Mercurial > repos > q2d2 > qiime2__rescript__edit_taxonomy

comparison qiime2__rescript__edit_taxonomy.xml @ 0:f4ea39668a42 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__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:23:23 +0000
parents
children 11ba954f155c
comparison
equal deleted inserted replaced
-1:000000000000 0:f4ea39668a42
1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2024, 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: 2024.2.1)
10 for:
11 qiime2 (version: 2024.2.0)
12 -->
13 <tool name="qiime2 rescript edit-taxonomy" id="qiime2__rescript__edit_taxonomy" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Edit taxonomy strings with find and replace terms.</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements>
18 <version_command>q2galaxy version rescript</version_command>
19 <command detect_errors="exit_code">q2galaxy run rescript edit_taxonomy '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles>
23 <inputs>
24 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomy strings data to be edited.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[Taxonomy]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
29 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <conditional name="replacement_map">
32 <param name="type" type="select" label="replacement_map: MetadataColumn[Categorical]" help="[optional] A tab-delimitad metadata file in which the strings in the 'id' column are replaced by the 'replacement-strings' in the second column. All strings in the 'id' column must be unique!">
33 <option value="none" selected="true">None (default)</option>
34 <option value="tsv">Metadata from TSV</option>
35 <option value="qza">Metadata from Artifact</option>
36 </param>
37 <when value="none"/>
38 <when value="tsv">
39 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
40 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
41 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
42 </param>
43 </when>
44 <when value="qza">
45 <param name="source" type="data" format="qza" label="Metadata Source"/>
46 <param name="column" type="text" label="Column Name">
47 <validator type="empty_field"/>
48 </param>
49 </when>
50 </conditional>
51 <repeat name="search_strings" help="[optional] Only used in conjuntion with 'replacement-strings'. Each string in this list is searched for and replaced with a string in the list of 'replace-ment-strings'. That is the first string in 'search-strings' is replaced with the first string in 'replacement-strings', and so on. The number of 'search-strings' must be equal to the number of replacement strings." title="search_strings: List[Str]">
52 <param name="element" type="text" label="element: Str" help="[required]">
53 <sanitizer>
54 <valid initial="string.printable"/>
55 </sanitizer>
56 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
57 </param>
58 </repeat>
59 <repeat name="replacement_strings" help="[optional] Only used in conjuntion with 'search-strings'. This must contain the same number of replacement strings as search strings. See 'search-strings' parameter text for more details." title="replacement_strings: List[Str]">
60 <param name="element" type="text" label="element: Str" help="[required]">
61 <sanitizer>
62 <valid initial="string.printable"/>
63 </sanitizer>
64 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
65 </param>
66 </repeat>
67 <param name="use_regex" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="use_regex: Bool" help="[default: No] Toggle regular expressions. By default, only litereal substring matching is performed."/>
68 </section>
69 </inputs>
70 <outputs>
71 <data name="edited_taxonomy" format="qza" label="${tool.name} on ${on_string}: edited_taxonomy.qza" from_work_dir="edited_taxonomy.qza"/>
72 </outputs>
73 <tests/>
74 <help>
75 QIIME 2: rescript edit-taxonomy
76 ===============================
77 Edit taxonomy strings with find and replace terms.
78
79
80 Outputs:
81 --------
82 :edited_taxonomy.qza: Taxonomy in which the original strings are replaced by user-supplied strings.
83
84 |
85
86 Description:
87 ------------
88 A method that allows the user to edit taxonomy strings. This is often used to fix inconsistent and/or inccorect taxonomic annotations. The user can either provide two separate lists of strings, i.e. 'search-strings', and 'replacement-strings', on the command line, and/or a single tab-delimited replacement map file containing a list of these strings. In both cases the number of search strings must match the number of replacement strings. That is the first string in 'search-strings' is replaced with the first string in 'replacement-strings', and so on. In the case that both search / replacement strings, and a replacement map file are provided, they will be merged.
89
90
91 |
92
93 </help>
94 <citations>
95 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
96 <citation type="doi">10.1038/s41587-019-0209-9</citation>
97 </citations>
98 </tool>