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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 19:59:34 +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 lineplot" id="qiime2__vizard__lineplot" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
14 <description>Lineplot</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 lineplot '$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 <param name="x_measure" type="text" label="x_measure: Str" help="[required] Numeric measure from the input Metadata that should be plotted on the x-axis.">
42 <sanitizer>
43 <valid initial="string.printable"/>
44 </sanitizer>
45 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
46 </param>
47 <param name="y_measure" type="text" label="y_measure: Str" help="[required] Numeric measure from the input Metadata that should be plotted on the y-axis.">
48 <sanitizer>
49 <valid initial="string.printable"/>
50 </sanitizer>
51 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
52 </param>
53 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
54 <param name="replicate_method" type="select" label="replicate_method: Str % Choices('none', 'median', 'mean')" display="radio">
55 <option value="none" selected="true">none</option>
56 <option value="median">median</option>
57 <option value="mean">mean</option>
58 </param>
59 <conditional name="__q2galaxy__GUI__conditional__group_by__" label="group_by: Str">
60 <param name="__q2galaxy__GUI__select__" type="select" label="group_by: Str" help="[optional] Categorical measure from the input Metadata that should be used for grouping the lineplot.">
61 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
62 <option value="__q2galaxy__::control::provide">Provide a value</option>
63 </param>
64 <when value="__q2galaxy__::control::default">
65 <param name="group_by" type="hidden" value="__q2galaxy__::literal::None"/>
66 </when>
67 <when value="__q2galaxy__::control::provide">
68 <param name="group_by" type="text">
69 <sanitizer>
70 <valid initial="string.printable"/>
71 </sanitizer>
72 </param>
73 </when>
74 </conditional>
75 <conditional name="__q2galaxy__GUI__conditional__title__" label="title: Str">
76 <param name="__q2galaxy__GUI__select__" type="select" label="title: Str" help="[optional] The title of the lineplot.">
77 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
78 <option value="__q2galaxy__::control::provide">Provide a value</option>
79 </param>
80 <when value="__q2galaxy__::control::default">
81 <param name="title" type="hidden" value="__q2galaxy__::literal::None"/>
82 </when>
83 <when value="__q2galaxy__::control::provide">
84 <param name="title" type="text">
85 <sanitizer>
86 <valid initial="string.printable"/>
87 </sanitizer>
88 </param>
89 </when>
90 </conditional>
91 </section>
92 </inputs>
93 <outputs>
94 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
95 </outputs>
96 <tests>
97 <test>
98 <repeat name="metadata">
99 <conditional name="__q2galaxy__GUI__conditional__metadata__">
100 <param name="type" value="tsv"/>
101 <param name="source" value="lineplot.test0.metadata.tsv" ftype="qiime2.tabular"/>
102 </conditional>
103 </repeat>
104 <param name="x_measure" value="x"/>
105 <param name="y_measure" value="y"/>
106 <param name="replicate_method" value="median"/>
107 <param name="group_by" value="group"/>
108 <param name="title" value="Lineplot with median replicate method__comma__ grouped by `group`."/>
109 <output name="visualization" ftype="qzv"/>
110 </test>
111 <test>
112 <repeat name="metadata">
113 <conditional name="__q2galaxy__GUI__conditional__metadata__">
114 <param name="type" value="tsv"/>
115 <param name="source" value="lineplot.test1.metadata.tsv" ftype="qiime2.tabular"/>
116 </conditional>
117 </repeat>
118 <param name="x_measure" value="x"/>
119 <param name="y_measure" value="y"/>
120 <param name="replicate_method" value="mean"/>
121 <param name="group_by" value="group"/>
122 <param name="title" value="Lineplot with mean replicate method__comma__ grouped by `group`."/>
123 <output name="visualization" ftype="qzv"/>
124 </test>
125 <test>
126 <repeat name="metadata">
127 <conditional name="__q2galaxy__GUI__conditional__metadata__">
128 <param name="type" value="tsv"/>
129 <param name="source" value="lineplot.test2.metadata.tsv" ftype="qiime2.tabular"/>
130 </conditional>
131 </repeat>
132 <param name="x_measure" value="x"/>
133 <param name="y_measure" value="y"/>
134 <param name="replicate_method" value="median"/>
135 <param name="title" value="Lineplot with median replicate method (no grouping)."/>
136 <output name="visualization" ftype="qzv"/>
137 </test>
138 <test>
139 <repeat name="metadata">
140 <conditional name="__q2galaxy__GUI__conditional__metadata__">
141 <param name="type" value="tsv"/>
142 <param name="source" value="lineplot.test3.metadata.tsv" ftype="qiime2.tabular"/>
143 </conditional>
144 </repeat>
145 <param name="x_measure" value="x"/>
146 <param name="y_measure" value="y"/>
147 <param name="replicate_method" value="mean"/>
148 <param name="title" value="Lineplot with mean replicate method (no grouping)."/>
149 <output name="visualization" ftype="qzv"/>
150 </test>
151 <test>
152 <repeat name="metadata">
153 <conditional name="__q2galaxy__GUI__conditional__metadata__">
154 <param name="type" value="tsv"/>
155 <param name="source" value="lineplot.test4.metadata.tsv" ftype="qiime2.tabular"/>
156 </conditional>
157 </repeat>
158 <param name="x_measure" value="a"/>
159 <param name="y_measure" value="y"/>
160 <param name="group_by" value="group"/>
161 <param name="title" value="Lineplot with no replicate method__comma__ grouped by `group`."/>
162 <output name="visualization" ftype="qzv"/>
163 </test>
164 <test>
165 <repeat name="metadata">
166 <conditional name="__q2galaxy__GUI__conditional__metadata__">
167 <param name="type" value="tsv"/>
168 <param name="source" value="lineplot.test5.metadata.tsv" ftype="qiime2.tabular"/>
169 </conditional>
170 </repeat>
171 <param name="x_measure" value="b"/>
172 <param name="y_measure" value="y"/>
173 <param name="title" value="Lineplot with no replicate method (no grouping)."/>
174 <output name="visualization" ftype="qzv"/>
175 </test>
176 </tests>
177 <help>
178 QIIME 2: vizard lineplot
179 ========================
180 Lineplot
181
182
183 Outputs:
184 --------
185 :visualization.qzv: &lt;no description&gt;
186
187 |
188
189 Description:
190 ------------
191 Basic lineplot for visualizing two numeric Metadata measures with optional grouping. All numeric columns present in the Metadata will be available as drop-down options on the Y-axis, but the chosen `x_measure` remains fixed.
192
193 Examples:
194 ---------
195
196 lineplot_median_replicates_with_grouping
197 ****************************************
198 Using the ``qiime2 vizard lineplot`` tool:
199 #. For *"metadata"*:
200
201 - Perform the following steps.
202
203 #. Leave as ``Metadata from TSV``
204 #. Set *"Metadata Source"* to ``metadata.tsv``
205
206
207 #. Set *"x_measure"* to ``x``
208 #. Set *"y_measure"* to ``y``
209 #. Expand the ``additional options`` section
210
211 #. Set *"replicate_method"* to ``median``
212 #. Set *"group_by"* to ``group``
213 #. Set *"title"* to ``Lineplot with median replicate method, grouped by `group`.``
214
215 #. Press the ``Execute`` button.
216
217 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
218 (Renaming is optional, but it will make any subsequent steps easier to complete.)
219
220 .. list-table::
221 :align: left
222 :header-rows: 1
223
224 * - History Name
225 - *"Name"* to set (be sure to press ``Save``)
226 * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``
227 - ``lineplot.qzv``
228
229 lineplot_mean_replicates_with_grouping
230 **************************************
231 Using the ``qiime2 vizard lineplot`` tool:
232 #. For *"metadata"*:
233
234 - Perform the following steps.
235
236 #. Leave as ``Metadata from TSV``
237 #. Set *"Metadata Source"* to ``metadata.tsv``
238
239
240 #. Set *"x_measure"* to ``x``
241 #. Set *"y_measure"* to ``y``
242 #. Expand the ``additional options`` section
243
244 #. Set *"replicate_method"* to ``mean``
245 #. Set *"group_by"* to ``group``
246 #. Set *"title"* to ``Lineplot with mean replicate method, grouped by `group`.``
247
248 #. Press the ``Execute`` button.
249
250 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
251 (Renaming is optional, but it will make any subsequent steps easier to complete.)
252
253 .. list-table::
254 :align: left
255 :header-rows: 1
256
257 * - History Name
258 - *"Name"* to set (be sure to press ``Save``)
259 * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``
260 - ``lineplot.qzv``
261
262 lineplot_median_replicates_no_grouping
263 **************************************
264 Using the ``qiime2 vizard lineplot`` tool:
265 #. For *"metadata"*:
266
267 - Perform the following steps.
268
269 #. Leave as ``Metadata from TSV``
270 #. Set *"Metadata Source"* to ``metadata.tsv``
271
272
273 #. Set *"x_measure"* to ``x``
274 #. Set *"y_measure"* to ``y``
275 #. Expand the ``additional options`` section
276
277 #. Set *"replicate_method"* to ``median``
278 #. Set *"title"* to ``Lineplot with median replicate method (no grouping).``
279
280 #. Press the ``Execute`` button.
281
282 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
283 (Renaming is optional, but it will make any subsequent steps easier to complete.)
284
285 .. list-table::
286 :align: left
287 :header-rows: 1
288
289 * - History Name
290 - *"Name"* to set (be sure to press ``Save``)
291 * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``
292 - ``lineplot.qzv``
293
294 lineplot_mean_replicates_no_grouping
295 ************************************
296 Using the ``qiime2 vizard lineplot`` tool:
297 #. For *"metadata"*:
298
299 - Perform the following steps.
300
301 #. Leave as ``Metadata from TSV``
302 #. Set *"Metadata Source"* to ``metadata.tsv``
303
304
305 #. Set *"x_measure"* to ``x``
306 #. Set *"y_measure"* to ``y``
307 #. Expand the ``additional options`` section
308
309 #. Set *"replicate_method"* to ``mean``
310 #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).``
311
312 #. Press the ``Execute`` button.
313
314 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
315 (Renaming is optional, but it will make any subsequent steps easier to complete.)
316
317 .. list-table::
318 :align: left
319 :header-rows: 1
320
321 * - History Name
322 - *"Name"* to set (be sure to press ``Save``)
323 * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``
324 - ``lineplot.qzv``
325
326 lineplot_no_replicates_with_grouping
327 ************************************
328 Using the ``qiime2 vizard lineplot`` tool:
329 #. For *"metadata"*:
330
331 - Perform the following steps.
332
333 #. Leave as ``Metadata from TSV``
334 #. Set *"Metadata Source"* to ``metadata.tsv``
335
336
337 #. Set *"x_measure"* to ``a``
338 #. Set *"y_measure"* to ``y``
339 #. Expand the ``additional options`` section
340
341 #. Set *"group_by"* to ``group``
342 #. Set *"title"* to ``Lineplot with no replicate method, grouped by `group`.``
343
344 #. Press the ``Execute`` button.
345
346 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
347 (Renaming is optional, but it will make any subsequent steps easier to complete.)
348
349 .. list-table::
350 :align: left
351 :header-rows: 1
352
353 * - History Name
354 - *"Name"* to set (be sure to press ``Save``)
355 * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``
356 - ``lineplot.qzv``
357
358 lineplot_no_replicates_no_grouping
359 **********************************
360 Using the ``qiime2 vizard lineplot`` tool:
361 #. For *"metadata"*:
362
363 - Perform the following steps.
364
365 #. Leave as ``Metadata from TSV``
366 #. Set *"Metadata Source"* to ``metadata.tsv``
367
368
369 #. Set *"x_measure"* to ``b``
370 #. Set *"y_measure"* to ``y``
371 #. Expand the ``additional options`` section
372
373 - Set *"title"* to ``Lineplot with no replicate method (no grouping).``
374
375 #. Press the ``Execute`` button.
376
377 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
378 (Renaming is optional, but it will make any subsequent steps easier to complete.)
379
380 .. list-table::
381 :align: left
382 :header-rows: 1
383
384 * - History Name
385 - *"Name"* to set (be sure to press ``Save``)
386 * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``
387 - ``lineplot.qzv``
388
389
390 |
391
392 </help>
393 <citations>
394 <citation type="doi">10.1038/s41587-019-0209-9</citation>
395 </citations>
396 </tool>