Mercurial > repos > q2d2 > qiime2__rescript__edit_taxonomy
changeset 0:f4ea39668a42 draft
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 |
| files | qiime2__rescript__edit_taxonomy.xml test-data/.gitkeep |
| diffstat | 1 files changed, 98 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__edit_taxonomy.xml Thu Apr 25 21:23:23 2024 +0000 @@ -0,0 +1,98 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2024, QIIME 2 development team. + +Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) +--> +<!-- +This tool was automatically generated by: + q2galaxy (version: 2024.2.1) +for: + qiime2 (version: 2024.2.0) +--> +<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"> + <description>Edit taxonomy strings with find and replace terms.</description> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + </requirements> + <version_command>q2galaxy version rescript</version_command> + <command detect_errors="exit_code">q2galaxy run rescript edit_taxonomy '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomy strings data to be edited."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Taxonomy]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <conditional name="replacement_map"> + <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!"> + <option value="none" selected="true">None (default)</option> + <option value="tsv">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="none"/> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> + <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> + </param> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + <param name="column" type="text" label="Column Name"> + <validator type="empty_field"/> + </param> + </when> + </conditional> + <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]"> + <param name="element" type="text" label="element: Str" help="[required]"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + </repeat> + <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]"> + <param name="element" type="text" label="element: Str" help="[required]"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + </repeat> + <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."/> + </section> + </inputs> + <outputs> + <data name="edited_taxonomy" format="qza" label="${tool.name} on ${on_string}: edited_taxonomy.qza" from_work_dir="edited_taxonomy.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: rescript edit-taxonomy +=============================== +Edit taxonomy strings with find and replace terms. + + +Outputs: +-------- +:edited_taxonomy.qza: Taxonomy in which the original strings are replaced by user-supplied strings. + +| + +Description: +------------ +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. + + +| + +</help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1009581</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>