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annotate qiime2__emperor__plot.xml @ 1:7c9ec8b8b7f8 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:50:44 +0000
parents e6978c621d70
children bc3a80afa08d
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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: 2022.11.1)
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10 for:
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11 qiime2 (version: 2022.11.1)
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12 -->
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13 <tool name="qiime2 emperor plot" id="qiime2__emperor__plot" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Visualize and Interact with Principal Coordinates Analysis Plots</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.11</container>
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17 </requirements>
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18 <version_command>q2galaxy version emperor</version_command>
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19 <command detect_errors="exit_code">q2galaxy run emperor plot '$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="pcoa" type="data" format="qza" label="pcoa: PCoAResults" help="[required] The principal coordinates matrix to be plotted.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="PCoAResults"/>
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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 ['PCoAResults']</validator>
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29 </param>
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30 <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata">
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31 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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32 <param name="type" type="select" label="metadata: Metadata">
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33 <option value="tsv" selected="true">Metadata from TSV</option>
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34 <option value="qza">Metadata from Artifact</option>
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35 </param>
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36 <when value="tsv">
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37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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38 </when>
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39 <when value="qza">
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40 <param name="source" type="data" format="qza" label="Metadata Source"/>
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41 </when>
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42 </conditional>
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43 </repeat>
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44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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45 <repeat name="custom_axes" help="[optional] Numeric sample metadata columns that should be included as axes in the Emperor plot." title="custom_axes: List[Str]">
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46 <param name="element" type="text" label="element: Str" help="[required]">
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47 <sanitizer>
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48 <valid initial="string.printable"/>
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49 </sanitizer>
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50 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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51 </param>
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52 </repeat>
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53 <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No] This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: &quot;This sample has no metadata&quot;. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata."/>
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54 <param name="ignore_pcoa_features" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_pcoa_features: Bool" help="[default: No] Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised."/>
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55 </section>
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56 </inputs>
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57 <outputs>
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58 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="pcoa" value="plot.test0.pcoa-result.qza" ftype="qza"/>
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63 <repeat name="metadata">
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64 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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65 <param name="type" value="tsv"/>
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66 <param name="source" value="plot.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
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67 </conditional>
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68 </repeat>
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69 <output name="visualization" ftype="qzv">
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70 <assert_contents>
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71 <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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72 <has_line_matching expression="type: Visualization"/>
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73 </has_archive_member>
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74 </assert_contents>
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75 </output>
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76 </test>
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77 </tests>
0
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78 <help>
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79 QIIME 2: emperor plot
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80 =====================
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81 Visualize and Interact with Principal Coordinates Analysis Plots
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82
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83
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84 Outputs:
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85 --------
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86 :visualization.qzv: &lt;no description&gt;
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87
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88 |
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89
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90 Description:
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91 ------------
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92 Generates an interactive ordination plot where the user can visually integrate sample metadata.
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93
1
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94 Examples:
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95 ---------
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96
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97 emperor_plot
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98 ************
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99 Using the ``qiime2 emperor plot`` tool:
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100 #. Set *"pcoa"* to ``#: pcoa-result.qza``
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101 #. For *"metadata"*:
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102
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103 - Perform the following steps.
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104
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105 #. Leave as ``Metadata from TSV``
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106 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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107
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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 emperor plot [...] : visualization.qzv``
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121 - ``plot.qzv``
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122
0
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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">10.1186/2047-217X-2-16</citation>
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129 <citation type="doi">10.1016/j.chom.2016.12.009</citation>
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130 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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131 </citations>
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132 </tool>