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annotate qiime2__diversity_lib__jaccard.xml @ 0:1eca9b532c76 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:47:51 +0000
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1eca9b532c76 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2022, 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: 2022.8.1)
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10 for:
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11 qiime2 (version: 2022.8.1)
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12 -->
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13 <tool name="qiime2 diversity-lib jaccard" id="qiime2__diversity_lib__jaccard" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Jaccard Distance</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.8</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="aggressive">q2galaxy run diversity_lib jaccard '$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 | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which Jaccard distance 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 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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28 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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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 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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33 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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34 <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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35 <option value="auto">auto (Str)</option>
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36 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
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37 </param>
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38 <when value="auto">
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39 <param name="n_jobs" type="hidden" value="auto"/>
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40 </when>
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41 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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42 <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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43 </when>
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44 </conditional>
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45 </section>
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46 </inputs>
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47 <outputs>
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48 <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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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="table" value="jaccard.test0.feature-table.qza" ftype="qza"/>
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53 <output name="distance_matrix" ftype="qza">
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54 <assert_contents>
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55 <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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56 <has_line_matching expression="type: DistanceMatrix"/>
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57 </has_archive_member>
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58 </assert_contents>
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59 </output>
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60 </test>
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61 <test>
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62 <param name="table" value="jaccard.test1.feature-table.qza" ftype="qza"/>
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63 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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64 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
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65 <param name="n_jobs" value="1"/>
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66 </conditional>
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67 <output name="distance_matrix" ftype="qza">
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68 <assert_contents>
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69 <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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70 <has_line_matching expression="type: DistanceMatrix"/>
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71 </has_archive_member>
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72 </assert_contents>
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73 </output>
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74 </test>
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75 <test>
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76 <param name="table" value="jaccard.test2.feature-table.qza" ftype="qza"/>
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77 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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78 <param name="__q2galaxy__GUI__select__" value="auto"/>
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79 <param name="n_jobs" value="auto"/>
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80 </conditional>
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81 <output name="distance_matrix" ftype="qza">
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82 <assert_contents>
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83 <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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84 <has_line_matching expression="type: DistanceMatrix"/>
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85 </has_archive_member>
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
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90 <help>
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91 QIIME 2: diversity-lib jaccard
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92 ==============================
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93 Jaccard Distance
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94
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95
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96 Outputs:
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97 --------
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98 :distance_matrix.qza: Distance matrix for Jaccard index
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99
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100 |
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101
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102 Description:
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103 ------------
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104 Compute Jaccard distance for each sample in a feature table. Jaccard is calculated usingpresence/absence data. Data of type FeatureTable[Frequency | Relative Frequency] is reducedto presence/absence prior to calculation.
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105
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106 Examples:
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107 ---------
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108
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109 run on one core (by default)
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110 ****************************
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111 Using the ``qiime2 diversity-lib jaccard`` tool:
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112 #. Set *"table"* to ``#: feature-table.qza``
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113 #. Press the ``Execute`` button.
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114
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115 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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116 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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117
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118 .. list-table::
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119 :align: left
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120 :header-rows: 1
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121
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122 * - History Name
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123 - *"Name"* to set (be sure to press ``Save``)
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124 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
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125 - ``jaccard-dm.qza``
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126
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127 to run on n cores, replace 1 here with your preferred integer
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128 *************************************************************
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129 Using the ``qiime2 diversity-lib jaccard`` tool:
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130 #. Set *"table"* to ``#: feature-table.qza``
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131 #. Expand the ``additional options`` section
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132
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133 - Leave *"n_jobs"* as its default value of ``1``
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134
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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 jaccard [...] : distance_matrix.qza``
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147 - ``jaccard-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 jaccard`` tool:
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152 #. Set *"table"* to ``#: feature-table.qza``
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153 #. Expand the ``additional options`` section
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154
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155 - Set *"n_jobs"* to ``auto``
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156
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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 jaccard [...] : distance_matrix.qza``
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169 - ``jaccard-dm.qza``
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170
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171
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172 |
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173
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174 </help>
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175 <citations>
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176 <citation type="bibtex">@article{cite1,
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177 author = {Jaccard, P},
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178 journal = {Bull. Soc. Vard. Sci. Nat},
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179 pages = {223--270},
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180 title = {Nouvelles recherches sur la distribution floral},
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181 volume = {44},
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182 year = {1908}
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183 }
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184 </citation>
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185 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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186 </citations>
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187 </tool>