diff qiime2__diversity__tsne.xml @ 0:404eadefe2fd draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__diversity__tsne.xml	Mon Aug 29 19:36:39 2022 +0000
@@ -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>