Mercurial > repos > q2d2 > qiime2__feature_table__filter_features_conditionally
annotate qiime2__feature_table__filter_features_conditionally.xml @ 0:90e36d8f2299 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
---|---|
date | Mon, 29 Aug 2022 19:56:18 +0000 |
parents | |
children | dbeb5a365844 |
rev | line source |
---|---|
0
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
1 <?xml version='1.0' encoding='utf-8'?> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
2 <!-- |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
3 Copyright (c) 2022, QIIME 2 development team. |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
4 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
6 --> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
7 <!-- |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
8 This tool was automatically generated by: |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
9 q2galaxy (version: 2022.8.1) |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
10 for: |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
11 qiime2 (version: 2022.8.1) |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
12 --> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
13 <tool name="qiime2 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
14 <description>Filter features from a table based on abundance and prevalence</description> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
15 <requirements> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
16 <container type="docker">quay.io/qiime2/core:2022.8</container> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
17 </requirements> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
18 <version_command>q2galaxy version feature_table</version_command> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
19 <command detect_errors="aggressive">q2galaxy run feature_table filter_features_conditionally '$inputs'</command> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
20 <configfiles> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
21 <inputs name="inputs" data_style="paths"/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
22 </configfiles> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
23 <inputs> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which features should be filtered."> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
25 <options options_filter_attribute="metadata.semantic_type"> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
26 <filter type="add_value" value="FeatureTable[Composition]"/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
28 <filter type="add_value" value="FeatureTable[Frequency]"/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
29 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
30 </options> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
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> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
32 </param> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
33 <param name="abundance" type="float" min="0" max="0.999999" value="" label="abundance: Float % Range(0, 1)" help="[required] The minimum relative abundance for a feature to be retained."/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
34 <param name="prevalence" type="float" min="0" max="0.999999" value="" label="prevalence: Float % Range(0, 1)" help="[required] The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained."/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
35 </inputs> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
36 <outputs> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
37 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
38 </outputs> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
39 <tests/> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
40 <help> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
41 QIIME 2: feature-table filter-features-conditionally |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
42 ==================================================== |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
43 Filter features from a table based on abundance and prevalence |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
44 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
45 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
46 Outputs: |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
47 -------- |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
48 :filtered_table.qza: The resulting feature table filtered by feature. |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
49 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
50 | |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
51 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
52 Description: |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
53 ------------ |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
54 Filter features based on the relative abundance in a certain portion of samples (i.e., features must have a relative abundance of at least `abundance` in at least `prevalence` number of samples). Any samples with a frequency of zero after feature filtering will also be removed. |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
55 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
56 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
57 | |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
58 |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
59 </help> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
60 <citations> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
61 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
62 </citations> |
90e36d8f2299
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
q2d2
parents:
diff
changeset
|
63 </tool> |