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author q2d2
date Mon, 03 Jun 2024 23:30:54 +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:
1
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9 q2galaxy (version: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 rescript edit-taxonomy" id="qiime2__rescript__edit_taxonomy" version="2024.5.0+q2galaxy.2024.5.0" 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 <requirements>
1
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version rescript</version_command>
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19 <command detect_errors="exit_code">q2galaxy run rescript edit_taxonomy '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomy strings data to be edited.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <conditional name="replacement_map">
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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!">
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33 <option value="none" selected="true">None (default)</option>
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34 <option value="tsv">Metadata from TSV</option>
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35 <option value="qza">Metadata from Artifact</option>
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36 </param>
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37 <when value="none"/>
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38 <when value="tsv">
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39 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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40 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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41 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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42 </param>
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43 </when>
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44 <when value="qza">
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45 <param name="source" type="data" format="qza" label="Metadata Source"/>
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46 <param name="column" type="text" label="Column Name">
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47 <validator type="empty_field"/>
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48 </param>
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49 </when>
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50 </conditional>
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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]">
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52 <param name="element" type="text" label="element: Str" help="[required]">
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53 <sanitizer>
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54 <valid initial="string.printable"/>
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55 </sanitizer>
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56 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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57 </param>
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58 </repeat>
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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]">
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60 <param name="element" type="text" label="element: Str" help="[required]">
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61 <sanitizer>
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62 <valid initial="string.printable"/>
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63 </sanitizer>
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64 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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65 </param>
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66 </repeat>
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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."/>
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68 </section>
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69 </inputs>
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70 <outputs>
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71 <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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72 </outputs>
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73 <tests/>
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74 <help>
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75 QIIME 2: rescript edit-taxonomy
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76 ===============================
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77 Edit taxonomy strings with find and replace terms.
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78
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80 Outputs:
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81 --------
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82 :edited_taxonomy.qza: Taxonomy in which the original strings are replaced by user-supplied strings.
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83
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84 |
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86 Description:
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87 ------------
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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.
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89
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91 |
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93 </help>
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94 <citations>
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95 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
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96 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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97 </citations>
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98 </tool>