view qiime2__feature_table__group.xml @ 0:834bb534ba6d draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2022, 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: 2022.8.1)
for:
    qiime2 (version: 2022.8.1)
-->
<tool name="qiime2 feature-table group" id="qiime2__feature_table__group" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Group samples or features by a metadata column</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version feature_table</version_command>
    <command detect_errors="aggressive">q2galaxy run feature_table group '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The table to group samples or features on.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio">
            <option value="__q2galaxy__::literal::None">Selection required</option>
            <option value="feature">feature</option>
            <option value="sample">sample</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
        </param>
        <conditional name="metadata">
            <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required]  A column defining the groups. Each unique value will become a new ID for the table on the given `axis`.">
                <option value="tsv" selected="true">Metadata from TSV</option>
                <option value="qza">Metadata from Artifact</option>
            </param>
            <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>
        <param name="mode" type="select" label="mode: Str % Choices('mean-ceiling', 'median-ceiling', 'sum')" display="radio">
            <option value="__q2galaxy__::literal::None">Selection required</option>
            <option value="mean-ceiling">mean-ceiling</option>
            <option value="median-ceiling">median-ceiling</option>
            <option value="sum">sum</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
        </param>
    </inputs>
    <outputs>
        <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: feature-table group
============================
Group samples or features by a metadata column


Outputs:
--------
:grouped_table.qza: A table that has been grouped along the given `axis`. IDs on that axis are replaced by values in the `metadata` column.

|  

Description:
------------
Group samples or features in a feature table using metadata to define the mapping of IDs to a group.


|  

</help>
    <citations>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>