Mercurial > repos > q2d2 > qiime2__diversity__alpha_correlation
annotate qiime2__diversity__alpha_correlation.xml @ 2:5850f79a2b9f draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 65e4952f33eb335528e8553150e9097e5ea8f556
author | q2d2 |
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date | Thu, 08 Jun 2023 19:37:54 +0000 |
parents | 9235f6a16926 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 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 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
1
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3 Copyright (c) 2023, QIIME 2 development team. |
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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 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 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 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 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 commit 65e4952f33eb335528e8553150e9097e5ea8f556
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9 q2galaxy (version: 2023.5.0) |
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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 commit 65e4952f33eb335528e8553150e9097e5ea8f556
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11 qiime2 (version: 2023.5.1) |
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12 --> |
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13 <tool name="qiime2 diversity alpha-correlation" id="qiime2__diversity__alpha_correlation" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> |
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14 <description>Alpha diversity correlation</description> |
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15 <requirements> |
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16 <container type="docker">quay.io/qiime2/core:2023.5</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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_correlation '$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 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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24 <param name="alpha_diversity" type="data" format="qza" label="alpha_diversity: SampleData[AlphaDiversity]" help="[required] Vector of alpha diversity values by sample."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 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 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="SampleData[AlphaDiversity]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 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 commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 </param> |
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30 <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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45 <param name="method" type="select" label="method: Str % Choices('spearman', 'pearson')" display="radio"> |
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46 <option value="spearman" selected="true">spearman</option> |
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47 <option value="pearson">pearson</option> |
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48 </param> |
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49 <param name="intersect_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="intersect_ids: Bool" help="[default: No] If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs."/> |
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50 </section> |
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51 </inputs> |
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52 <outputs> |
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53 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> |
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54 </outputs> |
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55 <tests> |
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56 <test> |
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57 <param name="alpha_diversity" value="alpha_correlation.test0.alpha-div-faith-pd.qza" ftype="qza"/> |
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58 <repeat name="metadata"> |
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59 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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60 <param name="type" value="tsv"/> |
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61 <param name="source" value="alpha_correlation.test0.metadata.tsv" ftype="qiime2.tabular"/> |
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62 </conditional> |
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63 </repeat> |
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64 <output name="visualization" ftype="qzv"> |
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65 <assert_contents> |
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66 <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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67 <has_line_matching expression="type: Visualization"/> |
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68 </has_archive_member> |
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69 </assert_contents> |
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70 </output> |
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71 </test> |
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72 </tests> |
0
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73 <help> |
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74 QIIME 2: diversity alpha-correlation |
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75 ==================================== |
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76 Alpha diversity correlation |
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77 |
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78 |
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79 Outputs: |
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80 -------- |
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81 :visualization.qzv: <no description> |
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82 |
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83 | |
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84 |
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85 Description: |
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86 ------------ |
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87 Determine whether numeric sample metadata columns are correlated with alpha diversity. |
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88 |
1
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89 Examples: |
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90 --------- |
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91 |
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92 alpha_correlation_faith_pd |
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93 ************************** |
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94 Using the ``qiime2 diversity alpha-correlation`` tool: |
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95 #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza`` |
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96 #. For *"metadata"*: |
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97 |
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98 - Perform the following steps. |
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99 |
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100 #. Leave as ``Metadata from TSV`` |
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101 #. Set *"Metadata Source"* to ``metadata.tsv`` |
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102 |
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103 |
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104 #. Press the ``Execute`` button. |
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105 |
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106 |
0
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107 |
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108 | |
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109 |
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110 </help> |
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111 <citations> |
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112 <citation type="doi">https://doi.org/10.1098/rspl.1895.0041</citation> |
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113 <citation type="doi">https://doi.org/10.2307/1422689</citation> |
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114 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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115 </citations> |
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116 </tool> |