Mercurial > repos > q2d2 > qiime2__diversity__mantel

annotate qiime2__diversity__mantel.xml @ 3:57fa02b53979 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 20:58:47 +0000
parents 196948449667
children 9a97bf1e0e05
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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:
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9 q2galaxy (version: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 diversity mantel" id="qiime2__diversity__mantel" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Apply the Mantel test to two distance matrices</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</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="exit_code">q2galaxy run diversity mantel '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="dm1" type="data" format="qza" label="dm1: 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 <param name="dm2" type="data" format="qza" label="dm2: DistanceMatrix" help="[required] Matrix of distances between pairs of samples.">
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31 <options options_filter_attribute="metadata.semantic_type">
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32 <filter type="add_value" value="DistanceMatrix"/>
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33 </options>
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34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator>
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35 </param>
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36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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37 <param name="method" type="select" label="method: Str % Choices('spearman', 'pearson')" display="radio">
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38 <option value="spearman" selected="true">spearman</option>
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39 <option value="pearson">pearson</option>
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40 </param>
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41 <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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42 <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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43 <param name="label1" type="text" value="Distance Matrix 1" label="label1: Str" help="[default: 'Distance Matrix 1'] Label for `dm1` in the output visualization.">
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44 <sanitizer>
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45 <valid initial="string.printable"/>
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46 </sanitizer>
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47 </param>
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48 <param name="label2" type="text" value="Distance Matrix 2" label="label2: Str" help="[default: 'Distance Matrix 2'] Label for `dm2` in the output visualization.">
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49 <sanitizer>
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50 <valid initial="string.printable"/>
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51 </sanitizer>
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52 </param>
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53 </section>
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54 </inputs>
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55 <outputs>
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56 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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57 </outputs>
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58 <tests/>
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59 <help>
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60 QIIME 2: diversity mantel
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61 =========================
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62 Apply the Mantel test to two distance matrices
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63
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64
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65 Outputs:
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66 --------
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67 :visualization.qzv: &lt;no description&gt;
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68
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69 |
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70
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71 Description:
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72 ------------
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73 Apply a two-sided Mantel test to identify correlation between two distance matrices.
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74
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75 Note: the directionality of the comparison has no bearing on the results. Thus, comparing distance matrix X to distance matrix Y is equivalent to comparing Y to X.
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76
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77 Note: the order of samples within the two distance matrices does not need to be the same; the distance matrices will be reordered before applying the Mantel test.
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78
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79 See the scikit-bio docs for more details about the Mantel test:
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80
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81 http://scikit-bio.org/docs/latest/generated/skbio.stats.distance.mantel
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82
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83
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84 |
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85
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86 </help>
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87 <citations>
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88 <citation type="bibtex">@article{cite1,
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89 author = {Mantel, Nathan},
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90 journal = {Cancer research},
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91 number = {2 Part 1},
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92 pages = {209--220},
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93 publisher = {AACR},
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94 title = {The detection of disease clustering and a generalized regression approach},
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95 volume = {27},
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96 year = {1967}
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97 }
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98 </citation>
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99 <citation type="doi">https://doi.org/10.1098/rspl.1895.0041</citation>
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100 <citation type="doi">https://doi.org/10.2307/1422689</citation>
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101 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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102 </citations>
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103 </tool>