Mercurial > repos > q2d2 > qiime2__vizard__lineplot

comparison qiime2__vizard__lineplot.xml @ 1:0b666cc4e746 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__vizard commit b1fccfb38b4873cd4699743033449014a2978e7d
author q2d2
date Mon, 05 May 2025 19:05:23 +0000
parents df9f1ff48c29
children d18e90f69613
comparison
equal deleted inserted replaced
0:df9f1ff48c29 1:0b666cc4e746
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2024, QIIME 2 development team. 3 Copyright (c) 2025, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2024.10.0) 9 q2galaxy (version: 2025.4.0)
10 for: 10 for:
11 qiime2 (version: 2024.10.1) 11 qiime2 (version: 2025.4.0)
12 --> 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"> 13 <tool name="qiime2 vizard lineplot" id="qiime2__vizard__lineplot" version="0.0.1.dev0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
14 <description>Lineplot</description> 14 <description>Lineplot</description>
15 <xrefs> 15 <xrefs>
16 <xref type="bio.tools">qiime2</xref> 16 <xref type="bio.tools">qiime2</xref>
17 </xrefs> 17 </xrefs>
18 <requirements> 18 <requirements>
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container> 19 <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
20 </requirements> 20 </requirements>
21 <version_command>q2galaxy version vizard</version_command> 21 <version_command>q2galaxy version vizard</version_command>
22 <command detect_errors="exit_code">q2galaxy run vizard lineplot '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run vizard lineplot '$inputs'</command>
23 <configfiles> 23 <configfiles>
24 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
42 <sanitizer> 42 <sanitizer>
43 <valid initial="string.printable"/> 43 <valid initial="string.printable"/>
44 </sanitizer> 44 </sanitizer>
45 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator> 45 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
46 </param> 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"> 47 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
48 <conditional name="__q2galaxy__GUI__conditional__y_measure__" label="y_measure: Str">
49 <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.">
50 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
51 <option value="__q2galaxy__::control::provide">Provide a value</option>
52 </param>
53 <when value="__q2galaxy__::control::default">
54 <param name="y_measure" type="hidden" value="__q2galaxy__::literal::None"/>
55 </when>
56 <when value="__q2galaxy__::control::provide">
57 <param name="y_measure" type="text">
58 <sanitizer>
59 <valid initial="string.printable"/>
60 </sanitizer>
61 </param>
62 </when>
63 </conditional>
54 <param name="replicate_method" type="select" label="replicate_method: Str % Choices('none', 'median', 'mean')" display="radio"> 64 <param name="replicate_method" type="select" label="replicate_method: Str % Choices('none', 'median', 'mean')" display="radio">
55 <option value="none" selected="true">none</option> 65 <option value="none" selected="true">none</option>
56 <option value="median">median</option> 66 <option value="median">median</option>
57 <option value="mean">mean</option> 67 <option value="mean">mean</option>
58 </param> 68 </param>
203 #. Leave as ``Metadata from TSV`` 213 #. Leave as ``Metadata from TSV``
204 #. Set *"Metadata Source"* to ``metadata.tsv`` 214 #. Set *"Metadata Source"* to ``metadata.tsv``
205 215
206 216
207 #. Set *"x_measure"* to ``x`` 217 #. Set *"x_measure"* to ``x``
208 #. Set *"y_measure"* to ``y`` 218 #. Expand the ``additional options`` section
209 #. Expand the ``additional options`` section 219
210 220 #. Set *"y_measure"* to ``y``
211 #. Set *"replicate_method"* to ``median`` 221 #. Set *"replicate_method"* to ``median``
212 #. Set *"group_by"* to ``group`` 222 #. Set *"group_by"* to ``group``
213 #. Set *"title"* to ``Lineplot with median replicate method, grouped by `group`.`` 223 #. Set *"title"* to ``Lineplot with median replicate method, grouped by `group`.``
214 224
215 #. Press the ``Execute`` button. 225 #. Press the ``Execute`` button.
236 #. Leave as ``Metadata from TSV`` 246 #. Leave as ``Metadata from TSV``
237 #. Set *"Metadata Source"* to ``metadata.tsv`` 247 #. Set *"Metadata Source"* to ``metadata.tsv``
238 248
239 249
240 #. Set *"x_measure"* to ``x`` 250 #. Set *"x_measure"* to ``x``
241 #. Set *"y_measure"* to ``y`` 251 #. Expand the ``additional options`` section
242 #. Expand the ``additional options`` section 252
243 253 #. Set *"y_measure"* to ``y``
244 #. Set *"replicate_method"* to ``mean`` 254 #. Set *"replicate_method"* to ``mean``
245 #. Set *"group_by"* to ``group`` 255 #. Set *"group_by"* to ``group``
246 #. Set *"title"* to ``Lineplot with mean replicate method, grouped by `group`.`` 256 #. Set *"title"* to ``Lineplot with mean replicate method, grouped by `group`.``
247 257
248 #. Press the ``Execute`` button. 258 #. Press the ``Execute`` button.
269 #. Leave as ``Metadata from TSV`` 279 #. Leave as ``Metadata from TSV``
270 #. Set *"Metadata Source"* to ``metadata.tsv`` 280 #. Set *"Metadata Source"* to ``metadata.tsv``
271 281
272 282
273 #. Set *"x_measure"* to ``x`` 283 #. Set *"x_measure"* to ``x``
274 #. Set *"y_measure"* to ``y`` 284 #. Expand the ``additional options`` section
275 #. Expand the ``additional options`` section 285
276 286 #. Set *"y_measure"* to ``y``
277 #. Set *"replicate_method"* to ``median`` 287 #. Set *"replicate_method"* to ``median``
278 #. Set *"title"* to ``Lineplot with median replicate method (no grouping).`` 288 #. Set *"title"* to ``Lineplot with median replicate method (no grouping).``
279 289
280 #. Press the ``Execute`` button. 290 #. Press the ``Execute`` button.
281 291
301 #. Leave as ``Metadata from TSV`` 311 #. Leave as ``Metadata from TSV``
302 #. Set *"Metadata Source"* to ``metadata.tsv`` 312 #. Set *"Metadata Source"* to ``metadata.tsv``
303 313
304 314
305 #. Set *"x_measure"* to ``x`` 315 #. Set *"x_measure"* to ``x``
306 #. Set *"y_measure"* to ``y`` 316 #. Expand the ``additional options`` section
307 #. Expand the ``additional options`` section 317
308 318 #. Set *"y_measure"* to ``y``
309 #. Set *"replicate_method"* to ``mean`` 319 #. Set *"replicate_method"* to ``mean``
310 #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).`` 320 #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).``
311 321
312 #. Press the ``Execute`` button. 322 #. Press the ``Execute`` button.
313 323
333 #. Leave as ``Metadata from TSV`` 343 #. Leave as ``Metadata from TSV``
334 #. Set *"Metadata Source"* to ``metadata.tsv`` 344 #. Set *"Metadata Source"* to ``metadata.tsv``
335 345
336 346
337 #. Set *"x_measure"* to ``a`` 347 #. Set *"x_measure"* to ``a``
338 #. Set *"y_measure"* to ``y`` 348 #. Expand the ``additional options`` section
339 #. Expand the ``additional options`` section 349
340 350 #. Set *"y_measure"* to ``y``
341 #. Set *"group_by"* to ``group`` 351 #. Set *"group_by"* to ``group``
342 #. Set *"title"* to ``Lineplot with no replicate method, grouped by `group`.`` 352 #. Set *"title"* to ``Lineplot with no replicate method, grouped by `group`.``
343 353
344 #. Press the ``Execute`` button. 354 #. Press the ``Execute`` button.
345 355
365 #. Leave as ``Metadata from TSV`` 375 #. Leave as ``Metadata from TSV``
366 #. Set *"Metadata Source"* to ``metadata.tsv`` 376 #. Set *"Metadata Source"* to ``metadata.tsv``
367 377
368 378
369 #. Set *"x_measure"* to ``b`` 379 #. Set *"x_measure"* to ``b``
370 #. Set *"y_measure"* to ``y`` 380 #. Expand the ``additional options`` section
371 #. Expand the ``additional options`` section 381
372 382 #. Set *"y_measure"* to ``y``
373 - Set *"title"* to ``Lineplot with no replicate method (no grouping).`` 383 #. Set *"title"* to ``Lineplot with no replicate method (no grouping).``
374 384
375 #. Press the ``Execute`` button. 385 #. Press the ``Execute`` button.
376 386
377 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: 387 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.) 388 (Renaming is optional, but it will make any subsequent steps easier to complete.)