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annotate qiime2__diversity_lib__bray_curtis.xml @ 3:6e6d848f2b5b draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:02:45 +0000
parents a1422e558f73
children 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: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 diversity-lib bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Bray-Curtis Dissimilarity</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</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 bray_curtis '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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27 <filter type="add_value" value="FeatureTable[Frequency]"/>
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28 </options>
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="table" value="bray_curtis.test0.feature-table.qza" ftype="qza"/>
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38 <output name="distance_matrix" ftype="qza">
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39 <assert_contents>
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40 <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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41 <has_line_matching expression="type: DistanceMatrix"/>
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42 </has_archive_member>
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43 </assert_contents>
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44 </output>
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45 </test>
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46 <test>
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47 <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/>
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48 <output name="distance_matrix" ftype="qza">
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49 <assert_contents>
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50 <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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51 <has_line_matching expression="type: DistanceMatrix"/>
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52 </has_archive_member>
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53 </assert_contents>
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54 </output>
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55 </test>
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56 <test>
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57 <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/>
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58 <output name="distance_matrix" ftype="qza">
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59 <assert_contents>
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60 <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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61 <has_line_matching expression="type: DistanceMatrix"/>
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62 </has_archive_member>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help>
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68 QIIME 2: diversity-lib bray-curtis
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69 ==================================
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70 Bray-Curtis Dissimilarity
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71
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72
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73 Outputs:
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74 --------
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75 :distance_matrix.qza: Distance matrix for Bray-Curtis dissimilarity
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76
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77 |
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78
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79 Description:
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80 ------------
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81 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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82
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83 Examples:
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84 ---------
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85
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86 run on one core (by default)
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87 ****************************
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88 Using the ``qiime2 diversity-lib bray-curtis`` tool:
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89 #. Set *"table"* to ``#: feature-table.qza``
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90 #. Press the ``Execute`` button.
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91
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92 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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93 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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94
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95 .. list-table::
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96 :align: left
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97 :header-rows: 1
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98
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99 * - History Name
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100 - *"Name"* to set (be sure to press ``Save``)
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101 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
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102 - ``bray-curtis-dm.qza``
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103
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104 to run on n cores, replace 1 here with your preferred integer
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105 *************************************************************
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106 Using the ``qiime2 diversity-lib bray-curtis`` tool:
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107 #. Set *"table"* to ``#: feature-table.qza``
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108 #. Press the ``Execute`` button.
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109
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110 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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111 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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112
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113 .. list-table::
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114 :align: left
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115 :header-rows: 1
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116
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117 * - History Name
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118 - *"Name"* to set (be sure to press ``Save``)
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119 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
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120 - ``bray-curtis-dm.qza``
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121
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122 use 'auto' to run on all of host system's available CPU cores
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123 *************************************************************
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124 Using the ``qiime2 diversity-lib bray-curtis`` tool:
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125 #. Set *"table"* to ``#: feature-table.qza``
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126 #. Press the ``Execute`` button.
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127
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128 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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129 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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130
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131 .. list-table::
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132 :align: left
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133 :header-rows: 1
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134
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135 * - History Name
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136 - *"Name"* to set (be sure to press ``Save``)
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137 * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
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138 - ``bray-curtis-dm.qza``
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139
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140
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141 |
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142
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143 </help>
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144 <citations>
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145 <citation type="bibtex">@article{cite1,
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146 author = {Sørensen, Thorvald},
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147 journal = {Biol. Skr.},
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148 pages = {1--34},
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149 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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150 volume = {5},
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151 year = {1948}
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152 }
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153 </citation>
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154 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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155 </citations>
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156 </tool>