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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:45:08 +0000
parents a80fde700012
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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: 2024.10.0)
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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 diversity-lib jaccard" id="qiime2__diversity_lib__jaccard" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Jaccard Distance</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 diversity_lib</version_command>
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22 <command detect_errors="exit_code">q2galaxy run diversity_lib jaccard '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which Jaccard distance should be computed.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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31 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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32 </options>
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33 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="table" value="jaccard.test0.feature-table.qza" ftype="qza"/>
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42 <output name="distance_matrix" ftype="qza">
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43 <assert_contents>
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44 <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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45 <has_line_matching expression="type: DistanceMatrix"/>
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46 </has_archive_member>
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47 </assert_contents>
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48 </output>
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49 </test>
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50 <test>
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51 <param name="table" value="jaccard.test1.feature-table.qza" ftype="qza"/>
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52 <output name="distance_matrix" ftype="qza">
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53 <assert_contents>
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54 <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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55 <has_line_matching expression="type: DistanceMatrix"/>
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56 </has_archive_member>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 <test>
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61 <param name="table" value="jaccard.test2.feature-table.qza" ftype="qza"/>
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62 <output name="distance_matrix" ftype="qza">
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63 <assert_contents>
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64 <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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65 <has_line_matching expression="type: DistanceMatrix"/>
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66 </has_archive_member>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help>
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72 QIIME 2: diversity-lib jaccard
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73 ==============================
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74 Jaccard Distance
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75
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76
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77 Outputs:
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78 --------
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79 :distance_matrix.qza: Distance matrix for Jaccard index
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80
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81 |
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82
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83 Description:
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84 ------------
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85 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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86
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87 Examples:
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88 ---------
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89
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90 run on one core (by default)
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91 ****************************
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92 Using the ``qiime2 diversity-lib jaccard`` tool:
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93 #. Set *"table"* to ``#: feature-table.qza``
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94 #. Press the ``Execute`` button.
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95
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96 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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97 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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98
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99 .. list-table::
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100 :align: left
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101 :header-rows: 1
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102
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103 * - History Name
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104 - *"Name"* to set (be sure to press ``Save``)
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105 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
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106 - ``jaccard-dm.qza``
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107
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108 to run on n cores, replace 1 here with your preferred integer
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109 *************************************************************
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110 Using the ``qiime2 diversity-lib jaccard`` tool:
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111 #. Set *"table"* to ``#: feature-table.qza``
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112 #. Press the ``Execute`` button.
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113
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114 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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115 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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116
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117 .. list-table::
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118 :align: left
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119 :header-rows: 1
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120
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121 * - History Name
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122 - *"Name"* to set (be sure to press ``Save``)
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123 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
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124 - ``jaccard-dm.qza``
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125
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126 use 'auto' to run on all of host system's available CPU cores
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127 *************************************************************
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128 Using the ``qiime2 diversity-lib jaccard`` tool:
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129 #. Set *"table"* to ``#: feature-table.qza``
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130 #. Press the ``Execute`` button.
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131
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132 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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133 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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134
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135 .. list-table::
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136 :align: left
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137 :header-rows: 1
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138
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139 * - History Name
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140 - *"Name"* to set (be sure to press ``Save``)
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141 * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza``
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142 - ``jaccard-dm.qza``
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143
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144
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145 |
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146
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147 </help>
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148 <citations>
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149 <citation type="bibtex">@article{cite1,
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150 author = {Jaccard, P},
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151 journal = {Bull. Soc. Vard. Sci. Nat},
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152 pages = {223--270},
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153 title = {Nouvelles recherches sur la distribution floral},
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154 volume = {44},
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155 year = {1908}
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156 }
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157 </citation>
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158 <citation type="doi">10.1038/s41587-019-0209-9</citation>
1eca9b532c76 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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159 </citations>
1eca9b532c76 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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160 </tool>