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author q2d2
date Thu, 08 Jun 2023 19:36:29 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 diversity tsne" id="qiime2__diversity__tsne" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>t-distributed stochastic neighbor embedding</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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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 tsne '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] The distance matrix on which t-SNE should be computed.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="DistanceMatrix"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <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."/>
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32 <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."/>
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33 <param name="n_iter" type="integer" min="1" value="1000" label="n_iter: Int % Range(1, None)" help="[default: 1000]"/>
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34 <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."/>
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35 <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."/>
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36 <param name="random_state" type="integer" optional="true" label="random_state: Int" help="[optional] Seed used by random number generator."/>
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37 </section>
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38 </inputs>
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39 <outputs>
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40 <data name="tsne" format="qza" label="${tool.name} on ${on_string}: tsne.qza" from_work_dir="tsne.qza"/>
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41 </outputs>
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42 <tests/>
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43 <help>
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44 QIIME 2: diversity tsne
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45 =======================
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46 t-distributed stochastic neighbor embedding
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47
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48
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49 Outputs:
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50 --------
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51 :tsne.qza: The resulting t-SNE matrix.
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52
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53 |
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54
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55 Description:
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56 ------------
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57 Apply t-distributed stochastic neighbor embedding.
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58
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59
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60 |
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61
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62 </help>
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63 <citations>
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64 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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65 </citations>
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66 </tool>