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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:59:12 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2024, 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: 2024.10.0)
10 for:
11 qiime2 (version: 2024.10.1)
12 -->
13 <tool name="qiime2 vizard scatterplot-2d" id="qiime2__vizard__scatterplot_2d" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
14 <description>2D Scatterplot</description>
15 <xrefs>
16 <xref type="bio.tools">qiime2</xref>
17 </xrefs>
18 <requirements>
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
20 </requirements>
21 <version_command>q2galaxy version vizard</version_command>
22 <command detect_errors="exit_code">q2galaxy run vizard scatterplot_2d '$inputs'</command>
23 <configfiles>
24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
25 </configfiles>
26 <inputs>
27 <repeat name="metadata" min="1" help="[required] Any metadata-like input with at least two numeric measures for visualizing." title="metadata: Metadata">
28 <conditional name="__q2galaxy__GUI__conditional__metadata__">
29 <param name="type" type="select" label="metadata: Metadata">
30 <option value="tsv" selected="true">Metadata from TSV</option>
31 <option value="qza">Metadata from Artifact</option>
32 </param>
33 <when value="tsv">
34 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
35 </when>
36 <when value="qza">
37 <param name="source" type="data" format="qza" label="Metadata Source"/>
38 </when>
39 </conditional>
40 </repeat>
41 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
42 <conditional name="__q2galaxy__GUI__conditional__x_measure__" label="x_measure: Str">
43 <param name="__q2galaxy__GUI__select__" type="select" label="x_measure: Str" help="[optional] Numeric measure from the input Metadata that should be plotted on the x-axis.">
44 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
45 <option value="__q2galaxy__::control::provide">Provide a value</option>
46 </param>
47 <when value="__q2galaxy__::control::default">
48 <param name="x_measure" type="hidden" value="__q2galaxy__::literal::None"/>
49 </when>
50 <when value="__q2galaxy__::control::provide">
51 <param name="x_measure" type="text">
52 <sanitizer>
53 <valid initial="string.printable"/>
54 </sanitizer>
55 </param>
56 </when>
57 </conditional>
58 <conditional name="__q2galaxy__GUI__conditional__y_measure__" label="y_measure: Str">
59 <param name="__q2galaxy__GUI__select__" type="select" label="y_measure: Str" help="[optional] Numeric measure from the input Metadata that should be plotted on the y-axis.">
60 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
61 <option value="__q2galaxy__::control::provide">Provide a value</option>
62 </param>
63 <when value="__q2galaxy__::control::default">
64 <param name="y_measure" type="hidden" value="__q2galaxy__::literal::None"/>
65 </when>
66 <when value="__q2galaxy__::control::provide">
67 <param name="y_measure" type="text">
68 <sanitizer>
69 <valid initial="string.printable"/>
70 </sanitizer>
71 </param>
72 </when>
73 </conditional>
74 <conditional name="__q2galaxy__GUI__conditional__color_by__" label="color_by: Str">
75 <param name="__q2galaxy__GUI__select__" type="select" label="color_by: Str" help="[optional] Categorical measure from the input Metadata that should be used for color-coding the scatterplot.">
76 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
77 <option value="__q2galaxy__::control::provide">Provide a value</option>
78 </param>
79 <when value="__q2galaxy__::control::default">
80 <param name="color_by" type="hidden" value="__q2galaxy__::literal::None"/>
81 </when>
82 <when value="__q2galaxy__::control::provide">
83 <param name="color_by" type="text">
84 <sanitizer>
85 <valid initial="string.printable"/>
86 </sanitizer>
87 </param>
88 </when>
89 </conditional>
90 <conditional name="__q2galaxy__GUI__conditional__title__" label="title: Str">
91 <param name="__q2galaxy__GUI__select__" type="select" label="title: Str" help="[optional] The title of the scatterplot.">
92 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
93 <option value="__q2galaxy__::control::provide">Provide a value</option>
94 </param>
95 <when value="__q2galaxy__::control::default">
96 <param name="title" type="hidden" value="__q2galaxy__::literal::None"/>
97 </when>
98 <when value="__q2galaxy__::control::provide">
99 <param name="title" type="text">
100 <sanitizer>
101 <valid initial="string.printable"/>
102 </sanitizer>
103 </param>
104 </when>
105 </conditional>
106 </section>
107 </inputs>
108 <outputs>
109 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
110 </outputs>
111 <tests>
112 <test>
113 <repeat name="metadata">
114 <conditional name="__q2galaxy__GUI__conditional__metadata__">
115 <param name="type" value="tsv"/>
116 <param name="source" value="scatterplot_2d.test0.metadata.tsv" ftype="qiime2.tabular"/>
117 </conditional>
118 </repeat>
119 <output name="visualization" ftype="qzv"/>
120 </test>
121 <test>
122 <repeat name="metadata">
123 <conditional name="__q2galaxy__GUI__conditional__metadata__">
124 <param name="type" value="tsv"/>
125 <param name="source" value="scatterplot_2d.test1.metadata.tsv" ftype="qiime2.tabular"/>
126 </conditional>
127 </repeat>
128 <param name="x_measure" value="x"/>
129 <param name="y_measure" value="y"/>
130 <param name="color_by" value="group"/>
131 <output name="visualization" ftype="qzv"/>
132 </test>
133 </tests>
134 <help>
135 QIIME 2: vizard scatterplot-2d
136 ==============================
137 2D Scatterplot
138
139
140 Outputs:
141 --------
142 :visualization.qzv: &lt;no description&gt;
143
144 |
145
146 Description:
147 ------------
148 Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.
149
150 Examples:
151 ---------
152
153 scatterplot_defaults
154 ********************
155 Using the ``qiime2 vizard scatterplot-2d`` tool:
156 #. For *"metadata"*:
157
158 - Perform the following steps.
159
160 #. Leave as ``Metadata from TSV``
161 #. Set *"Metadata Source"* to ``metadata.tsv``
162
163
164 #. Press the ``Execute`` button.
165
166 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
167 (Renaming is optional, but it will make any subsequent steps easier to complete.)
168
169 .. list-table::
170 :align: left
171 :header-rows: 1
172
173 * - History Name
174 - *"Name"* to set (be sure to press ``Save``)
175 * - ``#: qiime2 vizard scatterplot-2d [...] : visualization.qzv``
176 - ``scatterplot.qzv``
177
178 scatterplot_all_measures
179 ************************
180 Using the ``qiime2 vizard scatterplot-2d`` tool:
181 #. For *"metadata"*:
182
183 - Perform the following steps.
184
185 #. Leave as ``Metadata from TSV``
186 #. Set *"Metadata Source"* to ``metadata.tsv``
187
188
189 #. Expand the ``additional options`` section
190
191 #. Set *"x_measure"* to ``x``
192 #. Set *"y_measure"* to ``y``
193 #. Set *"color_by"* to ``group``
194
195 #. Press the ``Execute`` button.
196
197 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
198 (Renaming is optional, but it will make any subsequent steps easier to complete.)
199
200 .. list-table::
201 :align: left
202 :header-rows: 1
203
204 * - History Name
205 - *"Name"* to set (be sure to press ``Save``)
206 * - ``#: qiime2 vizard scatterplot-2d [...] : visualization.qzv``
207 - ``scatterplot.qzv``
208
209
210 |
211
212 </help>
213 <citations>
214 <citation type="doi">10.1038/s41587-019-0209-9</citation>
215 </citations>
216 </tool>