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author q2d2
date Wed, 30 Oct 2024 19:46:54 +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) 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: 2024.10.0)
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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 diversity-lib observed-features" id="qiime2__diversity_lib__observed_features" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Observed Features</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 diversity_lib</version_command>
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22 <command detect_errors="exit_code">q2galaxy run diversity_lib observed_features '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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31 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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32 </options>
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33 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="table" value="observed_features.test0.feature-table.qza" ftype="qza"/>
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42 <output name="vector" ftype="qza">
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43 <assert_contents>
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44 <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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45 <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
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46 </has_archive_member>
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47 <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}\/data\/alpha-diversity.tsv">
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48 <has_line_matching expression="S1&#9;1"/>
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49 <has_line_matching expression="S2&#9;1"/>
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50 <has_line_matching expression="S3&#9;2"/>
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51 <has_line_matching expression="S4&#9;2"/>
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52 <has_line_matching expression="S5&#9;3"/>
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53 </has_archive_member>
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54 </assert_contents>
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55 </output>
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56 </test>
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57 </tests>
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58 <help>
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59 QIIME 2: diversity-lib observed-features
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60 ========================================
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61 Observed Features
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64 Outputs:
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65 --------
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66 :vector.qza: Vector containing per-sample counts of observed features.
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67
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68 |
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70 Description:
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71 ------------
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72 Compute the number of observed features for each sample in a feature table
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74 Examples:
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75 ---------
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76
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77 basic
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78 *****
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79 Using the ``qiime2 diversity-lib observed-features`` tool:
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80 #. Set *"table"* to ``#: feature-table.qza``
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81 #. Press the ``Execute`` button.
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82
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83 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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84 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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85
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86 .. list-table::
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87 :align: left
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88 :header-rows: 1
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89
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90 * - History Name
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91 - *"Name"* to set (be sure to press ``Save``)
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92 * - ``#: qiime2 diversity-lib observed-features [...] : vector.qza``
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93 - ``obs-feat-vector.qza``
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96 |
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97
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98 </help>
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99 <citations>
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100 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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101 </citations>
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102 </tool>