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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:48:06 +0000
parents 4098a583c0d7
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, 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:
2
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 feature-table split" id="qiime2__feature_table__split" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Split one feature table into many</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version feature_table</version_command>
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22 <command detect_errors="exit_code">q2galaxy run feature_table split '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The table to split.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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31 <filter type="add_value" value="FeatureTable[Composition]"/>
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32 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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33 </options>
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34 <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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35 </param>
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36 <conditional name="metadata">
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37 <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] A column defining the groups. Each unique value will define a split feature table.">
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38 <option value="tsv" selected="true">Metadata from TSV</option>
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39 <option value="qza">Metadata from Artifact</option>
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40 </param>
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41 <when value="tsv">
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42 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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43 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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44 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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45 </param>
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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 <param name="column" type="text" label="Column Name">
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50 <validator type="empty_field"/>
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51 </param>
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52 </when>
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53 </conditional>
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54 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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55 <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 a split feature table are dropped."/>
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56 </section>
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57 </inputs>
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58 <outputs>
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59 <collection name="tables" type="list">
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60 <discover_datasets directory="tables" pattern="__name_and_ext__"/>
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61 </collection>
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62 </outputs>
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63 <tests/>
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64 <help>
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65 QIIME 2: feature-table split
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66 ============================
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67 Split one feature table into many
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68
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69
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70 Outputs:
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71 --------
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72 :tables.qza: Directory where feature tables split based on metadata values should be written.
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73
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74 |
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75
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76 Description:
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77 ------------
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78 Splits one feature table into many feature tables, where splits are defined by values in metadata column.
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79
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81 |
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83 </help>
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84 <citations>
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85 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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86 </citations>
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87 </tool>