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comparison qiime2__taxa__barplot.xml @ 2:124673b2e9e7 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:52:38 +0000
parents 5750bac5b744
children 0c992800a5cc
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1:5750bac5b744 2:124673b2e9e7
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2022.11.1) 9 q2galaxy (version: 2023.5.0)
10 for: 10 for:
11 qiime2 (version: 2022.11.1) 11 qiime2 (version: 2023.5.1)
12 --> 12 -->
13 <tool name="qiime2 taxa barplot" id="qiime2__taxa__barplot" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 taxa barplot" id="qiime2__taxa__barplot" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
14 <description>Visualize taxonomy with an interactive bar plot</description> 14 <description>Visualize taxonomy with an interactive bar plot</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.11</container> 16 <container type="docker">quay.io/qiime2/core:2023.5</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version taxa</version_command> 18 <version_command>q2galaxy version taxa</version_command>
19 <command detect_errors="exit_code">q2galaxy run taxa barplot '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run taxa barplot '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="paths"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table to visualize at various taxonomic levels."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | PresenceAbsence]" help="[required] Feature table to visualize at various taxonomic levels.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
26 <filter type="add_value" value="FeatureTable[Frequency]"/> 27 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 </options> 28 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> 29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]']</validator>
29 </param>
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.">
31 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="FeatureData[Taxonomy]"/>
33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
35 </param> 30 </param>
36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 31 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
32 <param name="taxonomy" type="data" format="qza" optional="true" label="taxonomy: FeatureData[Taxonomy]" help="[optional] 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. If no taxonomy is provided, the feature IDs will be used as labels.">
33 <options options_filter_attribute="metadata.semantic_type">
34 <filter type="add_value" value="FeatureData[Taxonomy]"/>
35 </options>
36 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
37 </param>
37 <repeat name="metadata" help="[optional] The sample metadata." title="metadata: Metadata"> 38 <repeat name="metadata" help="[optional] The sample metadata." title="metadata: Metadata">
38 <conditional name="__q2galaxy__GUI__conditional__metadata__"> 39 <conditional name="__q2galaxy__GUI__conditional__metadata__">
39 <param name="type" type="select" label="metadata: Metadata"> 40 <param name="type" type="select" label="metadata: Metadata">
40 <option value="tsv" selected="true">Metadata from TSV</option> 41 <option value="tsv" selected="true">Metadata from TSV</option>
41 <option value="qza">Metadata from Artifact</option> 42 <option value="qza">Metadata from Artifact</option>
46 <when value="qza"> 47 <when value="qza">
47 <param name="source" type="data" format="qza" label="Metadata Source"/> 48 <param name="source" type="data" format="qza" label="Metadata Source"/>
48 </when> 49 </when>
49 </conditional> 50 </conditional>
50 </repeat> 51 </repeat>
52 <conditional name="__q2galaxy__GUI__conditional__level_delimiter__" label="level_delimiter: Str">
53 <param name="__q2galaxy__GUI__select__" type="select" label="level_delimiter: Str" help="[optional] Attempt to parse hierarchical taxonomic information from feature IDs by separating levels with this character. This parameter is ignored if a taxonomy is provided as input.">
54 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
55 <option value="__q2galaxy__::control::provide">Provide a value</option>
56 </param>
57 <when value="__q2galaxy__::control::default">
58 <param name="level_delimiter" type="hidden" value="__q2galaxy__::literal::None"/>
59 </when>
60 <when value="__q2galaxy__::control::provide">
61 <param name="level_delimiter" type="text">
62 <sanitizer>
63 <valid initial="string.printable"/>
64 </sanitizer>
65 </param>
66 </when>
67 </conditional>
51 </section> 68 </section>
52 </inputs> 69 </inputs>
53 <outputs> 70 <outputs>
54 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> 71 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
55 </outputs> 72 </outputs>
93 110
94 barplot 111 barplot
95 ******* 112 *******
96 Using the ``qiime2 taxa barplot`` tool: 113 Using the ``qiime2 taxa barplot`` tool:
97 #. Set *"table"* to ``#: table.qza`` 114 #. Set *"table"* to ``#: table.qza``
98 #. Set *"taxonomy"* to ``#: taxonomy.qza``
99 #. Expand the ``additional options`` section 115 #. Expand the ``additional options`` section
100 116
101 - For *"metadata"*: 117 #. Set *"taxonomy"* to ``#: taxonomy.qza``
118 #. For *"metadata"*:
102 119
103 - Press the ``+ Insert metadata`` button to set up the next steps. 120 - Press the ``+ Insert metadata`` button to set up the next steps.
104 121
105 #. Leave as ``Metadata from TSV`` 122 #. Leave as ``Metadata from TSV``
106 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` 123 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
107 124
108 125
109 126
110 #. Press the ``Execute`` button. 127 #. Press the ``Execute`` button.
111 128