annotate qiime2__feature_table__group.xml @ 0:834bb534ba6d draft

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 19:54:40 +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 group" id="qiime2__feature_table__group" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Group samples or features by a metadata column</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 group '$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[Frequency]" help="[required] The table to group samples or features on.">
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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 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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29 </param>
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30 <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio">
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31 <option value="__q2galaxy__::literal::None">Selection required</option>
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32 <option value="feature">feature</option>
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33 <option value="sample">sample</option>
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34 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</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 become a new ID for the table on the given `axis`.">
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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 <param name="mode" type="select" label="mode: Str % Choices('mean-ceiling', 'median-ceiling', 'sum')" display="radio">
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55 <option value="__q2galaxy__::literal::None">Selection required</option>
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56 <option value="mean-ceiling">mean-ceiling</option>
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57 <option value="median-ceiling">median-ceiling</option>
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58 <option value="sum">sum</option>
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59 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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60 </param>
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61 </inputs>
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62 <outputs>
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63 <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/>
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64 </outputs>
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65 <tests/>
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66 <help>
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67 QIIME 2: feature-table group
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68 ============================
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69 Group samples or features by a metadata column
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70
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71
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72 Outputs:
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73 --------
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74 :grouped_table.qza: A table that has been grouped along the given `axis`. IDs on that axis are replaced by values in the `metadata` column.
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75
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76 |
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77
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78 Description:
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79 ------------
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80 Group samples or features in a feature table using metadata to define the mapping of IDs to a group.
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81
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82
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83 |
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84
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85 </help>
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86 <citations>
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87 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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88 </citations>
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89 </tool>