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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 19:46:33 +0000
parents 4111b5b17fd4
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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 bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Bray-Curtis Dissimilarity</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 bray_curtis '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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31 </options>
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32 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="table" value="bray_curtis.test0.feature-table.qza" ftype="qza"/>
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41 <output name="distance_matrix" ftype="qza">
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42 <assert_contents>
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43 <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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44 <has_line_matching expression="type: DistanceMatrix"/>
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45 </has_archive_member>
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46 </assert_contents>
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47 </output>
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48 </test>
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49 <test>
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50 <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/>
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51 <output name="distance_matrix" ftype="qza">
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52 <assert_contents>
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53 <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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54 <has_line_matching expression="type: DistanceMatrix"/>
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55 </has_archive_member>
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56 </assert_contents>
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57 </output>
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58 </test>
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59 <test>
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60 <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/>
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61 <output name="distance_matrix" ftype="qza">
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62 <assert_contents>
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63 <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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64 <has_line_matching expression="type: DistanceMatrix"/>
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65 </has_archive_member>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help>
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71 QIIME 2: diversity-lib bray-curtis
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72 ==================================
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73 Bray-Curtis Dissimilarity
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74
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75
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76 Outputs:
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77 --------
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78 :distance_matrix.qza: Distance matrix for Bray-Curtis dissimilarity
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79
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80 |
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81
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82 Description:
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83 ------------
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84 Compute Bray-Curtis dissimilarity for each sample in a feature table. Note: Frequency and relative frequency data produce different results unless overall sample sizes are identical. Please consider the impact on your results if you use Bray-Curtis with count data that has not been adjusted (normalized).
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85
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86 Examples:
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87 ---------
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88
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89 run on one core (by default)
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90 ****************************
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91 Using the ``qiime2 diversity-lib bray-curtis`` tool:
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92 #. Set *"table"* to ``#: feature-table.qza``
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93 #. Press the ``Execute`` button.
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94
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95 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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96 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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97
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98 .. list-table::
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99 :align: left
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100 :header-rows: 1
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101
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102 * - History Name
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103 - *"Name"* to set (be sure to press ``Save``)
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104 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
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105 - ``bray-curtis-dm.qza``
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106
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107 to run on n cores, replace 1 here with your preferred integer
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108 *************************************************************
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109 Using the ``qiime2 diversity-lib bray-curtis`` tool:
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110 #. Set *"table"* to ``#: feature-table.qza``
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111 #. Press the ``Execute`` button.
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112
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113 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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114 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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115
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116 .. list-table::
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117 :align: left
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118 :header-rows: 1
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119
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120 * - History Name
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121 - *"Name"* to set (be sure to press ``Save``)
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122 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
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123 - ``bray-curtis-dm.qza``
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124
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125 use 'auto' to run on all of host system's available CPU cores
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126 *************************************************************
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127 Using the ``qiime2 diversity-lib bray-curtis`` tool:
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128 #. Set *"table"* to ``#: feature-table.qza``
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129 #. Press the ``Execute`` button.
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130
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131 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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132 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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133
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134 .. list-table::
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135 :align: left
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136 :header-rows: 1
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137
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138 * - History Name
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139 - *"Name"* to set (be sure to press ``Save``)
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140 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
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141 - ``bray-curtis-dm.qza``
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142
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143
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144 |
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145
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146 </help>
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147 <citations>
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148 <citation type="bibtex">@article{cite1,
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149 author = {Sørensen, Thorvald},
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150 journal = {Biol. Skr.},
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151 pages = {1--34},
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152 title = {A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
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153 volume = {5},
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154 year = {1948}
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155 }
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156 </citation>
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157 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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158 </citations>
7330b10c19a7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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159 </tool>