Mercurial > repos > q2d2 > qiime2__emperor__biplot

comparison qiime2__emperor__biplot.xml @ 0:72079afffe4c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:48:59 +0000
parents
children 5aced4a38720
comparison
equal deleted inserted replaced
-1:000000000000 0:72079afffe4c
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 emperor biplot" id="qiime2__emperor__biplot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version emperor</version_command>
19 <command detect_errors="aggressive">q2galaxy run emperor biplot '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="biplot" type="data" format="qza" label="biplot: PCoAResults % Properties('biplot')" help="[required] The principal coordinates matrix to be plotted.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="PCoAResults % Properties('biplot')"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ["PCoAResults % Properties('biplot')"]</validator>
29 </param>
30 <repeat name="sample_metadata" min="1" help="[required] The sample metadata" title="sample_metadata: Metadata">
31 <conditional name="__q2galaxy__GUI__conditional__sample_metadata__">
32 <param name="type" type="select" label="sample_metadata: Metadata">
33 <option value="tsv" selected="true">Metadata from TSV</option>
34 <option value="qza">Metadata from Artifact</option>
35 </param>
36 <when value="tsv">
37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
38 </when>
39 <when value="qza">
40 <param name="source" type="data" format="qza" label="Metadata Source"/>
41 </when>
42 </conditional>
43 </repeat>
44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
45 <repeat name="feature_metadata" help="[optional] The feature metadata (useful to manipulate the arrows in the plot)." title="feature_metadata: Metadata">
46 <conditional name="__q2galaxy__GUI__conditional__feature_metadata__">
47 <param name="type" type="select" label="feature_metadata: Metadata">
48 <option value="tsv" selected="true">Metadata from TSV</option>
49 <option value="qza">Metadata from Artifact</option>
50 </param>
51 <when value="tsv">
52 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
53 </when>
54 <when value="qza">
55 <param name="source" type="data" format="qza" label="Metadata Source"/>
56 </when>
57 </conditional>
58 </repeat>
59 <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No] This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: &quot;This sample has no metadata&quot;. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata."/>
60 <param name="invert" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="invert: Bool" help="[default: No] If specified, the point and arrow coordinates will be swapped."/>
61 <param name="number_of_features" type="integer" min="1" value="5" label="number_of_features: Int % Range(1, None)" help="[default: 5] The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin)."/>
62 </section>
63 </inputs>
64 <outputs>
65 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
66 </outputs>
67 <tests/>
68 <help>
69 QIIME 2: emperor biplot
70 =======================
71 Visualize and Interact with Principal Coordinates Analysis Biplot
72
73
74 Outputs:
75 --------
76 :visualization.qzv: &lt;no description&gt;
77
78 |
79
80 Description:
81 ------------
82 Generates an interactive ordination biplot where the user can visually integrate sample and feature metadata. Vectors representing the n most important features are then plotted in the emperor visualization (5 largest, by default).
83
84
85 |
86
87 </help>
88 <citations>
89 <citation type="doi">10.1186/2047-217X-2-16</citation>
90 <citation type="doi">10.1016/j.chom.2016.12.009</citation>
91 <citation type="doi">10.1038/s41587-019-0209-9</citation>
92 </citations>
93 </tool>