Mercurial > repos > q2d2 > qiime2__feature_table__summarize

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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 19:51:09 +0000
parents 517cc51856dd
children
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bfe9f18ac641 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'?>
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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:
5
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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 summarize" id="qiime2__feature_table__summarize" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Summarize table</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 summarize '$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[Frequency | PresenceAbsence]" help="[required] The feature table to be summarized.">
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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[PresenceAbsence]"/>
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31 </options>
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32 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]']</validator>
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33 </param>
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34 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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35 <repeat name="sample_metadata" help="[optional] The sample metadata." title="sample_metadata: Metadata">
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36 <conditional name="__q2galaxy__GUI__conditional__sample_metadata__">
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37 <param name="type" type="select" label="sample_metadata: Metadata">
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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 </when>
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44 <when value="qza">
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45 <param name="source" type="data" format="qza" label="Metadata Source"/>
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46 </when>
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47 </conditional>
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48 </repeat>
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49 </section>
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50 </inputs>
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51 <outputs>
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52 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="table" value="summarize.test0.feature-table.qza" ftype="qza"/>
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57 <output name="visualization" ftype="qzv">
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58 <assert_contents>
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59 <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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60 <has_line_matching expression="type: Visualization"/>
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61 </has_archive_member>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66 <help>
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67 QIIME 2: feature-table summarize
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68 ================================
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69 Summarize table
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72 Outputs:
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73 --------
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74 :visualization.qzv: &lt;no description&gt;
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76 |
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78 Description:
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79 ------------
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80 Generate visual and tabular summaries of a feature table.
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81
1
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82 Examples:
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83 ---------
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84
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85 feature_table_summarize
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86 ***********************
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87 Using the ``qiime2 feature-table summarize`` tool:
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88 #. Set *"table"* to ``#: feature-table.qza``
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89 #. Press the ``Execute`` button.
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90
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91 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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92 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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93
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94 .. list-table::
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95 :align: left
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96 :header-rows: 1
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97
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98 * - History Name
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99 - *"Name"* to set (be sure to press ``Save``)
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100 * - ``#: qiime2 feature-table summarize [...] : visualization.qzv``
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101 - ``table.qzv``
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102
0
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103
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104 |
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105
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106 </help>
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107 <citations>
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108 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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109 </citations>
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110 </tool>