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annotate qiime2__diversity__alpha_rarefaction.xml @ 4:a19425489a68 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:19:03 +0000
parents fff91b5ed450
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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 diversity alpha-rarefaction" id="qiime2__diversity__alpha_rarefaction" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Alpha rarefaction curves</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 diversity</version_command>
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19 <command detect_errors="exit_code">q2galaxy run diversity alpha_rarefaction '$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="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table to compute rarefaction curves from.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[Frequency]"/>
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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 ['FeatureTable[Frequency]']</validator>
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29 </param>
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30 <param name="max_depth" type="integer" min="1" value="" label="max_depth: Int % Range(1, None)" help="[required] The maximum rarefaction depth. Must be greater than min_depth."/>
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31 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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32 <param name="phylogeny" type="data" format="qza" optional="true" label="phylogeny: Phylogeny[Rooted]" help="[optional] Optional phylogeny for phylogenetic metrics.">
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33 <options options_filter_attribute="metadata.semantic_type">
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34 <filter type="add_value" value="Phylogeny[Rooted]"/>
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35 </options>
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36 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
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37 </param>
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38 <repeat name="metrics" help="[optional] The metrics to be measured. By default computes observed_features, shannon, and if phylogeny is provided, faith_pd." title="metrics: Set[Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'dominance', 'doubles', 'enspie', 'faith_pd', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_features', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles')]">
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39 <param name="element" type="select" label="element: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'dominance', 'doubles', 'enspie', 'faith_pd', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_features', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles')">
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40 <option value="__q2galaxy__::literal::None">Selection required</option>
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41 <option value="ace">ace</option>
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42 <option value="berger_parker_d">berger_parker_d</option>
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43 <option value="brillouin_d">brillouin_d</option>
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44 <option value="chao1">chao1</option>
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45 <option value="dominance">dominance</option>
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46 <option value="doubles">doubles</option>
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47 <option value="enspie">enspie</option>
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48 <option value="faith_pd">faith_pd</option>
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49 <option value="fisher_alpha">fisher_alpha</option>
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50 <option value="gini_index">gini_index</option>
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51 <option value="goods_coverage">goods_coverage</option>
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52 <option value="heip_e">heip_e</option>
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53 <option value="lladser_pe">lladser_pe</option>
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54 <option value="margalef">margalef</option>
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55 <option value="mcintosh_d">mcintosh_d</option>
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56 <option value="mcintosh_e">mcintosh_e</option>
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57 <option value="menhinick">menhinick</option>
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58 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
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59 <option value="observed_features">observed_features</option>
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60 <option value="pielou_e">pielou_e</option>
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61 <option value="robbins">robbins</option>
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62 <option value="shannon">shannon</option>
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63 <option value="simpson">simpson</option>
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64 <option value="simpson_e">simpson_e</option>
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65 <option value="singles">singles</option>
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66 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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67 </param>
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68 </repeat>
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69 <repeat name="metadata" help="[optional] The sample metadata." title="metadata: Metadata">
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70 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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71 <param name="type" type="select" label="metadata: Metadata">
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72 <option value="tsv" selected="true">Metadata from TSV</option>
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73 <option value="qza">Metadata from Artifact</option>
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74 </param>
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75 <when value="tsv">
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76 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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77 </when>
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78 <when value="qza">
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79 <param name="source" type="data" format="qza" label="Metadata Source"/>
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80 </when>
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81 </conditional>
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82 </repeat>
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83 <param name="min_depth" type="integer" min="1" value="1" label="min_depth: Int % Range(1, None)" help="[default: 1] The minimum rarefaction depth."/>
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84 <param name="steps" type="integer" min="2" value="10" label="steps: Int % Range(2, None)" help="[default: 10] The number of rarefaction depths to include between min_depth and max_depth."/>
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85 <param name="iterations" type="integer" min="1" value="10" label="iterations: Int % Range(1, None)" help="[default: 10] The number of rarefied feature tables to compute at each step."/>
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86 </section>
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87 </inputs>
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88 <outputs>
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89 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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90 </outputs>
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91 <tests/>
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92 <help>
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93 QIIME 2: diversity alpha-rarefaction
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94 ====================================
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95 Alpha rarefaction curves
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96
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97
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98 Outputs:
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99 --------
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100 :visualization.qzv: &lt;no description&gt;
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101
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102 |
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103
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104 Description:
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105 ------------
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106 Generate interactive alpha rarefaction curves by computing rarefactions between `min_depth` and `max_depth`. The number of intermediate depths to compute is controlled by the `steps` parameter, with n `iterations` being computed at each rarefaction depth. If sample metadata is provided, samples may be grouped based on distinct values within a metadata column.
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107
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108
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109 |
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110
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111 </help>
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112 <citations>
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113 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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114 </citations>
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115 </tool>