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author q2d2
date Mon, 05 May 2025 18:56:17 +0000
parents d10f755328ea
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2025, 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: 2025.4.0)
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10 for:
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11 qiime2 (version: 2025.4.0)
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12 -->
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13 <tool name="qiime2 longitudinal linear-mixed-effects" id="qiime2__longitudinal__linear_mixed_effects" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Linear mixed effects modeling</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:2025.4</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 linear_mixed_effects '$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 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
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28 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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29 <param name="type" type="select" label="metadata: Metadata">
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30 <option value="tsv" selected="true">Metadata from TSV</option>
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31 <option value="qza">Metadata from Artifact</option>
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32 </param>
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33 <when value="tsv">
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34 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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35 </when>
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36 <when value="qza">
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37 <param name="source" type="data" format="qza" label="Metadata Source"/>
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38 </when>
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39 </conditional>
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40 </repeat>
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41 <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (time) variable information.">
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42 <sanitizer>
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43 <valid initial="string.printable"/>
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44 </sanitizer>
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45 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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46 </param>
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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="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional] Feature table containing metric.">
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55 <options options_filter_attribute="metadata.semantic_type">
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56 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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57 </options>
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58 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
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59 </param>
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60 <conditional name="__q2galaxy__GUI__conditional__metric__" label="metric: Str">
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61 <param name="__q2galaxy__GUI__select__" type="select" label="metric: Str" help="[optional] Dependent variable column name. Must be a column name located in the metadata or feature table files.">
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62 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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63 <option value="__q2galaxy__::control::provide">Provide a value</option>
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64 </param>
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65 <when value="__q2galaxy__::control::default">
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66 <param name="metric" type="hidden" value="__q2galaxy__::literal::None"/>
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67 </when>
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68 <when value="__q2galaxy__::control::provide">
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69 <param name="metric" type="text">
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70 <sanitizer>
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71 <valid initial="string.printable"/>
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72 </sanitizer>
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73 </param>
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74 </when>
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75 </conditional>
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76 <conditional name="__q2galaxy__GUI__conditional__group_columns__" label="group_columns: Str">
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77 <param name="__q2galaxy__GUI__select__" type="select" label="group_columns: Str" help="[optional] Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of &quot;metric&quot;.">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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78 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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79 <option value="__q2galaxy__::control::provide">Provide a value</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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80 </param>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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81 <when value="__q2galaxy__::control::default">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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82 <param name="group_columns" type="hidden" value="__q2galaxy__::literal::None"/>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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83 </when>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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84 <when value="__q2galaxy__::control::provide">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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85 <param name="group_columns" type="text">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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86 <sanitizer>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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87 <valid initial="string.printable"/>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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88 </sanitizer>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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89 </param>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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90 </when>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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91 </conditional>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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92 <conditional name="__q2galaxy__GUI__conditional__random_effects__" label="random_effects: Str">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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93 <param name="__q2galaxy__GUI__select__" type="select" label="random_effects: Str" help="[optional] Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of &quot;metric&quot;. To add a random slope, the same value passed to &quot;state_column&quot; should be passed here. A random intercept for each individual is set by default and does not need to be passed here.">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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94 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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95 <option value="__q2galaxy__::control::provide">Provide a value</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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96 </param>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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97 <when value="__q2galaxy__::control::default">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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98 <param name="random_effects" type="hidden" value="__q2galaxy__::literal::None"/>
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99 </when>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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100 <when value="__q2galaxy__::control::provide">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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101 <param name="random_effects" type="text">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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102 <sanitizer>
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103 <valid initial="string.printable"/>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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104 </sanitizer>
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105 </param>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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106 </when>
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107 </conditional>
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108 <param name="palette" type="select" label="palette: Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis')">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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109 <option value="Set1" selected="true">Set1</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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110 <option value="Set2">Set2</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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111 <option value="Set3">Set3</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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112 <option value="Pastel1">Pastel1</option>
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113 <option value="Pastel2">Pastel2</option>
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114 <option value="Paired">Paired</option>
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115 <option value="Accent">Accent</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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116 <option value="Dark2">Dark2</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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117 <option value="tab10">tab10</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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118 <option value="tab20">tab20</option>
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119 <option value="tab20b">tab20b</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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120 <option value="tab20c">tab20c</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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121 <option value="viridis">viridis</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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122 <option value="plasma">plasma</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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123 <option value="inferno">inferno</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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124 <option value="magma">magma</option>
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125 <option value="terrain">terrain</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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126 <option value="rainbow">rainbow</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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127 <option value="cividis">cividis</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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128 </param>
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129 <param name="lowess" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="lowess: Bool" help="[default: No] Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting."/>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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130 <param name="ci" type="float" min="0" max="99.999999" value="95" label="ci: Float % Range(0, 100)" help="[default: 95] Size of the confidence interval for the regression estimate."/>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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131 <conditional name="__q2galaxy__GUI__conditional__formula__" label="formula: Str">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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132 <param name="__q2galaxy__GUI__select__" type="select" label="formula: Str" help="[optional] R-style formula to use for model specification. A formula must be used if the &quot;metric&quot; parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format &quot;a ~ b + c&quot;, where &quot;a&quot; is the metric (dependent variable) and &quot;b&quot; and &quot;c&quot; are independent covariates. Use &quot;+&quot; to add a variable; &quot;+ a:b&quot; to add an interaction between variables a and b; &quot;*&quot; to include a variable and all interactions; and &quot;-&quot; to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises.">
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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133 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
8fe7ffdd3a71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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134 <option value="__q2galaxy__::control::provide">Provide a value</option>
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135 </param>
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136 <when value="__q2galaxy__::control::default">
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137 <param name="formula" type="hidden" value="__q2galaxy__::literal::None"/>
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138 </when>
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139 <when value="__q2galaxy__::control::provide">
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140 <param name="formula" type="text">
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141 <sanitizer>
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142 <valid initial="string.printable"/>
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143 </sanitizer>
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144 </param>
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145 </when>
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146 </conditional>
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147 </section>
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148 </inputs>
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149 <outputs>
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150 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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151 </outputs>
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152 <tests/>
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153 <help>
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154 QIIME 2: longitudinal linear-mixed-effects
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155 ==========================================
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156 Linear mixed effects modeling
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157
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158
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159 Outputs:
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160 --------
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161 :visualization.qzv: &lt;no description&gt;
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162
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163 |
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164
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165 Description:
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166 ------------
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167 Linear mixed effects models evaluate the contribution of exogenous covariates "group_columns" and "random_effects" to a single dependent variable, "metric". Perform LME and plot line plots of each group column. A feature table artifact is required input, though whether "metric" is derived from the feature table or metadata is optional.
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168
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169
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170 |
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171
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172 </help>
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173 <citations>
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174 <citation type="bibtex">@inproceedings{cite1,
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175 author = {Seabold, Skipper and Perktold, Josef},
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176 booktitle = {Proceedings of the 9th Python in Science Conference},
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177 organization = {SciPy society Austin},
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178 pages = {61},
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179 title = {Statsmodels: Econometric and statistical modeling with python},
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180 volume = {57},
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181 year = {2010}
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182 }
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183 </citation>
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184 <citation type="doi">10.1128/mSystems.00219-18</citation>
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185 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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186 </citations>
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187 </tool>