Mercurial > repos > q2d2 > qiime2__feature_table__filter_samples
annotate qiime2__feature_table__filter_samples.xml @ 4:40647f5aa13b draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:24:54 +0000 |
parents | 4a129fe72b67 |
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e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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4a129fe72b67
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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3 Copyright (c) 2024, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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40647f5aa13b
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
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9 q2galaxy (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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40647f5aa13b
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
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11 qiime2 (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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40647f5aa13b
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
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13 <tool name="qiime2 feature-table filter-samples" id="qiime2__feature_table__filter_samples" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> |
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e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Filter samples from table</description> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version feature_table</version_command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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19 <command detect_errors="exit_code">q2galaxy run feature_table filter_samples '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 <configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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."> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="FeatureTable[Composition]"/> |
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4a129fe72b67
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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27 <filter type="add_value" value="FeatureTable[Frequency]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 65e4952f33eb335528e8553150e9097e5ea8f556
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28 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> |
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40647f5aa13b
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
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29 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 </options> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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."/> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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)."/> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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."/> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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)."/> |
e2b704eca815
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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40 <param name="type" type="select" label="metadata: Metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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41 <option value="tsv" selected="true">Metadata from TSV</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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42 <option value="qza">Metadata from Artifact</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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43 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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44 <when value="tsv"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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45 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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46 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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47 <when value="qza"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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48 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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49 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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50 </conditional> |
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51 </repeat> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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52 <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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54 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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55 <option value="__q2galaxy__::control::provide">Provide a value</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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59 </when> |
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60 <when value="__q2galaxy__::control::provide"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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 <param name="allow_empty_table" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allow_empty_table: Bool" help="[default: No] If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty."/> |
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71 </section> |
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72 </inputs> |
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73 <outputs> |
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74 <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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75 </outputs> |
1
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76 <tests> |
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77 <test> |
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78 <param name="table" value="filter_samples.test0.feature-table.qza" ftype="qza"/> |
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79 <repeat name="metadata"> |
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80 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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81 <param name="type" value="tsv"/> |
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82 <param name="source" value="filter_samples.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> |
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83 </conditional> |
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84 </repeat> |
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85 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__"/> |
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86 <output name="filtered_table" ftype="qza"> |
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87 <assert_contents> |
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88 <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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89 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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90 </has_archive_member> |
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91 </assert_contents> |
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92 </output> |
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93 </test> |
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94 <test> |
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95 <param name="table" value="filter_samples.test1.feature-table.qza" ftype="qza"/> |
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96 <repeat name="metadata"> |
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97 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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98 <param name="type" value="tsv"/> |
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99 <param name="source" value="filter_samples.test1.sample-metadata.tsv" ftype="qiime2.tabular"/> |
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100 </conditional> |
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101 </repeat> |
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102 <param name="where" value="__ob__body-site__cb__ IN (__dq__left palm__dq____comma__ __dq__right palm__dq__)"/> |
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103 <output name="filtered_table" ftype="qza"> |
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104 <assert_contents> |
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105 <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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106 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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107 </has_archive_member> |
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108 </assert_contents> |
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109 </output> |
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110 </test> |
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111 <test> |
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112 <param name="table" value="filter_samples.test2.feature-table.qza" ftype="qza"/> |
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113 <repeat name="metadata"> |
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114 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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115 <param name="type" value="tsv"/> |
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116 <param name="source" value="filter_samples.test2.sample-metadata.tsv" ftype="qiime2.tabular"/> |
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117 </conditional> |
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118 </repeat> |
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119 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND __ob__body-site__cb__=__dq__gut__dq__"/> |
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120 <output name="filtered_table" ftype="qza"> |
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121 <assert_contents> |
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122 <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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123 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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124 </has_archive_member> |
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125 </assert_contents> |
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126 </output> |
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127 </test> |
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128 <test> |
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129 <param name="table" value="filter_samples.test3.feature-table.qza" ftype="qza"/> |
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130 <repeat name="metadata"> |
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131 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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132 <param name="type" value="tsv"/> |
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133 <param name="source" value="filter_samples.test3.sample-metadata.tsv" ftype="qiime2.tabular"/> |
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134 </conditional> |
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135 </repeat> |
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136 <param name="where" value="__ob__body-site__cb__=__dq__gut__dq__ OR __ob__reported-antibiotic-usage__cb__=__dq__Yes__dq__"/> |
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137 <output name="filtered_table" ftype="qza"> |
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138 <assert_contents> |
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139 <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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140 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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141 </has_archive_member> |
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142 </assert_contents> |
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143 </output> |
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144 </test> |
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145 <test> |
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146 <param name="table" value="filter_samples.test4.feature-table.qza" ftype="qza"/> |
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147 <repeat name="metadata"> |
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148 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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149 <param name="type" value="tsv"/> |
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150 <param name="source" value="filter_samples.test4.sample-metadata.tsv" ftype="qiime2.tabular"/> |
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151 </conditional> |
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152 </repeat> |
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153 <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND NOT __ob__body-site__cb__=__dq__gut__dq__"/> |
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154 <output name="filtered_table" ftype="qza"> |
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155 <assert_contents> |
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156 <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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157 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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158 </has_archive_member> |
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159 </assert_contents> |
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160 </output> |
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161 </test> |
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162 <test> |
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163 <param name="table" value="filter_samples.test5.feature-table.qza" ftype="qza"/> |
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164 <param name="min_features" value="10"/> |
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165 <output name="filtered_table" ftype="qza"> |
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166 <assert_contents> |
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167 <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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168 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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169 </has_archive_member> |
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170 </assert_contents> |
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171 </output> |
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172 </test> |
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173 <test> |
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174 <param name="table" value="filter_samples.test6.feature-table.qza" ftype="qza"/> |
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175 <param name="min_frequency" value="1500"/> |
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176 <output name="filtered_table" ftype="qza"> |
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177 <assert_contents> |
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178 <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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179 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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180 </has_archive_member> |
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181 </assert_contents> |
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182 </output> |
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183 </test> |
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184 </tests> |
0
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185 <help> |
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186 QIIME 2: feature-table filter-samples |
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187 ===================================== |
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188 Filter samples from table |
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189 |
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190 |
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191 Outputs: |
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192 -------- |
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193 :filtered_table.qza: The resulting feature table filtered by sample. |
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194 |
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195 | |
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196 |
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197 Description: |
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198 ------------ |
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199 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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200 |
1
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201 Examples: |
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202 --------- |
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203 |
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204 filter_to_subject1 |
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205 ****************** |
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206 Using the ``qiime2 feature-table filter-samples`` tool: |
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207 #. Set *"table"* to ``#: feature-table.qza`` |
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208 #. Expand the ``additional options`` section |
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209 |
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210 #. For *"metadata"*: |
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211 |
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212 - Press the ``+ Insert metadata`` button to set up the next steps. |
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213 |
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214 #. Leave as ``Metadata from TSV`` |
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215 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` |
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216 |
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217 |
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218 #. Set *"where"* to ``[subject]="subject-1"`` |
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219 |
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220 #. Press the ``Execute`` button. |
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221 |
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222 |
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223 filter_to_skin |
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224 ************** |
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225 Using the ``qiime2 feature-table filter-samples`` tool: |
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226 #. Set *"table"* to ``#: feature-table.qza`` |
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227 #. Expand the ``additional options`` section |
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228 |
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229 #. For *"metadata"*: |
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230 |
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231 - Press the ``+ Insert metadata`` button to set up the next steps. |
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232 |
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233 #. Leave as ``Metadata from TSV`` |
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234 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` |
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235 |
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236 |
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237 #. Set *"where"* to ``[body-site] IN ("left palm", "right palm")`` |
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238 |
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239 #. Press the ``Execute`` button. |
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240 |
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241 |
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242 filter_to_subject1_gut |
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243 ********************** |
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244 Using the ``qiime2 feature-table filter-samples`` tool: |
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245 #. Set *"table"* to ``#: feature-table.qza`` |
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246 #. Expand the ``additional options`` section |
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247 |
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248 #. For *"metadata"*: |
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249 |
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250 - Press the ``+ Insert metadata`` button to set up the next steps. |
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251 |
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252 #. Leave as ``Metadata from TSV`` |
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253 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` |
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254 |
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255 |
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256 #. Set *"where"* to ``[subject]="subject-1" AND [body-site]="gut"`` |
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257 |
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258 #. Press the ``Execute`` button. |
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259 |
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260 |
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261 filter_to_gut_or_abx |
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262 ******************** |
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263 Using the ``qiime2 feature-table filter-samples`` tool: |
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264 #. Set *"table"* to ``#: feature-table.qza`` |
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265 #. Expand the ``additional options`` section |
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266 |
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267 #. For *"metadata"*: |
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268 |
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269 - Press the ``+ Insert metadata`` button to set up the next steps. |
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270 |
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271 #. Leave as ``Metadata from TSV`` |
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272 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` |
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273 |
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274 |
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275 #. Set *"where"* to ``[body-site]="gut" OR [reported-antibiotic-usage]="Yes"`` |
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276 |
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277 #. Press the ``Execute`` button. |
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278 |
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279 |
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280 filter_to_subject1_not_gut |
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281 ************************** |
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282 Using the ``qiime2 feature-table filter-samples`` tool: |
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283 #. Set *"table"* to ``#: feature-table.qza`` |
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284 #. Expand the ``additional options`` section |
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285 |
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286 #. For *"metadata"*: |
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287 |
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288 - Press the ``+ Insert metadata`` button to set up the next steps. |
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289 |
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290 #. Leave as ``Metadata from TSV`` |
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291 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` |
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292 |
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293 |
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294 #. Set *"where"* to ``[subject]="subject-1" AND NOT [body-site]="gut"`` |
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295 |
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296 #. Press the ``Execute`` button. |
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297 |
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298 |
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299 filter_min_features |
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300 ******************* |
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301 Using the ``qiime2 feature-table filter-samples`` tool: |
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302 #. Set *"table"* to ``#: feature-table.qza`` |
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303 #. Expand the ``additional options`` section |
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304 |
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305 - Set *"min_features"* to ``10`` |
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306 |
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307 #. Press the ``Execute`` button. |
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308 |
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309 |
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310 filter_min_frequency |
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311 ******************** |
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312 Using the ``qiime2 feature-table filter-samples`` tool: |
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313 #. Set *"table"* to ``#: feature-table.qza`` |
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314 #. Expand the ``additional options`` section |
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315 |
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316 - Set *"min_frequency"* to ``1500`` |
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317 |
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318 #. Press the ``Execute`` button. |
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319 |
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320 |
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321 |
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322 | |
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323 |
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324 </help> |
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325 <citations> |
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326 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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327 </citations> |
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328 </tool> |