| Next changeset 1:1e30542264c3 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__diversity__tsne.xml test-data/.gitkeep |
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| diff -r 000000000000 -r 404eadefe2fd qiime2__diversity__tsne.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__diversity__tsne.xml Mon Aug 29 19:36:39 2022 +0000 |
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| @@ -0,0 +1,66 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, QIIME 2 development team. + +Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) +--> +<!-- +This tool was automatically generated by: + q2galaxy (version: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 diversity tsne" id="qiime2__diversity__tsne" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>t-distributed stochastic neighbor embedding</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version diversity</version_command> + <command detect_errors="aggressive">q2galaxy run diversity tsne '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] The distance matrix on which t-SNE should be computed."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="DistanceMatrix"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="number_of_dimensions" type="integer" min="2" value="2" label="number_of_dimensions: Int % Range(2, None)" help="[default: 2] Dimensions to reduce the distance matrix to."/> + <param name="perplexity" type="float" min="1" value="25.0" label="perplexity: Float % Range(1, None)" help="[default: 25.0] Provide the balance between local and global structure. Low values concentrate on local structure. Large values sacrifice local details for a broader global embedding. The default value is 25 to achieve better results for small microbiome datasets."/> + <param name="n_iter" type="integer" min="1" value="1000" label="n_iter: Int % Range(1, None)" help="[default: 1000]"/> + <param name="learning_rate" type="float" min="10.0" value="200.0" label="learning_rate: Float % Range(10.0, None)" help="[default: 200.0] Controls how much the weights are adjusted at each update."/> + <param name="early_exaggeration" type="float" min="0" value="12.0" label="early_exaggeration: Float % Range(0, None)" help="[default: 12.0] Affects the tightness of the shown clusters. Larger values increase the distance between natural clusters in the embedded space."/> + <param name="random_state" type="integer" optional="true" label="random_state: Int" help="[optional] Seed used by random number generator."/> + </section> + </inputs> + <outputs> + <data name="tsne" format="qza" label="${tool.name} on ${on_string}: tsne.qza" from_work_dir="tsne.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: diversity tsne +======================= +t-distributed stochastic neighbor embedding + + +Outputs: +-------- +:tsne.qza: The resulting t-SNE matrix. + +| + +Description: +------------ +Apply t-distributed stochastic neighbor embedding. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool> |