``Save``)
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189 * - ``#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza``
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190 - ``unweighted-unifrac-dm.qza``
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191
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192
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193 |
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194
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195 </help>
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196 <citations>
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197 <citation type="doi">10.1128/AEM.71.12.8228-8235.2005</citation>
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198 <citation type="doi">10.1128/AEM.01996-06</citation>
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199 <citation type="doi">10.1038/ismej.2009.97</citation>
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200 <citation type="doi">10.1038/ismej.2010.133</citation>
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201 <citation type="doi">10.1038/s41592-018-0187-8</citation>
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202 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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203 </citations>
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204 </tool>