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author q2d2
date Wed, 30 Oct 2024 19:44:28 +0000
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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 shannon-entropy" id="qiime2__diversity_lib__shannon_entropy" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Shannon's Entropy</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 shannon_entropy '$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 Shannon's Entropy 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 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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35 <param name="drop_undefined_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="drop_undefined_samples: Bool" help="[default: No] Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector."/>
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36 </section>
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37 </inputs>
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38 <outputs>
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39 <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="table" value="shannon_entropy.test0.feature-table.qza" ftype="qza"/>
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44 <output name="vector" ftype="qza">
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45 <assert_contents>
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46 <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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47 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
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48 </has_archive_member>
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49 </assert_contents>
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50 </output>
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51 </test>
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52 <test>
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53 <param name="table" value="shannon_entropy.test1.feature-table.qza" ftype="qza"/>
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54 <param name="drop_undefined_samples" value="__q2galaxy__::literal::True"/>
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55 <output name="vector" ftype="qza">
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56 <assert_contents>
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57 <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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58 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
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59 </has_archive_member>
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60 </assert_contents>
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61 </output>
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62 </test>
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63 </tests>
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64 <help>
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65 QIIME 2: diversity-lib shannon-entropy
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66 ======================================
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67 Shannon's Entropy
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68
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69
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70 Outputs:
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71 --------
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72 :vector.qza: Vector containing per-sample values for Shannon's Entropy.
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73
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74 |
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75
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76 Description:
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77 ------------
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78 Compute Shannon's Entropy for each sample in a feature table
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79
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80 Examples:
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81 ---------
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82
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83 basic
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84 *****
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85 Using the ``qiime2 diversity-lib shannon-entropy`` tool:
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86 #. Set *"table"* to ``#: feature-table.qza``
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87 #. Press the ``Execute`` button.
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88
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89 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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90 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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91
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92 .. list-table::
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93 :align: left
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94 :header-rows: 1
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95
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96 * - History Name
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97 - *"Name"* to set (be sure to press ``Save``)
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98 * - ``#: qiime2 diversity-lib shannon-entropy [...] : vector.qza``
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99 - ``shannon-vector.qza``
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100
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101 dropping undefined samples
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102 **************************
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103 Using the ``qiime2 diversity-lib shannon-entropy`` tool:
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104 #. Set *"table"* to ``#: feature-table.qza``
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105 #. Expand the ``additional options`` section
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106
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107 - Set *"drop_undefined_samples"* to ``Yes``
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108
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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 shannon-entropy [...] : vector.qza``
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121 - ``shannon-vector.qza``
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122
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123
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124 |
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125
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126 </help>
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127 <citations>
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128 <citation type="doi">10.1002/j.1538-7305.1948.tb01338.x</citation>
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129 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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130 </citations>
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131 </tool>