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comparison qiime2__feature_table__filter_samples.xml @ 0:e2b704eca815 draft

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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 19:55:05 +0000
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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>