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comparison qiime2__taxa__collapse.xml @ 1:96d3a6a511bc draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 23:01:09 +0000
parents 3e34b8065c52
children 16e425d54e64
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0:3e34b8065c52 1:96d3a6a511bc
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2022, QIIME 2 development team. 3 Copyright (c) 2023, 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: 2022.8.1) 9 q2galaxy (version: 2022.11.1)
10 for: 10 for:
11 qiime2 (version: 2022.8.1) 11 qiime2 (version: 2022.11.1)
12 --> 12 -->
13 <tool name="qiime2 taxa collapse" id="qiime2__taxa__collapse" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 taxa collapse" id="qiime2__taxa__collapse" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Collapse features by their taxonomy at the specified level</description> 14 <description>Collapse features by their taxonomy at the specified level</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container> 16 <container type="docker">quay.io/qiime2/core:2022.11</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="aggressive">q2galaxy run taxa collapse '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run taxa collapse '$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 be collapsed."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table to be collapsed.">
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."/> 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."/>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data name="collapsed_table" format="qza" label="${tool.name} on ${on_string}: collapsed_table.qza" from_work_dir="collapsed_table.qza"/> 39 <data name="collapsed_table" format="qza" label="${tool.name} on ${on_string}: collapsed_table.qza" from_work_dir="collapsed_table.qza"/>
40 </outputs> 40 </outputs>
41 <tests/> 41 <tests>
42 <test>
43 <param name="table" value="collapse.test0.table.qza" ftype="qza"/>
44 <param name="taxonomy" value="collapse.test0.taxonomy.qza" ftype="qza"/>
45 <param name="level" value="6"/>
46 <output name="collapsed_table" ftype="qza">
47 <assert_contents>
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">
49 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
50 </has_archive_member>
51 </assert_contents>
52 </output>
53 </test>
54 </tests>
42 <help> 55 <help>
43 QIIME 2: taxa collapse 56 QIIME 2: taxa collapse
44 ====================== 57 ======================
45 Collapse features by their taxonomy at the specified level 58 Collapse features by their taxonomy at the specified level
46 59
53 66
54 Description: 67 Description:
55 ------------ 68 ------------
56 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. 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.
57 70
71 Examples:
72 ---------
73
74 collapse
75 ********
76 Using the ``qiime2 taxa collapse`` tool:
77 #. Set *"table"* to ``#: table.qza``
78 #. Set *"taxonomy"* to ``#: taxonomy.qza``
79 #. Set *"level"* to ``6``
80 #. Press the ``Execute`` button.
81
82 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
83 (Renaming is optional, but it will make any subsequent steps easier to complete.)
84
85 .. list-table::
86 :align: left
87 :header-rows: 1
88
89 * - History Name
90 - *"Name"* to set (be sure to press ``Save``)
91 * - ``#: qiime2 taxa collapse [...] : collapsed_table.qza``
92 - ``collapsed-table-l6.qza``
93
58 94
59 | 95 |
60 96
61 </help> 97 </help>
62 <citations> 98 <citations>