Mercurial > repos > q2d2 > qiime2__feature_table__filter_samples

annotate qiime2__feature_table__filter_samples.xml @ 2:540707a41f82 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:47:56 +0000
parents 552388e54b68
children 4a129fe72b67
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, QIIME 2 development team.
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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: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 feature-table filter-samples" id="qiime2__feature_table__filter_samples" version="2023.5.0+q2galaxy.2023.5.0.2" 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:2023.5</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="exit_code">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[Frequency]"/>
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27 <filter type="add_value" value="FeatureTable[Composition]"/>
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28 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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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>
1
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75 <tests>
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76 <test>
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77 <param name="table" value="filter_samples.test0.feature-table.qza" ftype="qza"/>
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78 <repeat name="metadata">
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79 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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80 <param name="type" value="tsv"/>
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81 <param name="source" value="filter_samples.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
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82 </conditional>
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83 </repeat>
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84 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__"/>
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85 <output name="filtered_table" ftype="qza">
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86 <assert_contents>
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87 <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">
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88 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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89 </has_archive_member>
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90 </assert_contents>
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91 </output>
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92 </test>
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93 <test>
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94 <param name="table" value="filter_samples.test1.feature-table.qza" ftype="qza"/>
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95 <repeat name="metadata">
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96 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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97 <param name="type" value="tsv"/>
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98 <param name="source" value="filter_samples.test1.sample-metadata.tsv" ftype="qiime2.tabular"/>
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99 </conditional>
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100 </repeat>
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101 <param name="where" value="__ob__body-site__cb__ IN (__dq__left palm__dq____comma__ __dq__right palm__dq__)"/>
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102 <output name="filtered_table" ftype="qza">
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103 <assert_contents>
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104 <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">
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105 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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106 </has_archive_member>
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107 </assert_contents>
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108 </output>
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109 </test>
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110 <test>
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111 <param name="table" value="filter_samples.test2.feature-table.qza" ftype="qza"/>
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112 <repeat name="metadata">
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113 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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114 <param name="type" value="tsv"/>
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115 <param name="source" value="filter_samples.test2.sample-metadata.tsv" ftype="qiime2.tabular"/>
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116 </conditional>
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117 </repeat>
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118 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND __ob__body-site__cb__=__dq__gut__dq__"/>
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119 <output name="filtered_table" ftype="qza">
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120 <assert_contents>
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121 <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">
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122 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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123 </has_archive_member>
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124 </assert_contents>
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125 </output>
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126 </test>
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127 <test>
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128 <param name="table" value="filter_samples.test3.feature-table.qza" ftype="qza"/>
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129 <repeat name="metadata">
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130 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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131 <param name="type" value="tsv"/>
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132 <param name="source" value="filter_samples.test3.sample-metadata.tsv" ftype="qiime2.tabular"/>
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133 </conditional>
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134 </repeat>
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135 <param name="where" value="__ob__body-site__cb__=__dq__gut__dq__ OR __ob__reported-antibiotic-usage__cb__=__dq__Yes__dq__"/>
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136 <output name="filtered_table" ftype="qza">
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137 <assert_contents>
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138 <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">
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139 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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140 </has_archive_member>
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141 </assert_contents>
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142 </output>
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143 </test>
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144 <test>
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145 <param name="table" value="filter_samples.test4.feature-table.qza" ftype="qza"/>
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146 <repeat name="metadata">
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147 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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148 <param name="type" value="tsv"/>
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149 <param name="source" value="filter_samples.test4.sample-metadata.tsv" ftype="qiime2.tabular"/>
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150 </conditional>
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151 </repeat>
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152 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND NOT __ob__body-site__cb__=__dq__gut__dq__"/>
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153 <output name="filtered_table" ftype="qza">
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154 <assert_contents>
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155 <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">
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156 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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157 </has_archive_member>
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158 </assert_contents>
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159 </output>
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160 </test>
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161 <test>
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162 <param name="table" value="filter_samples.test5.feature-table.qza" ftype="qza"/>
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163 <param name="min_features" value="10"/>
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164 <output name="filtered_table" ftype="qza">
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165 <assert_contents>
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166 <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">
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167 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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168 </has_archive_member>
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169 </assert_contents>
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170 </output>
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171 </test>
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172 <test>
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173 <param name="table" value="filter_samples.test6.feature-table.qza" ftype="qza"/>
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174 <param name="min_frequency" value="1500"/>
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175 <output name="filtered_table" ftype="qza">
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176 <assert_contents>
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177 <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">
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178 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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179 </has_archive_member>
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180 </assert_contents>
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181 </output>
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182 </test>
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183 </tests>
0
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184 <help>
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185 QIIME 2: feature-table filter-samples
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186 =====================================
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187 Filter samples from table
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188
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189
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190 Outputs:
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191 --------
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192 :filtered_table.qza: The resulting feature table filtered by sample.
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193
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194 |
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195
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196 Description:
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197 ------------
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198 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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199
1
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200 Examples:
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201 ---------
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202
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203 filter_to_subject1
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204 ******************
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205 Using the ``qiime2 feature-table filter-samples`` tool:
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206 #. Set *"table"* to ``#: feature-table.qza``
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207 #. Expand the ``additional options`` section
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208
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209 #. For *"metadata"*:
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210
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211 - Press the ``+ Insert metadata`` button to set up the next steps.
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212
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213 #. Leave as ``Metadata from TSV``
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214 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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215
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216
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217 #. Set *"where"* to ``[subject]="subject-1"``
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218
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219 #. Press the ``Execute`` button.
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220
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221
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222 filter_to_skin
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223 **************
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224 Using the ``qiime2 feature-table filter-samples`` tool:
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225 #. Set *"table"* to ``#: feature-table.qza``
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226 #. Expand the ``additional options`` section
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227
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228 #. For *"metadata"*:
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229
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230 - Press the ``+ Insert metadata`` button to set up the next steps.
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231
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232 #. Leave as ``Metadata from TSV``
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233 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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234
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235
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236 #. Set *"where"* to ``[body-site] IN ("left palm", "right palm")``
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237
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238 #. Press the ``Execute`` button.
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239
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240
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241 filter_to_subject1_gut
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242 **********************
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243 Using the ``qiime2 feature-table filter-samples`` tool:
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244 #. Set *"table"* to ``#: feature-table.qza``
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245 #. Expand the ``additional options`` section
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246
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247 #. For *"metadata"*:
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248
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249 - Press the ``+ Insert metadata`` button to set up the next steps.
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250
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251 #. Leave as ``Metadata from TSV``
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252 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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253
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254
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255 #. Set *"where"* to ``[subject]="subject-1" AND [body-site]="gut"``
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256
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257 #. Press the ``Execute`` button.
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258
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259
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260 filter_to_gut_or_abx
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261 ********************
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262 Using the ``qiime2 feature-table filter-samples`` tool:
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263 #. Set *"table"* to ``#: feature-table.qza``
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264 #. Expand the ``additional options`` section
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265
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266 #. For *"metadata"*:
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267
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268 - Press the ``+ Insert metadata`` button to set up the next steps.
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269
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270 #. Leave as ``Metadata from TSV``
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271 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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272
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273
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274 #. Set *"where"* to ``[body-site]="gut" OR [reported-antibiotic-usage]="Yes"``
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275
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276 #. Press the ``Execute`` button.
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277
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278
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279 filter_to_subject1_not_gut
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280 **************************
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281 Using the ``qiime2 feature-table filter-samples`` tool:
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282 #. Set *"table"* to ``#: feature-table.qza``
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283 #. Expand the ``additional options`` section
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284
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285 #. For *"metadata"*:
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286
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287 - Press the ``+ Insert metadata`` button to set up the next steps.
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288
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289 #. Leave as ``Metadata from TSV``
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290 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
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291
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292
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293 #. Set *"where"* to ``[subject]="subject-1" AND NOT [body-site]="gut"``
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294
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295 #. Press the ``Execute`` button.
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296
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297
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298 filter_min_features
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299 *******************
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300 Using the ``qiime2 feature-table filter-samples`` tool:
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301 #. Set *"table"* to ``#: feature-table.qza``
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302 #. Expand the ``additional options`` section
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303
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304 - Set *"min_features"* to ``10``
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305
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306 #. Press the ``Execute`` button.
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307
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308
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309 filter_min_frequency
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310 ********************
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311 Using the ``qiime2 feature-table filter-samples`` tool:
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312 #. Set *"table"* to ``#: feature-table.qza``
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313 #. Expand the ``additional options`` section
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314
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315 - Set *"min_frequency"* to ``1500``
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316
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317 #. Press the ``Execute`` button.
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318
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319
0
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320
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321 |
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322
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323 </help>
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324 <citations>
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325 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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326 </citations>
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327 </tool>