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annotate qiime2__diversity__beta_correlation.xml @ 0:2dcfb3ea0e51 draft

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author q2d2
date Mon, 29 Aug 2022 19:34:16 +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) 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 diversity beta-correlation" id="qiime2__diversity__beta_correlation" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Beta diversity correlation</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 diversity</version_command>
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19 <command detect_errors="aggressive">q2galaxy run diversity beta_correlation '$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="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] Matrix of distances between pairs of samples.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="DistanceMatrix"/>
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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 ['DistanceMatrix']</validator>
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29 </param>
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30 <conditional name="metadata">
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31 <param name="type" type="select" label="metadata: MetadataColumn[Numeric]" help="[required] Numeric metadata column from which to compute pairwise Euclidean distances">
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32 <option value="tsv" selected="true">Metadata from TSV</option>
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33 <option value="qza">Metadata from Artifact</option>
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34 </param>
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35 <when value="tsv">
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36 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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37 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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38 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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39 </param>
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40 </when>
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41 <when value="qza">
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42 <param name="source" type="data" format="qza" label="Metadata Source"/>
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43 <param name="column" type="text" label="Column Name">
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44 <validator type="empty_field"/>
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45 </param>
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46 </when>
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47 </conditional>
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48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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49 <param name="method" type="select" label="method: Str % Choices('spearman', 'pearson')" display="radio">
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50 <option value="spearman" selected="true">spearman</option>
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51 <option value="pearson">pearson</option>
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52 </param>
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53 <param name="permutations" type="integer" min="0" value="999" label="permutations: Int % Range(0, None)" help="[default: 999] The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."/>
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54 <param name="intersect_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="intersect_ids: Bool" help="[default: No] If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs."/>
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55 <param name="label1" type="text" value="Metadata" label="label1: Str" help="[default: 'Metadata'] Label for `distance_matrix` in the output visualization.">
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56 <sanitizer>
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57 <valid initial="string.printable"/>
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58 </sanitizer>
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59 </param>
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60 <param name="label2" type="text" value="Distance Matrix" label="label2: Str" help="[default: 'Distance Matrix'] Label for `metadata_distance_matrix` in the output visualization.">
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61 <sanitizer>
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62 <valid initial="string.printable"/>
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63 </sanitizer>
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64 </param>
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <data name="metadata_distance_matrix" format="qza" label="${tool.name} on ${on_string}: metadata_distance_matrix.qza" from_work_dir="metadata_distance_matrix.qza"/>
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69 <data name="mantel_scatter_visualization" format="qzv" label="${tool.name} on ${on_string}: mantel_scatter_visualization.qzv" from_work_dir="mantel_scatter_visualization.qzv"/>
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70 </outputs>
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71 <tests/>
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72 <help>
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73 QIIME 2: diversity beta-correlation
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74 ===================================
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75 Beta diversity correlation
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76
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77
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78 Outputs:
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79 --------
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80 :metadata_distance_matrix.qza: The Distance Matrix produced from the metadata column and used in the mantel test
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81 :mantel_scatter_visualization.qzv: Scatter plot rendering of the manteltest results
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83 |
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85 Description:
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86 ------------
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87 Create a distance matrix from a numeric metadata column and apply a two-sided Mantel test to identify correlation between two distance matrices. Actions used internally: `distance-matrix` from q2-metadata and `mantel` from q2-diversity.
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89
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90 |
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91
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92 </help>
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93 <citations>
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94 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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95 </citations>
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96 </tool>