Mercurial > repos > q2d2 > qiime2__diversity__procrustes_analysis
comparison qiime2__diversity__procrustes_analysis.xml @ 0:e015c75346ab 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 19:33:15 +0000 |
| parents | |
| children | 111d05bd9e0d |
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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 procrustes-analysis" id="qiime2__diversity__procrustes_analysis" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
| 14 <description>Procrustes Analysis</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 procrustes_analysis '$inputs'</command> | |
| 20 <configfiles> | |
| 21 <inputs name="inputs" data_style="paths"/> | |
| 22 </configfiles> | |
| 23 <inputs> | |
| 24 <param name="reference" type="data" format="qza" label="reference: PCoAResults" help="[required] The ordination matrix to which data is fitted to."> | |
| 25 <options options_filter_attribute="metadata.semantic_type"> | |
| 26 <filter type="add_value" value="PCoAResults"/> | |
| 27 </options> | |
| 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator> | |
| 29 </param> | |
| 30 <param name="other" type="data" format="qza" label="other: PCoAResults" help="[required] The ordination matrix that's fitted to the reference ordination."> | |
| 31 <options options_filter_attribute="metadata.semantic_type"> | |
| 32 <filter type="add_value" value="PCoAResults"/> | |
| 33 </options> | |
| 34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator> | |
| 35 </param> | |
| 36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
| 37 <param name="dimensions" type="integer" min="1" value="5" label="dimensions: Int % Range(1, None)" help="[default: 5] The number of dimensions to use when fitting the two matrices"/> | |
| 38 <conditional name="__q2galaxy__GUI__conditional__permutations__"> | |
| 39 <param name="__q2galaxy__GUI__select__" type="select" label="permutations: Int % Range(1, None) | Str % Choices('disable')" help="[default: 999] The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."> | |
| 40 <option value="disable">disable (Str)</option> | |
| 41 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> | |
| 42 </param> | |
| 43 <when value="disable"> | |
| 44 <param name="permutations" type="hidden" value="disable"/> | |
| 45 </when> | |
| 46 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> | |
| 47 <param name="permutations" type="integer" min="1" value="999" label="permutations: Int % Range(1, None)" help="[default: 999] The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."/> | |
| 48 </when> | |
| 49 </conditional> | |
| 50 </section> | |
| 51 </inputs> | |
| 52 <outputs> | |
| 53 <data name="transformed_reference" format="qza" label="${tool.name} on ${on_string}: transformed_reference.qza" from_work_dir="transformed_reference.qza"/> | |
| 54 <data name="transformed_other" format="qza" label="${tool.name} on ${on_string}: transformed_other.qza" from_work_dir="transformed_other.qza"/> | |
| 55 <data name="disparity_results" format="qza" label="${tool.name} on ${on_string}: disparity_results.qza" from_work_dir="disparity_results.qza"/> | |
| 56 </outputs> | |
| 57 <tests/> | |
| 58 <help> | |
| 59 QIIME 2: diversity procrustes-analysis | |
| 60 ====================================== | |
| 61 Procrustes Analysis | |
| 62 | |
| 63 | |
| 64 Outputs: | |
| 65 -------- | |
| 66 :transformed_reference.qza: A normalized version of the "reference" ordination matrix. | |
| 67 :transformed_other.qza: A normalized and fitted version of the "other" ordination matrix. | |
| 68 :disparity_results.qza: The sum of the squares of the pointwise differences between the two input datasets & its p value. | |
| 69 | |
| 70 | | |
| 71 | |
| 72 Description: | |
| 73 ------------ | |
| 74 Fit two ordination matrices with Procrustes analysis | |
| 75 | |
| 76 | |
| 77 | | |
| 78 | |
| 79 </help> | |
| 80 <citations> | |
| 81 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
| 82 </citations> | |
| 83 </tool> |