Mercurial > repos > q2d2 > qiime2__diversity_lib__beta_phylogenetic_passthrough
annotate qiime2__diversity_lib__beta_phylogenetic_passthrough.xml @ 0:faf299216a5e draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 19:44:51 +0000 |
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children | 423e0a6e9a1f |
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faf299216a5e
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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3 Copyright (c) 2022, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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9 q2galaxy (version: 2022.8.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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11 qiime2 (version: 2022.8.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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13 <tool name="qiime2 diversity-lib beta-phylogenetic-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_passthrough" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Beta Phylogenetic Passthrough</description> |
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15 <requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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16 <container type="docker">quay.io/qiime2/core:2022.8</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
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18 <version_command>q2galaxy version diversity_lib</version_command> |
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19 <command detect_errors="aggressive">q2galaxy run diversity_lib beta_phylogenetic_passthrough '$inputs'</command> |
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20 <configfiles> |
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21 <inputs name="inputs" data_style="paths"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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23 <inputs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples over which beta diversity should be computed."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="FeatureTable[Frequency]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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="phylogeny" type="data" format="qza" label="phylogeny: Phylogeny[Rooted]" help="[required] Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <filter type="add_value" value="Phylogeny[Rooted]"/> |
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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 ['Phylogeny[Rooted]']</validator> |
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35 </param> |
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36 <param name="metric" type="select" label="metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac')" display="radio"> |
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37 <option value="__q2galaxy__::literal::None">Selection required</option> |
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38 <option value="generalized_unifrac">generalized_unifrac</option> |
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39 <option value="unweighted_unifrac">unweighted_unifrac</option> |
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40 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option> |
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41 <option value="weighted_unifrac">weighted_unifrac</option> |
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42 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> |
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43 </param> |
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44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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45 <conditional name="__q2galaxy__GUI__conditional__threads__"> |
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46 <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."> |
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47 <option value="auto">auto (Str)</option> |
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48 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> |
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49 </param> |
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50 <when value="auto"> |
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51 <param name="threads" type="hidden" value="auto"/> |
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52 </when> |
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53 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> |
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54 <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."/> |
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55 </when> |
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56 </conditional> |
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57 <param name="variance_adjusted" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="variance_adjusted: Bool" help="[default: No] Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation."/> |
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58 <param name="alpha" type="float" min="0" max="1" optional="true" label="alpha: Float % Range(0, 1, inclusive_end=True)" help="[optional] This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized."/> |
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59 <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/> |
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60 </section> |
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61 </inputs> |
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62 <outputs> |
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63 <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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64 </outputs> |
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65 <tests> |
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66 <test> |
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67 <param name="table" value="beta_phylogenetic_passthrough.test0.feature-table.qza" ftype="qza"/> |
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68 <param name="phylogeny" value="beta_phylogenetic_passthrough.test0.phylogeny.qza" ftype="qza"/> |
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69 <param name="metric" value="weighted_normalized_unifrac"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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70 <output name="distance_matrix" ftype="qza"> |
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71 <assert_contents> |
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72 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
faf299216a5e
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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73 <has_line_matching expression="type: DistanceMatrix"/> |
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74 </has_archive_member> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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75 </assert_contents> |
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76 </output> |
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77 </test> |
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78 <test> |
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79 <param name="table" value="beta_phylogenetic_passthrough.test1.feature-table.qza" ftype="qza"/> |
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80 <param name="phylogeny" value="beta_phylogenetic_passthrough.test1.phylogeny.qza" ftype="qza"/> |
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81 <param name="metric" value="weighted_normalized_unifrac"/> |
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82 <conditional name="__q2galaxy__GUI__conditional__threads__"> |
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83 <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/> |
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84 <param name="threads" value="1"/> |
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85 </conditional> |
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86 <output name="distance_matrix" ftype="qza"> |
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87 <assert_contents> |
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88 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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89 <has_line_matching expression="type: DistanceMatrix"/> |
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90 </has_archive_member> |
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91 </assert_contents> |
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92 </output> |
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93 </test> |
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94 <test> |
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95 <param name="table" value="beta_phylogenetic_passthrough.test2.feature-table.qza" ftype="qza"/> |
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96 <param name="phylogeny" value="beta_phylogenetic_passthrough.test2.phylogeny.qza" ftype="qza"/> |
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97 <param name="metric" value="weighted_normalized_unifrac"/> |
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98 <conditional name="__q2galaxy__GUI__conditional__threads__"> |
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99 <param name="__q2galaxy__GUI__select__" value="auto"/> |
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100 <param name="threads" value="auto"/> |
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101 </conditional> |
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102 <output name="distance_matrix" ftype="qza"> |
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103 <assert_contents> |
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104 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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105 <has_line_matching expression="type: DistanceMatrix"/> |
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106 </has_archive_member> |
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107 </assert_contents> |
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108 </output> |
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109 </test> |
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110 <test> |
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111 <param name="table" value="beta_phylogenetic_passthrough.test3.feature-table.qza" ftype="qza"/> |
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112 <param name="phylogeny" value="beta_phylogenetic_passthrough.test3.phylogeny.qza" ftype="qza"/> |
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113 <param name="metric" value="weighted_normalized_unifrac"/> |
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114 <conditional name="__q2galaxy__GUI__conditional__threads__"> |
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115 <param name="__q2galaxy__GUI__select__" value="auto"/> |
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116 <param name="threads" value="auto"/> |
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117 </conditional> |
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118 <param name="bypass_tips" value="__q2galaxy__::literal::True"/> |
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119 <output name="distance_matrix" ftype="qza"> |
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120 <assert_contents> |
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121 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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122 <has_line_matching expression="type: DistanceMatrix"/> |
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123 </has_archive_member> |
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124 </assert_contents> |
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125 </output> |
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126 </test> |
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127 <test> |
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128 <param name="table" value="beta_phylogenetic_passthrough.test4.feature-table.qza" ftype="qza"/> |
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129 <param name="phylogeny" value="beta_phylogenetic_passthrough.test4.phylogeny.qza" ftype="qza"/> |
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130 <param name="metric" value="weighted_unifrac"/> |
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131 <conditional name="__q2galaxy__GUI__conditional__threads__"> |
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132 <param name="__q2galaxy__GUI__select__" value="auto"/> |
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133 <param name="threads" value="auto"/> |
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134 </conditional> |
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135 <param name="variance_adjusted" value="__q2galaxy__::literal::True"/> |
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136 <output name="distance_matrix" ftype="qza"> |
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137 <assert_contents> |
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138 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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139 <has_line_matching expression="type: DistanceMatrix"/> |
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140 </has_archive_member> |
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141 </assert_contents> |
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142 </output> |
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143 </test> |
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144 <test> |
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145 <param name="table" value="beta_phylogenetic_passthrough.test5.feature-table.qza" ftype="qza"/> |
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146 <param name="phylogeny" value="beta_phylogenetic_passthrough.test5.phylogeny.qza" ftype="qza"/> |
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147 <param name="metric" value="generalized_unifrac"/> |
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148 <output name="distance_matrix" ftype="qza"> |
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149 <assert_contents> |
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150 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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151 <has_line_matching expression="type: DistanceMatrix"/> |
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152 </has_archive_member> |
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153 </assert_contents> |
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154 </output> |
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155 </test> |
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156 <test> |
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157 <param name="table" value="beta_phylogenetic_passthrough.test6.feature-table.qza" ftype="qza"/> |
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158 <param name="phylogeny" value="beta_phylogenetic_passthrough.test6.phylogeny.qza" ftype="qza"/> |
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159 <param name="metric" value="generalized_unifrac"/> |
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160 <param name="alpha" value="0.75"/> |
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161 <output name="distance_matrix" ftype="qza"> |
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162 <assert_contents> |
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163 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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164 <has_line_matching expression="type: DistanceMatrix"/> |
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165 </has_archive_member> |
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166 </assert_contents> |
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167 </output> |
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168 </test> |
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169 </tests> |
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170 <help> |
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171 QIIME 2: diversity-lib beta-phylogenetic-passthrough |
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172 ==================================================== |
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173 Beta Phylogenetic Passthrough |
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174 |
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175 |
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176 Outputs: |
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177 -------- |
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178 :distance_matrix.qza: The resulting distance matrix. |
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179 |
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180 | |
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181 |
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182 Description: |
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183 ------------ |
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184 Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric. |
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185 |
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186 Examples: |
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187 --------- |
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188 |
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189 run on one core (by default) |
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190 **************************** |
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191 Using the ``qiime2 diversity-lib beta-phylogenetic-passthrough`` tool: |
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192 #. Set *"table"* to ``#: feature-table.qza`` |
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193 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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194 #. Set *"metric"* to ``weighted_normalized_unifrac`` |
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195 #. Press the ``Execute`` button. |
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196 |
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197 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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198 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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199 |
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200 .. list-table:: |
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201 :align: left |
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202 :header-rows: 1 |
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203 |
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204 * - History Name |
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205 - *"Name"* to set (be sure to press ``Save``) |
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206 * - ``#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`` |
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207 - ``weighted-normalized-unifrac-dm.qza`` |
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208 |
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209 to run on n cores, replace 1 here with your preferred integer |
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210 ************************************************************* |
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211 Using the ``qiime2 diversity-lib beta-phylogenetic-passthrough`` tool: |
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212 #. Set *"table"* to ``#: feature-table.qza`` |
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213 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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214 #. Set *"metric"* to ``weighted_normalized_unifrac`` |
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215 #. Expand the ``additional options`` section |
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216 |
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217 - Leave *"threads"* as its default value of ``1`` |
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218 |
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219 #. Press the ``Execute`` button. |
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220 |
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221 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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222 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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223 |
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224 .. list-table:: |
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225 :align: left |
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226 :header-rows: 1 |
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227 |
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228 * - History Name |
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229 - *"Name"* to set (be sure to press ``Save``) |
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230 * - ``#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`` |
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231 - ``weighted-normalized-unifrac-dm.qza`` |
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232 |
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233 use 'auto' to run on all of host system's available CPU cores |
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234 ************************************************************* |
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235 Using the ``qiime2 diversity-lib beta-phylogenetic-passthrough`` tool: |
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236 #. Set *"table"* to ``#: feature-table.qza`` |
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237 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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238 #. Set *"metric"* to ``weighted_normalized_unifrac`` |
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239 #. Expand the ``additional options`` section |
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240 |
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241 - Set *"threads"* to ``auto`` |
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242 |
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243 #. Press the ``Execute`` button. |
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244 |
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245 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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246 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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247 |
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248 .. list-table:: |
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249 :align: left |
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250 :header-rows: 1 |
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251 |
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252 * - History Name |
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253 - *"Name"* to set (be sure to press ``Save``) |
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254 * - ``#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`` |
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255 - ``weighted-normalized-unifrac-dm.qza`` |
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256 |
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257 use bypass_tips to trade specificity for reduced compute time |
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258 ************************************************************* |
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259 | bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time. |
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260 Using the ``qiime2 diversity-lib beta-phylogenetic-passthrough`` tool: |
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261 #. Set *"table"* to ``#: feature-table.qza`` |
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262 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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263 #. Set *"metric"* to ``weighted_normalized_unifrac`` |
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264 #. Expand the ``additional options`` section |
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265 |
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266 #. Set *"threads"* to ``auto`` |
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267 #. Set *"bypass_tips"* to ``Yes`` |
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268 |
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269 #. Press the ``Execute`` button. |
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270 |
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271 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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272 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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273 |
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274 .. list-table:: |
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275 :align: left |
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276 :header-rows: 1 |
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277 |
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278 * - History Name |
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279 - *"Name"* to set (be sure to press ``Save``) |
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280 * - ``#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`` |
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281 - ``weighted-normalized-unifrac-dm.qza`` |
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282 |
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283 variance adjustment |
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284 ******************* |
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285 | Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function. |
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286 Using the ``qiime2 diversity-lib beta-phylogenetic-passthrough`` tool: |
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287 #. Set *"table"* to ``#: feature-table.qza`` |
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288 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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289 #. Set *"metric"* to ``weighted_unifrac`` |
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290 #. Expand the ``additional options`` section |
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291 |
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292 #. Set *"threads"* to ``auto`` |
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293 #. Set *"variance_adjusted"* to ``Yes`` |
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294 |
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295 #. Press the ``Execute`` button. |
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296 |
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297 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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298 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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299 |
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300 .. list-table:: |
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301 :align: left |
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302 :header-rows: 1 |
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303 |
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304 * - History Name |
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305 - *"Name"* to set (be sure to press ``Save``) |
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306 * - ``#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`` |
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307 - ``var-adj-weighted-unifrac-dm.qza`` |
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308 |
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309 minimal generalized unifrac |
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310 *************************** |
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311 | Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized. |
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312 Using the ``qiime2 diversity-lib beta-phylogenetic-passthrough`` tool: |
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313 #. Set *"table"* to ``#: feature-table.qza`` |
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314 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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315 #. Set *"metric"* to ``generalized_unifrac`` |
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316 #. Press the ``Execute`` button. |
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317 |
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318 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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319 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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320 |
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321 .. list-table:: |
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322 :align: left |
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323 :header-rows: 1 |
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324 |
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325 * - History Name |
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326 - *"Name"* to set (be sure to press ``Save``) |
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327 * - ``#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`` |
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328 - ``generalized-unifrac-dm.qza`` |
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329 |
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330 generalized unifrac |
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331 ******************* |
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332 | passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions. |
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333 Using the ``qiime2 diversity-lib beta-phylogenetic-passthrough`` tool: |
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334 #. Set *"table"* to ``#: feature-table.qza`` |
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335 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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336 #. Set *"metric"* to ``generalized_unifrac`` |
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337 #. Expand the ``additional options`` section |
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338 |
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339 - Set *"alpha"* to ``0.75`` |
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340 |
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341 #. Press the ``Execute`` button. |
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342 |
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343 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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344 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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345 |
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346 .. list-table:: |
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347 :align: left |
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348 :header-rows: 1 |
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349 |
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350 * - History Name |
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351 - *"Name"* to set (be sure to press ``Save``) |
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352 * - ``#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`` |
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353 - ``generalized-unifrac-dm.qza`` |
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354 |
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355 |
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356 | |
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357 |
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358 </help> |
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359 <citations> |
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360 <citation type="doi">10.1128/AEM.71.12.8228-8235.2005</citation> |
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361 <citation type="doi">10.1128/AEM.01996-06</citation> |
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362 <citation type="doi">10.1038/ismej.2009.97</citation> |
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363 <citation type="doi">10.1038/ismej.2010.133</citation> |
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364 <citation type="doi">10.1038/s41592-018-0187-8</citation> |
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365 <citation type="doi">10.1186/1471-2105-12-118</citation> |
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366 <citation type="doi">10.1093/bioinformatics/bts342</citation> |
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367 <citation type="bibtex">@article{cite8, |
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368 author = {Sfiligoi, Igor and Armstrong, George and Gonzalez, Antonio and McDonald, Daniel and Knight, Rob}, |
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369 journal = {mSystems}, |
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370 title = {Optimizing UniFrac with OpenACC yields >1000x speed increase}, |
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371 year = {in press} |
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372 } |
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373 </citation> |
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374 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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375 </citations> |
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376 </tool> |