Mercurial > repos > q2d2 > qiime2__feature_table__filter_samples
comparison qiime2__feature_table__filter_samples.xml @ 1:552388e54b68 draft
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 |
comparison
equal
deleted
inserted
replaced
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> |