Mercurial > repos > q2d2 > qiime2__feature_table__filter_samples
comparison qiime2__feature_table__filter_samples.xml @ 0:e2b704eca815 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 19:55:05 +0000 |
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children | 552388e54b68 |
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1 <?xml version='1.0' encoding='utf-8'?> | |
2 <!-- | |
3 Copyright (c) 2022, QIIME 2 development team. | |
4 | |
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) | |
6 --> | |
7 <!-- | |
8 This tool was automatically generated by: | |
9 q2galaxy (version: 2022.8.1) | |
10 for: | |
11 qiime2 (version: 2022.8.1) | |
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"> | |
14 <description>Filter samples from table</description> | |
15 <requirements> | |
16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
17 </requirements> | |
18 <version_command>q2galaxy version feature_table</version_command> | |
19 <command detect_errors="aggressive">q2galaxy run feature_table filter_samples '$inputs'</command> | |
20 <configfiles> | |
21 <inputs name="inputs" data_style="paths"/> | |
22 </configfiles> | |
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."> | |
25 <options options_filter_attribute="metadata.semantic_type"> | |
26 <filter type="add_value" value="FeatureTable[Composition]"/> | |
27 <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> | |
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> | |
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."/> | |
35 <param name="max_frequency" type="integer" optional="true" label="max_frequency: Int" help="[optional] The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied)."/> | |
36 <param name="min_features" type="integer" value="0" label="min_features: Int" help="[default: 0] The minimum number of features that a sample must have to be retained."/> | |
37 <param name="max_features" type="integer" optional="true" label="max_features: Int" help="[optional] The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied)."/> | |
38 <repeat name="metadata" help="[optional] Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude_ids` when selecting samples to discard." title="metadata: Metadata"> | |
39 <conditional name="__q2galaxy__GUI__conditional__metadata__"> | |
40 <param name="type" type="select" label="metadata: Metadata"> | |
41 <option value="tsv" selected="true">Metadata from TSV</option> | |
42 <option value="qza">Metadata from Artifact</option> | |
43 </param> | |
44 <when value="tsv"> | |
45 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> | |
46 </when> | |
47 <when value="qza"> | |
48 <param name="source" type="data" format="qza" label="Metadata Source"/> | |
49 </when> | |
50 </conditional> | |
51 </repeat> | |
52 <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> | |
53 <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained."> | |
54 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> | |
55 <option value="__q2galaxy__::control::provide">Provide a value</option> | |
56 </param> | |
57 <when value="__q2galaxy__::control::default"> | |
58 <param name="where" type="hidden" value="__q2galaxy__::literal::None"/> | |
59 </when> | |
60 <when value="__q2galaxy__::control::provide"> | |
61 <param name="where" type="text"> | |
62 <sanitizer> | |
63 <valid initial="string.printable"/> | |
64 </sanitizer> | |
65 </param> | |
66 </when> | |
67 </conditional> | |
68 <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No] If true, the samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained."/> | |
69 <param name="filter_empty_features" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="filter_empty_features: Bool" help="[default: Yes] If true, features which are not present in any retained samples are dropped."/> | |
70 </section> | |
71 </inputs> | |
72 <outputs> | |
73 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> | |
74 </outputs> | |
75 <tests/> | |
76 <help> | |
77 QIIME 2: feature-table filter-samples | |
78 ===================================== | |
79 Filter samples from table | |
80 | |
81 | |
82 Outputs: | |
83 -------- | |
84 :filtered_table.qza: The resulting feature table filtered by sample. | |
85 | |
86 | | |
87 | |
88 Description: | |
89 ------------ | |
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. | |
91 | |
92 | |
93 | | |
94 | |
95 </help> | |
96 <citations> | |
97 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
98 </citations> | |
99 </tool> |