Mercurial > repos > q2d2 > qiime2__feature_table__filter_features_conditionally

comparison qiime2__feature_table__filter_features_conditionally.xml @ 1:dbeb5a365844 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__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:52:51 +0000
parents 90e36d8f2299
children 78538c1b0993
comparison
equal deleted inserted replaced
0:90e36d8f2299 1:dbeb5a365844
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-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"> 13 <tool name="qiime2 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Filter features from a table based on abundance and prevalence</description> 14 <description>Filter features from a table based on abundance and prevalence</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_features_conditionally '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run feature_table filter_features_conditionally '$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 features 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 features 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 <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."/> 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."/>
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."/> 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."/>
35 </inputs> 35 </inputs>
36 <outputs> 36 <outputs>
37 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> 37 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
38 </outputs> 38 </outputs>
39 <tests/> 39 <tests>
40 <test>
41 <param name="table" value="filter_features_conditionally.test0.feature-table.qza" ftype="qza"/>
42 <param name="abundance" value="0.01"/>
43 <param name="prevalence" value="0.34"/>
44 <output name="filtered_table" ftype="qza">
45 <assert_contents>
46 <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">
47 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
48 </has_archive_member>
49 </assert_contents>
50 </output>
51 </test>
52 </tests>
40 <help> 53 <help>
41 QIIME 2: feature-table filter-features-conditionally 54 QIIME 2: feature-table filter-features-conditionally
42 ==================================================== 55 ====================================================
43 Filter features from a table based on abundance and prevalence 56 Filter features from a table based on abundance and prevalence
44 57
51 64
52 Description: 65 Description:
53 ------------ 66 ------------
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. 67 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.
55 68
69 Examples:
70 ---------
71
72 feature_table_filter_features_conditionally
73 *******************************************
74 | Retain only features with at least 1%% abundance in at least 34%% of samples.
75 Using the ``qiime2 feature-table filter-features-conditionally`` tool:
76 #. Set *"table"* to ``#: feature-table.qza``
77 #. Set *"abundance"* to ``0.01``
78 #. Set *"prevalence"* to ``0.34``
79 #. Press the ``Execute`` button.
80
81
56 82
57 | 83 |
58 84
59 </help> 85 </help>
60 <citations> 86 <citations>