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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:58:46 +0000
parents d9d69991f2b2
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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:
5
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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 taxa barplot" id="qiime2__taxa__barplot" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Visualize taxonomy with an interactive bar plot</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 taxa</version_command>
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22 <command detect_errors="exit_code">q2galaxy run taxa barplot '$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 | PresenceAbsence]" help="[required] Feature table to visualize at various taxonomic levels.">
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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 </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[PresenceAbsence]']</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="taxonomy" type="data" format="qza" optional="true" label="taxonomy: FeatureData[Taxonomy]" help="[optional] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. If no taxonomy is provided, the feature IDs will be used as labels.">
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36 <options options_filter_attribute="metadata.semantic_type">
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37 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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38 </options>
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39 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
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40 </param>
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41 <repeat name="metadata" help="[optional] The sample metadata." title="metadata: Metadata">
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42 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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43 <param name="type" type="select" label="metadata: Metadata">
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44 <option value="tsv" selected="true">Metadata from TSV</option>
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45 <option value="qza">Metadata from Artifact</option>
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46 </param>
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47 <when value="tsv">
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48 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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49 </when>
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50 <when value="qza">
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51 <param name="source" type="data" format="qza" label="Metadata Source"/>
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52 </when>
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53 </conditional>
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54 </repeat>
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55 <conditional name="__q2galaxy__GUI__conditional__level_delimiter__" label="level_delimiter: Str">
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56 <param name="__q2galaxy__GUI__select__" type="select" label="level_delimiter: Str" help="[optional] Attempt to parse hierarchical taxonomic information from feature IDs by separating levels with this character. This parameter is ignored if a taxonomy is provided as input.">
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57 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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58 <option value="__q2galaxy__::control::provide">Provide a value</option>
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59 </param>
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60 <when value="__q2galaxy__::control::default">
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61 <param name="level_delimiter" type="hidden" value="__q2galaxy__::literal::None"/>
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62 </when>
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63 <when value="__q2galaxy__::control::provide">
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64 <param name="level_delimiter" type="text">
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65 <sanitizer>
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66 <valid initial="string.printable"/>
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67 </sanitizer>
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68 </param>
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69 </when>
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70 </conditional>
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71 </section>
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72 </inputs>
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73 <outputs>
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74 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="table" value="barplot.test0.table.qza" ftype="qza"/>
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79 <param name="taxonomy" value="barplot.test0.taxonomy.qza" ftype="qza"/>
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80 <repeat name="metadata">
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81 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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82 <param name="type" value="tsv"/>
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83 <param name="source" value="barplot.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
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84 </conditional>
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85 </repeat>
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86 <output name="visualization" ftype="qzv">
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87 <assert_contents>
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88 <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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89 <has_line_matching expression="type: Visualization"/>
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90 </has_archive_member>
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91 </assert_contents>
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92 </output>
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93 </test>
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94 </tests>
0
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95 <help>
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96 QIIME 2: taxa barplot
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97 =====================
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98 Visualize taxonomy with an interactive bar plot
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99
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100
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101 Outputs:
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102 --------
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103 :visualization.qzv: &lt;no description&gt;
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104
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105 |
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106
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107 Description:
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108 ------------
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109 This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export.
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110
1
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111 Examples:
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112 ---------
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113
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114 barplot
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115 *******
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116 Using the ``qiime2 taxa barplot`` tool:
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117 #. Set *"table"* to ``#: table.qza``
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118 #. Expand the ``additional options`` section
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119
2
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120 #. Set *"taxonomy"* to ``#: taxonomy.qza``
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121 #. For *"metadata"*:
1
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122
2
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123 - Press the ``+ Insert metadata`` button to set up the next steps.
1
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124
2
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125 #. Leave as ``Metadata from TSV``
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126 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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127
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128
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129
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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 taxa barplot [...] : visualization.qzv``
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142 - ``taxa-bar-plots.qzv``
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143
0
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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="doi">10.1038/s41587-019-0209-9</citation>
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150 </citations>
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151 </tool>