Mercurial > repos > q2d2 > qiime2__diversity_lib__alpha_passthrough

annotate qiime2__diversity_lib__alpha_passthrough.xml @ 2:98ae2621b590 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:39:18 +0000
parents 86034ce5e0b5
children 0292b5d33b9c
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, 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: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 diversity-lib alpha-passthrough" id="qiime2__diversity_lib__alpha_passthrough" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Alpha Passthrough (non-phylogenetic)</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2023.5</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 alpha_passthrough '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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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]" help="[required] The feature table containing the samples for which a selected metric 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[Frequency]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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29 </param>
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30 <param name="metric" type="select" label="metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong')">
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31 <option value="__q2galaxy__::literal::None">Selection required</option>
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32 <option value="ace">ace</option>
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33 <option value="berger_parker_d">berger_parker_d</option>
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34 <option value="brillouin_d">brillouin_d</option>
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35 <option value="chao1">chao1</option>
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36 <option value="chao1_ci">chao1_ci</option>
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37 <option value="dominance">dominance</option>
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38 <option value="doubles">doubles</option>
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39 <option value="enspie">enspie</option>
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40 <option value="esty_ci">esty_ci</option>
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41 <option value="fisher_alpha">fisher_alpha</option>
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42 <option value="gini_index">gini_index</option>
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43 <option value="goods_coverage">goods_coverage</option>
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44 <option value="heip_e">heip_e</option>
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45 <option value="kempton_taylor_q">kempton_taylor_q</option>
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46 <option value="lladser_pe">lladser_pe</option>
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47 <option value="margalef">margalef</option>
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48 <option value="mcintosh_d">mcintosh_d</option>
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49 <option value="mcintosh_e">mcintosh_e</option>
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50 <option value="menhinick">menhinick</option>
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51 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
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52 <option value="osd">osd</option>
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53 <option value="robbins">robbins</option>
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54 <option value="simpson">simpson</option>
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55 <option value="simpson_e">simpson_e</option>
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56 <option value="singles">singles</option>
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57 <option value="strong">strong</option>
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58 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="table" value="alpha_passthrough.test0.feature-table.qza" ftype="qza"/>
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67 <param name="metric" value="simpson"/>
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68 <output name="vector" ftype="qza">
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69 <assert_contents>
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70 <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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71 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
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72 </has_archive_member>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 </tests>
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77 <help>
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78 QIIME 2: diversity-lib alpha-passthrough
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79 ========================================
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80 Alpha Passthrough (non-phylogenetic)
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81
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82
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83 Outputs:
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84 --------
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85 :vector.qza: Vector containing per-sample values for the chosen metric.
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86
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87 |
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88
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89 Description:
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90 ------------
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91 Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.
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92
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93 Examples:
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94 ---------
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95
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96 basic
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97 *****
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98 Using the ``qiime2 diversity-lib alpha-passthrough`` tool:
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99 #. Set *"table"* to ``#: feature-table.qza``
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100 #. Set *"metric"* to ``simpson``
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101 #. Press the ``Execute`` button.
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102
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103 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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104 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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105
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106 .. list-table::
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107 :align: left
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108 :header-rows: 1
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109
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110 * - History Name
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111 - *"Name"* to set (be sure to press ``Save``)
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112 * - ``#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza``
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113 - ``simpson-vector.qza``
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114
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115
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116 |
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117
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118 </help>
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119 <citations>
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120 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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121 </citations>
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122 </tool>