Mercurial > repos > q2d2 > qiime2__emperor__biplot

annotate qiime2__emperor__biplot.xml @ 0:72079afffe4c draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:48:59 +0000
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children 5aced4a38720
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2022, QIIME 2 development team.
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4
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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: 2022.8.1)
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10 for:
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11 qiime2 (version: 2022.8.1)
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12 -->
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13 <tool name="qiime2 emperor biplot" id="qiime2__emperor__biplot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.8</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="aggressive">q2galaxy run emperor biplot '$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="biplot" type="data" format="qza" label="biplot: PCoAResults % Properties('biplot')" 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 % Properties('biplot')"/>
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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 % Properties('biplot')"]</validator>
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29 </param>
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30 <repeat name="sample_metadata" min="1" help="[required] The sample metadata" title="sample_metadata: Metadata">
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31 <conditional name="__q2galaxy__GUI__conditional__sample_metadata__">
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32 <param name="type" type="select" label="sample_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="feature_metadata" help="[optional] The feature metadata (useful to manipulate the arrows in the plot)." title="feature_metadata: Metadata">
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46 <conditional name="__q2galaxy__GUI__conditional__feature_metadata__">
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47 <param name="type" type="select" label="feature_metadata: Metadata">
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48 <option value="tsv" selected="true">Metadata from TSV</option>
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49 <option value="qza">Metadata from Artifact</option>
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50 </param>
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51 <when value="tsv">
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52 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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53 </when>
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54 <when value="qza">
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55 <param name="source" type="data" format="qza" label="Metadata Source"/>
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56 </when>
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57 </conditional>
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58 </repeat>
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59 <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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60 <param name="invert" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="invert: Bool" help="[default: No] If specified, the point and arrow coordinates will be swapped."/>
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61 <param name="number_of_features" type="integer" min="1" value="5" label="number_of_features: Int % Range(1, None)" help="[default: 5] The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin)."/>
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62 </section>
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63 </inputs>
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64 <outputs>
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65 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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66 </outputs>
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67 <tests/>
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68 <help>
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69 QIIME 2: emperor biplot
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70 =======================
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71 Visualize and Interact with Principal Coordinates Analysis Biplot
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72
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73
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74 Outputs:
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75 --------
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76 :visualization.qzv: &lt;no description&gt;
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77
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78 |
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80 Description:
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81 ------------
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82 Generates an interactive ordination biplot where the user can visually integrate sample and feature metadata. Vectors representing the n most important features are then plotted in the emperor visualization (5 largest, by default).
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84
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85 |
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87 </help>
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88 <citations>
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89 <citation type="doi">10.1186/2047-217X-2-16</citation>
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90 <citation type="doi">10.1016/j.chom.2016.12.009</citation>
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91 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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92 </citations>
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93 </tool>