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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:53:01 +0000
parents d17232fb5897
children
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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 longitudinal nmit" id="qiime2__longitudinal__nmit" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Nonparametric microbial interdependence test</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 longitudinal</version_command>
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22 <command detect_errors="exit_code">q2galaxy run longitudinal nmit '$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[RelativeFrequency]" help="[required] Feature table to use for microbial interdependence test.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
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32 </param>
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33 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
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34 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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35 <param name="type" type="select" label="metadata: Metadata">
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36 <option value="tsv" selected="true">Metadata from TSV</option>
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37 <option value="qza">Metadata from Artifact</option>
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38 </param>
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39 <when value="tsv">
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40 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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41 </when>
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42 <when value="qza">
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43 <param name="source" type="data" format="qza" label="Metadata Source"/>
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44 </when>
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45 </conditional>
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46 </repeat>
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47 <param name="individual_id_column" type="text" label="individual_id_column: Str" help="[required] Metadata column containing IDs for individual subjects.">
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48 <sanitizer>
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49 <valid initial="string.printable"/>
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50 </sanitizer>
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51 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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52 </param>
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53 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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54 <param name="corr_method" type="select" label="corr_method: Str % Choices('kendall', 'pearson', 'spearman')" display="radio">
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55 <option value="kendall" selected="true">kendall</option>
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56 <option value="pearson">pearson</option>
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57 <option value="spearman">spearman</option>
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58 </param>
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59 <param name="dist_method" type="select" label="dist_method: Str % Choices('fro', 'nuc')" display="radio">
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60 <option value="fro" selected="true">fro</option>
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61 <option value="nuc">nuc</option>
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62 </param>
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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67 </outputs>
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68 <tests/>
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69 <help>
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70 QIIME 2: longitudinal nmit
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71 ==========================
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72 Nonparametric microbial interdependence test
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73
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74
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75 Outputs:
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76 --------
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77 :distance_matrix.qza: The resulting distance matrix.
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78
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81 Description:
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82 ------------
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83 Perform nonparametric microbial interdependence test to determine longitudinal sample similarity as a function of temporal microbial composition. For more details and citation, please see doi.org/10.1002/gepi.22065
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86 |
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88 </help>
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89 <citations>
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90 <citation type="doi">10.1002/gepi.22065</citation>
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91 <citation type="doi">10.1128/mSystems.00219-18</citation>
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92 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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93 </citations>
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94 </tool>