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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'?>
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2 <!--
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3 Copyright (c) 2022, QIIME 2 development team.
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4
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2022.8.1)
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10 for:
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11 qiime2 (version: 2022.8.1)
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12 -->
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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">
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14 <description>Filter samples from table</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.8</container>
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17 </requirements>
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18 <version_command>q2galaxy version feature_table</version_command>
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19 <command detect_errors="aggressive">q2galaxy run feature_table filter_samples '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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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.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[Composition]"/>
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27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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28 <filter type="add_value" value="FeatureTable[Frequency]"/>
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29 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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30 </options>
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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>
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32 </param>
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33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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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."/>
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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)."/>
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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."/>
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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)."/>
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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">
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39 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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40 <param name="type" type="select" label="metadata: Metadata">
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41 <option value="tsv" selected="true">Metadata from TSV</option>
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42 <option value="qza">Metadata from Artifact</option>
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43 </param>
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44 <when value="tsv">
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45 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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46 </when>
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47 <when value="qza">
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48 <param name="source" type="data" format="qza" label="Metadata Source"/>
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49 </when>
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50 </conditional>
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51 </repeat>
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52 <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str">
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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.">
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54 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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55 <option value="__q2galaxy__::control::provide">Provide a value</option>
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56 </param>
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57 <when value="__q2galaxy__::control::default">
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58 <param name="where" type="hidden" value="__q2galaxy__::literal::None"/>
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59 </when>
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60 <when value="__q2galaxy__::control::provide">
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61 <param name="where" type="text">
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62 <sanitizer>
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63 <valid initial="string.printable"/>
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64 </sanitizer>
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65 </param>
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66 </when>
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67 </conditional>
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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."/>
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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."/>
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70 </section>
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71 </inputs>
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72 <outputs>
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73 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
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74 </outputs>
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75 <tests/>
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76 <help>
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77 QIIME 2: feature-table filter-samples
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78 =====================================
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79 Filter samples from table
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80
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81
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82 Outputs:
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83 --------
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84 :filtered_table.qza: The resulting feature table filtered by sample.
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85
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86 |
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87
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88 Description:
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89 ------------
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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.
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91
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92
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93 |
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94
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95 </help>
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96 <citations>
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97 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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98 </citations>
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99 </tool>