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author q2d2
date Mon, 03 Jun 2024 23:29:14 +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) 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: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 longitudinal pairwise-distances" id="qiime2__longitudinal__pairwise_distances" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Paired pairwise distance testing and boxplots</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version longitudinal</version_command>
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19 <command detect_errors="exit_code">q2galaxy run longitudinal pairwise_distances '$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="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 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
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31 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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32 <param name="type" type="select" label="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 <param name="group_column" type="text" label="group_column: Str" help="[required] Metadata column on which to separate groups for comparison">
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45 <sanitizer>
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46 <valid initial="string.printable"/>
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47 </sanitizer>
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48 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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49 </param>
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50 <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (e.g., Time) across which samples are paired.">
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51 <sanitizer>
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52 <valid initial="string.printable"/>
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53 </sanitizer>
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54 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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55 </param>
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56 <param name="state_1" type="text" label="state_1: Str" help="[required] Baseline state column value.">
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57 <sanitizer>
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58 <valid initial="string.printable"/>
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59 </sanitizer>
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60 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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61 </param>
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62 <param name="state_2" type="text" label="state_2: Str" help="[required] State column value to pair with baseline.">
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63 <sanitizer>
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64 <valid initial="string.printable"/>
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65 </sanitizer>
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66 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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67 </param>
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68 <param name="individual_id_column" type="text" label="individual_id_column: Str" help="[required] Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state_1 or state_2, that subject will be dropped and reported in standard output by default. Set replicate_handling=&quot;random&quot; to instead randomly select one member.">
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69 <sanitizer>
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70 <valid initial="string.printable"/>
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71 </sanitizer>
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72 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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73 </param>
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74 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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75 <param name="parametric" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parametric: Bool" help="[default: No] Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests."/>
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76 <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')">
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77 <option value="Set1" selected="true">Set1</option>
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78 <option value="Set2">Set2</option>
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79 <option value="Set3">Set3</option>
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80 <option value="Pastel1">Pastel1</option>
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81 <option value="Pastel2">Pastel2</option>
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82 <option value="Paired">Paired</option>
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83 <option value="Accent">Accent</option>
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84 <option value="Dark2">Dark2</option>
05288bdecab7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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85 <option value="tab10">tab10</option>
05288bdecab7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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86 <option value="tab20">tab20</option>
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87 <option value="tab20b">tab20b</option>
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88 <option value="tab20c">tab20c</option>
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89 <option value="viridis">viridis</option>
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90 <option value="plasma">plasma</option>
05288bdecab7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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91 <option value="inferno">inferno</option>
05288bdecab7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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92 <option value="magma">magma</option>
05288bdecab7 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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93 <option value="terrain">terrain</option>
05288bdecab7 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="rainbow">rainbow</option>
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95 <option value="cividis">cividis</option>
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96 </param>
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97 <param name="replicate_handling" type="select" label="replicate_handling: Str % Choices('error', 'random', 'drop')" display="radio">
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98 <option value="error" selected="true">error</option>
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99 <option value="random">random</option>
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100 <option value="drop">drop</option>
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101 </param>
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102 </section>
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103 </inputs>
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104 <outputs>
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105 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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106 </outputs>
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107 <tests/>
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108 <help>
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109 QIIME 2: longitudinal pairwise-distances
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110 ========================================
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111 Paired pairwise distance testing and boxplots
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112
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113
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114 Outputs:
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115 --------
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116 :visualization.qzv: &lt;no description&gt;
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117
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118 |
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119
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120 Description:
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121 ------------
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122 Performs pairwise distance testing between sample pairs from each subject. Sample pairs may represent a typical intervention study, e.g., samples collected pre- and post-treatment; paired samples from two different timepoints (e.g., in a longitudinal study design), or identical samples receiving different two different treatments. This action tests whether the pairwise distance between each subject pair differs between groups (e.g., groups of subjects receiving different treatments) and produces boxplots of paired distance distributions for each group.
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123
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124
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125 |
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126
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127 </help>
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128 <citations>
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129 <citation type="doi">10.1128/mSystems.00219-18</citation>
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130 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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131 </citations>
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132 </tool>