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comparison qiime2__feature_table__tabulate_seqs.xml @ 3:2feea4c63f4c draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:11:45 +0000
parents 6d5cd7bcc0d0
children 9fe85eec5420
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2:6d5cd7bcc0d0 3:2feea4c63f4c
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2023, QIIME 2 development team. 3 Copyright (c) 2024, QIIME 2 development team.
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: 2023.5.0) 9 q2galaxy (version: 2024.2.1)
10 for: 10 for:
11 qiime2 (version: 2023.5.1) 11 qiime2 (version: 2024.2.0)
12 --> 12 -->
13 <tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>View sequence associated with each feature</description> 14 <description>View sequence associated with each feature</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2023.5</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version feature_table</version_command> 18 <version_command>q2galaxy version feature_table</version_command>
19 <command detect_errors="exit_code">q2galaxy run feature_table tabulate_seqs '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run feature_table tabulate_seqs '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required] The feature sequences to be tabulated."> 24 <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required] The feature sequences to be tabulated.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
26 <filter type="add_value" value="FeatureData[Sequence]"/> 27 <filter type="add_value" value="FeatureData[Sequence]"/>
27 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
28 </options> 28 </options>
29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator> 29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator>
30 </param> 30 </param>
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: Collection[FeatureData[Taxonomy]]" help="[optional] The taxonomic classifications of the tabulated features." multiple="true">
33 <options options_filter_attribute="metadata.semantic_type">
34 <filter type="add_value" value="FeatureData[Taxonomy]"/>
35 </options>
36 </param>
37 <repeat name="metadata" help="[optional] Any additional metadata for the tabulated features." title="metadata: Metadata">
38 <conditional name="__q2galaxy__GUI__conditional__metadata__">
39 <param name="type" type="select" label="metadata: Metadata">
40 <option value="tsv" selected="true">Metadata from TSV</option>
41 <option value="qza">Metadata from Artifact</option>
42 </param>
43 <when value="tsv">
44 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
45 </when>
46 <when value="qza">
47 <param name="source" type="data" format="qza" label="Metadata Source"/>
48 </when>
49 </conditional>
50 </repeat>
51 <param name="merge_method" type="select" label="merge_method: Str % Choices('strict', 'union', 'intersect')" display="radio">
52 <option value="strict" selected="true">strict</option>
53 <option value="union">union</option>
54 <option value="intersect">intersect</option>
55 </param>
56 </section>
31 </inputs> 57 </inputs>
32 <outputs> 58 <outputs>
33 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> 59 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
34 </outputs> 60 </outputs>
35 <tests> 61 <tests>
36 <test> 62 <test>
37 <param name="data" value="tabulate_seqs.test0.rep-seqs.qza" ftype="qza"/> 63 <param name="data" value="tabulate_seqs.test0.rep-seqs.qza" ftype="qza"/>
64 <output name="visualization" ftype="qzv">
65 <assert_contents>
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">
67 <has_line_matching expression="type: Visualization"/>
68 </has_archive_member>
69 </assert_contents>
70 </output>
71 </test>
72 <test>
73 <param name="data" value="tabulate_seqs.test1.rep-seqs-single-taxon.qza" ftype="qza"/>
74 <param name="taxonomy" value="tabulate_seqs.test1.single-taxonomy.qza" ftype="qza"/>
75 <output name="visualization" ftype="qzv">
76 <assert_contents>
77 <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">
78 <has_line_matching expression="type: Visualization"/>
79 </has_archive_member>
80 </assert_contents>
81 </output>
82 </test>
83 <test>
84 <param name="data" value="tabulate_seqs.test2.rep-seqs-multi-taxon.qza" ftype="qza"/>
85 <param name="taxonomy" value="tabulate_seqs.test2.multi-taxonomy/GG1.qza,tabulate_seqs.test2.multi-taxonomy/GG2.qza" ftype="qza"/>
38 <output name="visualization" ftype="qzv"> 86 <output name="visualization" ftype="qzv">
39 <assert_contents> 87 <assert_contents>
40 <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"> 88 <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">
41 <has_line_matching expression="type: Visualization"/> 89 <has_line_matching expression="type: Visualization"/>
42 </has_archive_member> 90 </has_archive_member>
79 * - History Name 127 * - History Name
80 - *"Name"* to set (be sure to press ``Save``) 128 - *"Name"* to set (be sure to press ``Save``)
81 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv`` 129 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
82 - ``rep-seqs.qzv`` 130 - ``rep-seqs.qzv``
83 131
132 feature_table_tabulate_seqs_single_taxon
133 ****************************************
134 Using the ``qiime2 feature-table tabulate-seqs`` tool:
135 #. Set *"data"* to ``#: rep-seqs-single-taxon.qza``
136 #. Expand the ``additional options`` section
137
138 - Set *"taxonomy"* to ``#: ['single-taxonomy.qza']``
139
140 #. Press the ``Execute`` button.
141
142 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
143 (Renaming is optional, but it will make any subsequent steps easier to complete.)
144
145 .. list-table::
146 :align: left
147 :header-rows: 1
148
149 * - History Name
150 - *"Name"* to set (be sure to press ``Save``)
151 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
152 - ``rep-seqs.qzv``
153
154 feature_table_tabulate_seqs_multi_taxon
155 ***************************************
156 Using the ``qiime2 feature-table tabulate-seqs`` tool:
157 #. Set *"data"* to ``#: rep-seqs-multi-taxon.qza``
158 #. Expand the ``additional options`` section
159
160 - Set *"taxonomy"* to ``#: multi-taxonomy/``
161
162 #. Press the ``Execute`` button.
163
164 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
165 (Renaming is optional, but it will make any subsequent steps easier to complete.)
166
167 .. list-table::
168 :align: left
169 :header-rows: 1
170
171 * - History Name
172 - *"Name"* to set (be sure to press ``Save``)
173 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
174 - ``rep-seqs.qzv``
175
84 176
85 | 177 |
86 178
87 </help> 179 </help>
88 <citations> 180 <citations>