annotate qiime2__feature_table__merge.xml @ 3:6bad55f4a310 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

<?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 feature-table merge" id="qiime2__feature_table__merge" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Combine multiple tables</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version feature_table</version_command>
    <command detect_errors="exit_code">q2galaxy run feature_table merge '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]¹ | FeatureTable[RelativeFrequency]² | FeatureTable[PresenceAbsence]³]" help="[required]  The collection of feature tables to be merged." multiple="true">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
            </options>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="overlap_method" type="select" label="overlap_method: Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ | Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample')² | Str % Choices('error_on_overlapping_feature', 'error_on_overlapping_sample', 'union')³" help="[default: 'error_on_overlapping_sample']  Method for handling overlapping ids.">
                <option value="average">average (Str)</option>
                <option value="error_on_overlapping_feature">error_on_overlapping_feature (Str)</option>
                <option value="error_on_overlapping_sample" selected="true">error_on_overlapping_sample (Str)</option>
                <option value="sum">sum (Str)</option>
                <option value="union">union (Str)</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="merged_table" format="qza" label="${tool.name} on ${on_string}: merged_table.qza" from_work_dir="merged_table.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="tables" value="merge.test0.feature-table1.qza,merge.test0.feature-table2.qza" ftype="qza"/>
            <output name="merged_table" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="tables" value="merge.test1.feature-table1.qza,merge.test1.feature-table2.qza,merge.test1.feature-table3.qza" ftype="qza"/>
            <conditional name="__q2galaxy__GUI__conditional__overlap_method__">
                <param name="__q2galaxy__GUI__select__" value="sum"/>
                <param name="overlap_method" value="sum"/>
            </conditional>
            <output name="merged_table" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: feature-table merge
============================
Combine multiple tables


Outputs:
--------
:merged_table.qza: The resulting merged feature table.

|  

Description:
------------
Combines feature tables using the `overlap_method` provided.

Examples:
---------

feature_table_merge_two_tables
******************************
Using the ``qiime2 feature-table merge`` tool:
 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: feature-table1.qza``
    #. ``#: feature-table2.qza``

 #. Press the ``Execute`` button.


feature_table_merge_three_tables
********************************
Using the ``qiime2 feature-table merge`` tool:
 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: feature-table1.qza``
    #. ``#: feature-table2.qza``
    #. ``#: feature-table3.qza``

 #. Expand the ``additional options`` section

    - Set *"overlap_method"* to ``sum``

 #. Press the ``Execute`` button.



|  

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