Mercurial > repos > q2d2 > qiime2__feature_table__merge

comparison qiime2__feature_table__merge.xml @ 0:6a753c135e34 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:00:50 +0000
parents
children bbef44c4221b
comparison
equal deleted inserted replaced
-1:000000000000 0:6a753c135e34
1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
12 -->
13 <tool name="qiime2 feature-table merge" id="qiime2__feature_table__merge" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Combine multiple tables</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version feature_table</version_command>
19 <command detect_errors="aggressive">q2galaxy run feature_table merge '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]¹ | FeatureTable[RelativeFrequency]²]" help="[required] The collection of feature tables to be merged." multiple="true">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
28 </options>
29 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <param name="overlap_method" type="select" label="overlap_method: Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ | Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample')²" help="[default: 'error_on_overlapping_sample'] Method for handling overlapping ids.">
32 <option value="average">average (Str)</option>
33 <option value="error_on_overlapping_feature">error_on_overlapping_feature (Str)</option>
34 <option value="error_on_overlapping_sample" selected="true">error_on_overlapping_sample (Str)</option>
35 <option value="sum">sum (Str)</option>
36 </param>
37 </section>
38 </inputs>
39 <outputs>
40 <data name="merged_table" format="qza" label="${tool.name} on ${on_string}: merged_table.qza" from_work_dir="merged_table.qza"/>
41 </outputs>
42 <tests>
43 <test>
44 <param name="tables" value="merge.test0.feature-table1.qza,merge.test0.feature-table2.qza" ftype="qza"/>
45 <output name="merged_table" ftype="qza"/>
46 </test>
47 <test>
48 <param name="tables" value="merge.test1.feature-table1.qza,merge.test1.feature-table2.qza,merge.test1.feature-table3.qza" ftype="qza"/>
49 <conditional name="__q2galaxy__GUI__conditional__overlap_method__">
50 <param name="__q2galaxy__GUI__select__" value="sum"/>
51 <param name="overlap_method" value="sum"/>
52 </conditional>
53 <output name="merged_table" ftype="qza"/>
54 </test>
55 </tests>
56 <help>
57 QIIME 2: feature-table merge
58 ============================
59 Combine multiple tables
60
61
62 Outputs:
63 --------
64 :merged_table.qza: The resulting merged feature table.
65
66 |
67
68 Description:
69 ------------
70 Combines feature tables using the `overlap_method` provided.
71
72 Examples:
73 ---------
74
75 basic
76 *****
77 Using the ``qiime2 feature-table merge`` tool:
78 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:
79
80 #. ``#: feature-table1.qza``
81 #. ``#: feature-table2.qza``
82
83 #. Press the ``Execute`` button.
84
85
86 three_tables
87 ************
88 Using the ``qiime2 feature-table merge`` tool:
89 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:
90
91 #. ``#: feature-table1.qza``
92 #. ``#: feature-table2.qza``
93 #. ``#: feature-table3.qza``
94
95 #. Expand the ``additional options`` section
96
97 - Set *"overlap_method"* to ``sum``
98
99 #. Press the ``Execute`` button.
100
101
102
103 |
104
105 </help>
106 <citations>
107 <citation type="doi">10.1038/s41587-019-0209-9</citation>
108 </citations>
109 </tool>