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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:21:21 +0000
parents 760b9ecc9575
children
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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 jaccard" id="qiime2__diversity_lib__jaccard" version="2024.5.0+q2galaxy.2024.5.0" 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/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 jaccard '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which Jaccard distance should be computed.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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28 <filter type="add_value" value="FeatureTable[Frequency]"/>
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29 </options>
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30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="table" value="jaccard.test0.feature-table.qza" ftype="qza"/>
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39 <output name="distance_matrix" ftype="qza">
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40 <assert_contents>
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41 <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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42 <has_line_matching expression="type: DistanceMatrix"/>
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43 </has_archive_member>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 <test>
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48 <param name="table" value="jaccard.test1.feature-table.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="jaccard.test2.feature-table.qza" ftype="qza"/>
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59 <output name="distance_matrix" ftype="qza">
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60 <assert_contents>
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61 <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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62 <has_line_matching expression="type: DistanceMatrix"/>
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63 </has_archive_member>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 </tests>
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68 <help>
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69 QIIME 2: diversity-lib jaccard
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70 ==============================
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71 Jaccard Distance
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72
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73
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74 Outputs:
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75 --------
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76 :distance_matrix.qza: Distance matrix for Jaccard index
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77
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78 |
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79
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80 Description:
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81 ------------
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82 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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83
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84 Examples:
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85 ---------
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86
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87 run on one core (by default)
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88 ****************************
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89 Using the ``qiime2 diversity-lib jaccard`` tool:
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90 #. Set *"table"* to ``#: feature-table.qza``
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91 #. Press the ``Execute`` button.
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92
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93 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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94 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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95
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96 .. list-table::
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97 :align: left
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98 :header-rows: 1
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99
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100 * - History Name
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101 - *"Name"* to set (be sure to press ``Save``)
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102 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
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103 - ``jaccard-dm.qza``
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104
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105 to run on n cores, replace 1 here with your preferred integer
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106 *************************************************************
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107 Using the ``qiime2 diversity-lib jaccard`` tool:
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108 #. Set *"table"* to ``#: feature-table.qza``
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109 #. Press the ``Execute`` button.
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110
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111 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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112 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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113
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114 .. list-table::
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115 :align: left
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116 :header-rows: 1
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117
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118 * - History Name
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119 - *"Name"* to set (be sure to press ``Save``)
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120 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
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121 - ``jaccard-dm.qza``
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122
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123 use 'auto' to run on all of host system's available CPU cores
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124 *************************************************************
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125 Using the ``qiime2 diversity-lib jaccard`` tool:
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126 #. Set *"table"* to ``#: feature-table.qza``
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127 #. Press the ``Execute`` button.
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128
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129 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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130 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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131
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132 .. list-table::
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133 :align: left
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134 :header-rows: 1
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135
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136 * - History Name
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137 - *"Name"* to set (be sure to press ``Save``)
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138 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
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139 - ``jaccard-dm.qza``
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140
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141
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142 |
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143
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144 </help>
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145 <citations>
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146 <citation type="bibtex">@article{cite1,
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147 author = {Jaccard, P},
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148 journal = {Bull. Soc. Vard. Sci. Nat},
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149 pages = {223--270},
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150 title = {Nouvelles recherches sur la distribution floral},
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151 volume = {44},
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152 year = {1908}
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153 }
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154 </citation>
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155 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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156 </citations>
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157 </tool>