view qiime2__rescript__edit_taxonomy.xml @ 2:f69e24d4703b draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7

<?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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<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">
    <description>Edit taxonomy strings with find and replace terms.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</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) &gt; 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) &gt; 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>