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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 19:52:16 +0000
parents 02074619b5e8
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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 merge" id="qiime2__feature_table__merge" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Combine multiple tables</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 merge '$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="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]¹ | FeatureTable[RelativeFrequency]² | FeatureTable[PresenceAbsence]³]" help="[required] The collection of feature tables to be merged." multiple="true">
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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[PresenceAbsence]"/>
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32 </options>
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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 <param name="overlap_method" type="select" label="overlap_method: Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ | Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample')² | Str % Choices('error_on_overlapping_feature', 'error_on_overlapping_sample', 'union')³" help="[default: 'error_on_overlapping_sample'] Method for handling overlapping ids.">
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36 <option value="average">average (Str)</option>
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37 <option value="error_on_overlapping_feature">error_on_overlapping_feature (Str)</option>
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38 <option value="error_on_overlapping_sample" selected="true">error_on_overlapping_sample (Str)</option>
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39 <option value="sum">sum (Str)</option>
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40 <option value="union">union (Str)</option>
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41 </param>
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42 </section>
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43 </inputs>
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44 <outputs>
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45 <data name="merged_table" format="qza" label="${tool.name} on ${on_string}: merged_table.qza" from_work_dir="merged_table.qza"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="tables" value="merge.test0.feature-table1.qza,merge.test0.feature-table2.qza" ftype="qza"/>
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50 <output name="merged_table" ftype="qza">
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51 <assert_contents>
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52 <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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53 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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54 </has_archive_member>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="tables" value="merge.test1.feature-table1.qza,merge.test1.feature-table2.qza,merge.test1.feature-table3.qza" ftype="qza"/>
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60 <conditional name="__q2galaxy__GUI__conditional__overlap_method__">
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61 <param name="__q2galaxy__GUI__select__" value="sum"/>
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62 <param name="overlap_method" value="sum"/>
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63 </conditional>
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64 <output name="merged_table" ftype="qza">
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65 <assert_contents>
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66 <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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67 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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68 </has_archive_member>
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69 </assert_contents>
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70 </output>
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71 </test>
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72 </tests>
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73 <help>
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74 QIIME 2: feature-table merge
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75 ============================
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76 Combine multiple tables
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77
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78
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79 Outputs:
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80 --------
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81 :merged_table.qza: The resulting merged feature table.
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82
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83 |
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84
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85 Description:
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86 ------------
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87 Combines feature tables using the `overlap_method` provided.
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88
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89 Examples:
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90 ---------
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91
1
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92 feature_table_merge_two_tables
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93 ******************************
0
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94 Using the ``qiime2 feature-table merge`` tool:
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95 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:
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96
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97 #. ``#: feature-table1.qza``
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98 #. ``#: feature-table2.qza``
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99
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100 #. Press the ``Execute`` button.
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101
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102
1
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103 feature_table_merge_three_tables
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104 ********************************
0
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105 Using the ``qiime2 feature-table merge`` tool:
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106 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:
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107
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108 #. ``#: feature-table1.qza``
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109 #. ``#: feature-table2.qza``
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110 #. ``#: feature-table3.qza``
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111
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112 #. Expand the ``additional options`` section
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113
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114 - Set *"overlap_method"* to ``sum``
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115
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116 #. Press the ``Execute`` button.
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118
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119
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120 |
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121
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122 </help>
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123 <citations>
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124 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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125 </citations>
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126 </tool>