Mercurial > repos > q2d2 > qiime2__diversity__beta_group_significance
comparison qiime2__diversity__beta_group_significance.xml @ 0:e12bf91d8469 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
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| date | Mon, 29 Aug 2022 19:31:14 +0000 |
| parents | |
| children | ae04ef51094f |
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| 1 <?xml version='1.0' encoding='utf-8'?> | |
| 2 <!-- | |
| 3 Copyright (c) 2022, QIIME 2 development team. | |
| 4 | |
| 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) | |
| 6 --> | |
| 7 <!-- | |
| 8 This tool was automatically generated by: | |
| 9 q2galaxy (version: 2022.8.1) | |
| 10 for: | |
| 11 qiime2 (version: 2022.8.1) | |
| 12 --> | |
| 13 <tool name="qiime2 diversity beta-group-significance" id="qiime2__diversity__beta_group_significance" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
| 14 <description>Beta diversity group significance</description> | |
| 15 <requirements> | |
| 16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
| 17 </requirements> | |
| 18 <version_command>q2galaxy version diversity</version_command> | |
| 19 <command detect_errors="aggressive">q2galaxy run diversity beta_group_significance '$inputs'</command> | |
| 20 <configfiles> | |
| 21 <inputs name="inputs" data_style="paths"/> | |
| 22 </configfiles> | |
| 23 <inputs> | |
| 24 <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] Matrix of distances between pairs of samples."> | |
| 25 <options options_filter_attribute="metadata.semantic_type"> | |
| 26 <filter type="add_value" value="DistanceMatrix"/> | |
| 27 </options> | |
| 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator> | |
| 29 </param> | |
| 30 <conditional name="metadata"> | |
| 31 <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] Categorical sample metadata column."> | |
| 32 <option value="tsv" selected="true">Metadata from TSV</option> | |
| 33 <option value="qza">Metadata from Artifact</option> | |
| 34 </param> | |
| 35 <when value="tsv"> | |
| 36 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> | |
| 37 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> | |
| 38 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> | |
| 39 </param> | |
| 40 </when> | |
| 41 <when value="qza"> | |
| 42 <param name="source" type="data" format="qza" label="Metadata Source"/> | |
| 43 <param name="column" type="text" label="Column Name"> | |
| 44 <validator type="empty_field"/> | |
| 45 </param> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
| 49 <param name="method" type="select" label="method: Str % Choices('permanova', 'anosim', 'permdisp')" display="radio"> | |
| 50 <option value="permanova" selected="true">permanova</option> | |
| 51 <option value="anosim">anosim</option> | |
| 52 <option value="permdisp">permdisp</option> | |
| 53 </param> | |
| 54 <param name="pairwise" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="pairwise: Bool" help="[default: No] Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column."/> | |
| 55 <param name="permutations" type="integer" value="999" label="permutations: Int" help="[default: 999] The number of permutations to be run when computing p-values."/> | |
| 56 </section> | |
| 57 </inputs> | |
| 58 <outputs> | |
| 59 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> | |
| 60 </outputs> | |
| 61 <tests/> | |
| 62 <help> | |
| 63 QIIME 2: diversity beta-group-significance | |
| 64 ========================================== | |
| 65 Beta diversity group significance | |
| 66 | |
| 67 | |
| 68 Outputs: | |
| 69 -------- | |
| 70 :visualization.qzv: <no description> | |
| 71 | |
| 72 | | |
| 73 | |
| 74 Description: | |
| 75 ------------ | |
| 76 Determine whether groups of samples are significantly different from one another using a permutation-based statistical test. | |
| 77 | |
| 78 | |
| 79 | | |
| 80 | |
| 81 </help> | |
| 82 <citations> | |
| 83 <citation type="doi">https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x</citation> | |
| 84 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
| 85 </citations> | |
| 86 </tool> |