Mercurial > repos > q2d2 > qiime2__rescript__edit_taxonomy

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author q2d2
date Wed, 30 Oct 2024 19:55:52 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 rescript edit-taxonomy" id="qiime2__rescript__edit_taxonomy" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Edit taxonomy strings with find and replace terms.</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version rescript</version_command>
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22 <command detect_errors="exit_code">q2galaxy run rescript edit_taxonomy '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomy strings data to be edited.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
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32 </param>
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33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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34 <conditional name="replacement_map">
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35 <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!">
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36 <option value="none" selected="true">None (default)</option>
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37 <option value="tsv">Metadata from TSV</option>
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38 <option value="qza">Metadata from Artifact</option>
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39 </param>
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40 <when value="none"/>
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41 <when value="tsv">
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42 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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43 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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44 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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45 </param>
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46 </when>
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47 <when value="qza">
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48 <param name="source" type="data" format="qza" label="Metadata Source"/>
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49 <param name="column" type="text" label="Column Name">
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50 <validator type="empty_field"/>
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51 </param>
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52 </when>
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53 </conditional>
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54 <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]">
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55 <param name="element" type="text" label="element: Str" help="[required]">
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56 <sanitizer>
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57 <valid initial="string.printable"/>
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58 </sanitizer>
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59 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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60 </param>
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61 </repeat>
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62 <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]">
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63 <param name="element" type="text" label="element: Str" help="[required]">
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64 <sanitizer>
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65 <valid initial="string.printable"/>
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66 </sanitizer>
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67 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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68 </param>
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69 </repeat>
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70 <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."/>
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71 </section>
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72 </inputs>
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73 <outputs>
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74 <data name="edited_taxonomy" format="qza" label="${tool.name} on ${on_string}: edited_taxonomy.qza" from_work_dir="edited_taxonomy.qza"/>
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75 </outputs>
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76 <tests/>
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77 <help>
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78 QIIME 2: rescript edit-taxonomy
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79 ===============================
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80 Edit taxonomy strings with find and replace terms.
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81
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82
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83 Outputs:
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84 --------
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85 :edited_taxonomy.qza: Taxonomy in which the original strings are replaced by user-supplied strings.
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86
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87 |
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88
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89 Description:
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90 ------------
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91 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.
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92
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93
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94 |
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95
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96 </help>
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97 <citations>
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98 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
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99 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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100 </citations>
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101 </tool>