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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:52:20 +0000
parents e2b704eca815
children 540707a41f82
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0:e2b704eca815 1:552388e54b68
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2022, QIIME 2 development team. 3 Copyright (c) 2023, 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: 2022.8.1) 9 q2galaxy (version: 2022.11.1)
10 for: 10 for:
11 qiime2 (version: 2022.8.1) 11 qiime2 (version: 2022.11.1)
12 --> 12 -->
13 <tool name="qiime2 feature-table filter-samples" id="qiime2__feature_table__filter_samples" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 feature-table filter-samples" id="qiime2__feature_table__filter_samples" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Filter samples from table</description> 14 <description>Filter samples from table</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container> 16 <container type="docker">quay.io/qiime2/core:2022.11</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version feature_table</version_command> 18 <version_command>q2galaxy version feature_table</version_command>
19 <command detect_errors="aggressive">q2galaxy run feature_table filter_samples '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run feature_table filter_samples '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="paths"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which samples should be filtered."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which samples should be filtered.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
26 <filter type="add_value" value="FeatureTable[Composition]"/> 27 <filter type="add_value" value="FeatureTable[Composition]"/>
28 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> 29 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
28 <filter type="add_value" value="FeatureTable[Frequency]"/>
29 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
30 </options> 30 </options>
31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> 31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
32 </param> 32 </param>
33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
34 <param name="min_frequency" type="integer" value="0" label="min_frequency: Int" help="[default: 0] The minimum total frequency that a sample must have to be retained."/> 34 <param name="min_frequency" type="integer" value="0" label="min_frequency: Int" help="[default: 0] The minimum total frequency that a sample must have to be retained."/>
70 </section> 70 </section>
71 </inputs> 71 </inputs>
72 <outputs> 72 <outputs>
73 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> 73 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
74 </outputs> 74 </outputs>
75 <tests/> 75 <tests>
76 <test>
77 <param name="table" value="filter_samples.test0.feature-table.qza" ftype="qza"/>
78 <repeat name="metadata">
79 <conditional name="__q2galaxy__GUI__conditional__metadata__">
80 <param name="type" value="tsv"/>
81 <param name="source" value="filter_samples.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
82 </conditional>
83 </repeat>
84 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__"/>
85 <output name="filtered_table" ftype="qza">
86 <assert_contents>
87 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
88 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
89 </has_archive_member>
90 </assert_contents>
91 </output>
92 </test>
93 <test>
94 <param name="table" value="filter_samples.test1.feature-table.qza" ftype="qza"/>
95 <repeat name="metadata">
96 <conditional name="__q2galaxy__GUI__conditional__metadata__">
97 <param name="type" value="tsv"/>
98 <param name="source" value="filter_samples.test1.sample-metadata.tsv" ftype="qiime2.tabular"/>
99 </conditional>
100 </repeat>
101 <param name="where" value="__ob__body-site__cb__ IN (__dq__left palm__dq____comma__ __dq__right palm__dq__)"/>
102 <output name="filtered_table" ftype="qza">
103 <assert_contents>
104 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
105 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
106 </has_archive_member>
107 </assert_contents>
108 </output>
109 </test>
110 <test>
111 <param name="table" value="filter_samples.test2.feature-table.qza" ftype="qza"/>
112 <repeat name="metadata">
113 <conditional name="__q2galaxy__GUI__conditional__metadata__">
114 <param name="type" value="tsv"/>
115 <param name="source" value="filter_samples.test2.sample-metadata.tsv" ftype="qiime2.tabular"/>
116 </conditional>
117 </repeat>
118 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND __ob__body-site__cb__=__dq__gut__dq__"/>
119 <output name="filtered_table" ftype="qza">
120 <assert_contents>
121 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
122 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
123 </has_archive_member>
124 </assert_contents>
125 </output>
126 </test>
127 <test>
128 <param name="table" value="filter_samples.test3.feature-table.qza" ftype="qza"/>
129 <repeat name="metadata">
130 <conditional name="__q2galaxy__GUI__conditional__metadata__">
131 <param name="type" value="tsv"/>
132 <param name="source" value="filter_samples.test3.sample-metadata.tsv" ftype="qiime2.tabular"/>
133 </conditional>
134 </repeat>
135 <param name="where" value="__ob__body-site__cb__=__dq__gut__dq__ OR __ob__reported-antibiotic-usage__cb__=__dq__Yes__dq__"/>
136 <output name="filtered_table" ftype="qza">
137 <assert_contents>
138 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
139 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
140 </has_archive_member>
141 </assert_contents>
142 </output>
143 </test>
144 <test>
145 <param name="table" value="filter_samples.test4.feature-table.qza" ftype="qza"/>
146 <repeat name="metadata">
147 <conditional name="__q2galaxy__GUI__conditional__metadata__">
148 <param name="type" value="tsv"/>
149 <param name="source" value="filter_samples.test4.sample-metadata.tsv" ftype="qiime2.tabular"/>
150 </conditional>
151 </repeat>
152 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND NOT __ob__body-site__cb__=__dq__gut__dq__"/>
153 <output name="filtered_table" ftype="qza">
154 <assert_contents>
155 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
156 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
157 </has_archive_member>
158 </assert_contents>
159 </output>
160 </test>
161 <test>
162 <param name="table" value="filter_samples.test5.feature-table.qza" ftype="qza"/>
163 <param name="min_features" value="10"/>
164 <output name="filtered_table" ftype="qza">
165 <assert_contents>
166 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
167 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
168 </has_archive_member>
169 </assert_contents>
170 </output>
171 </test>
172 <test>
173 <param name="table" value="filter_samples.test6.feature-table.qza" ftype="qza"/>
174 <param name="min_frequency" value="1500"/>
175 <output name="filtered_table" ftype="qza">
176 <assert_contents>
177 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
178 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
179 </has_archive_member>
180 </assert_contents>
181 </output>
182 </test>
183 </tests>
76 <help> 184 <help>
77 QIIME 2: feature-table filter-samples 185 QIIME 2: feature-table filter-samples
78 ===================================== 186 =====================================
79 Filter samples from table 187 Filter samples from table
80 188
86 | 194 |
87 195
88 Description: 196 Description:
89 ------------ 197 ------------
90 Filter samples from table based on frequency and/or metadata. Any features with a frequency of zero after sample filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details. 198 Filter samples from table based on frequency and/or metadata. Any features with a frequency of zero after sample filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details.
199
200 Examples:
201 ---------
202
203 filter_to_subject1
204 ******************
205 Using the ``qiime2 feature-table filter-samples`` tool:
206 #. Set *"table"* to ``#: feature-table.qza``
207 #. Expand the ``additional options`` section
208
209 #. For *"metadata"*:
210
211 - Press the ``+ Insert metadata`` button to set up the next steps.
212
213 #. Leave as ``Metadata from TSV``
214 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
215
216
217 #. Set *"where"* to ``[subject]="subject-1"``
218
219 #. Press the ``Execute`` button.
220
221
222 filter_to_skin
223 **************
224 Using the ``qiime2 feature-table filter-samples`` tool:
225 #. Set *"table"* to ``#: feature-table.qza``
226 #. Expand the ``additional options`` section
227
228 #. For *"metadata"*:
229
230 - Press the ``+ Insert metadata`` button to set up the next steps.
231
232 #. Leave as ``Metadata from TSV``
233 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
234
235
236 #. Set *"where"* to ``[body-site] IN ("left palm", "right palm")``
237
238 #. Press the ``Execute`` button.
239
240
241 filter_to_subject1_gut
242 **********************
243 Using the ``qiime2 feature-table filter-samples`` tool:
244 #. Set *"table"* to ``#: feature-table.qza``
245 #. Expand the ``additional options`` section
246
247 #. For *"metadata"*:
248
249 - Press the ``+ Insert metadata`` button to set up the next steps.
250
251 #. Leave as ``Metadata from TSV``
252 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
253
254
255 #. Set *"where"* to ``[subject]="subject-1" AND [body-site]="gut"``
256
257 #. Press the ``Execute`` button.
258
259
260 filter_to_gut_or_abx
261 ********************
262 Using the ``qiime2 feature-table filter-samples`` tool:
263 #. Set *"table"* to ``#: feature-table.qza``
264 #. Expand the ``additional options`` section
265
266 #. For *"metadata"*:
267
268 - Press the ``+ Insert metadata`` button to set up the next steps.
269
270 #. Leave as ``Metadata from TSV``
271 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
272
273
274 #. Set *"where"* to ``[body-site]="gut" OR [reported-antibiotic-usage]="Yes"``
275
276 #. Press the ``Execute`` button.
277
278
279 filter_to_subject1_not_gut
280 **************************
281 Using the ``qiime2 feature-table filter-samples`` tool:
282 #. Set *"table"* to ``#: feature-table.qza``
283 #. Expand the ``additional options`` section
284
285 #. For *"metadata"*:
286
287 - Press the ``+ Insert metadata`` button to set up the next steps.
288
289 #. Leave as ``Metadata from TSV``
290 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
291
292
293 #. Set *"where"* to ``[subject]="subject-1" AND NOT [body-site]="gut"``
294
295 #. Press the ``Execute`` button.
296
297
298 filter_min_features
299 *******************
300 Using the ``qiime2 feature-table filter-samples`` tool:
301 #. Set *"table"* to ``#: feature-table.qza``
302 #. Expand the ``additional options`` section
303
304 - Set *"min_features"* to ``10``
305
306 #. Press the ``Execute`` button.
307
308
309 filter_min_frequency
310 ********************
311 Using the ``qiime2 feature-table filter-samples`` tool:
312 #. Set *"table"* to ``#: feature-table.qza``
313 #. Expand the ``additional options`` section
314
315 - Set *"min_frequency"* to ``1500``
316
317 #. Press the ``Execute`` button.
318
91 319
92 320
93 | 321 |
94 322
95 </help> 323 </help>