Mercurial > repos > q2d2 > qiime2__taxa__collapse

annotate qiime2__taxa__collapse.xml @ 4:f17ae5fa0c60 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:32:12 +0000
parents 615a560393c2
children e8ab6eff4cf8
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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:
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9 q2galaxy (version: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 taxa collapse" id="qiime2__taxa__collapse" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Collapse features by their taxonomy at the specified level</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version taxa</version_command>
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19 <command detect_errors="exit_code">q2galaxy run taxa collapse '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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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] Feature table to be collapsed.">
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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="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.">
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31 <options options_filter_attribute="metadata.semantic_type">
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32 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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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 ['FeatureData[Taxonomy]']</validator>
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35 </param>
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36 <param name="level" type="integer" value="" label="level: Int" help="[required] The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation."/>
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37 </inputs>
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38 <outputs>
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39 <data name="collapsed_table" format="qza" label="${tool.name} on ${on_string}: collapsed_table.qza" from_work_dir="collapsed_table.qza"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="table" value="collapse.test0.table.qza" ftype="qza"/>
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44 <param name="taxonomy" value="collapse.test0.taxonomy.qza" ftype="qza"/>
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45 <param name="level" value="6"/>
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46 <output name="collapsed_table" ftype="qza">
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47 <assert_contents>
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48 <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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49 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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50 </has_archive_member>
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51 </assert_contents>
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52 </output>
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53 </test>
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54 </tests>
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55 <help>
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56 QIIME 2: taxa collapse
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57 ======================
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58 Collapse features by their taxonomy at the specified level
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59
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60
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61 Outputs:
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62 --------
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63 :collapsed_table.qza: The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels.
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64
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65 |
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66
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67 Description:
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68 ------------
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69 Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.
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70
1
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71 Examples:
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72 ---------
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73
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74 collapse
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75 ********
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76 Using the ``qiime2 taxa collapse`` tool:
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77 #. Set *"table"* to ``#: table.qza``
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78 #. Set *"taxonomy"* to ``#: taxonomy.qza``
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79 #. Set *"level"* to ``6``
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80 #. Press the ``Execute`` button.
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81
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82 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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83 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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84
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85 .. list-table::
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86 :align: left
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87 :header-rows: 1
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88
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89 * - History Name
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90 - *"Name"* to set (be sure to press ``Save``)
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91 * - ``#: qiime2 taxa collapse [...] : collapsed_table.qza``
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92 - ``collapsed-table-l6.qza``
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93
0
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94
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95 |
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96
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97 </help>
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98 <citations>
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99 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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100 </citations>
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101 </tool>