annotate qiime2__metadata__merge.xml @ 1:9ec6c7da58d2 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata commit c7e80dcda727ce63b42aa8a946e9330310929797

<?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: 2024.5.0)
for:
    qiime2 (version: 2024.5.0)
-->
<tool name="qiime2 metadata merge" id="qiime2__metadata__merge" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
    <description>Merge metadata</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
    </requirements>
    <version_command>q2galaxy version metadata</version_command>
    <command detect_errors="exit_code">q2galaxy run metadata merge '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <repeat name="metadata1" min="1" help="[required]  First metadata file to merge." title="metadata1: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__metadata1__">
                <param name="type" type="select" label="metadata1: Metadata">
                    <option value="tsv" selected="true">Metadata from TSV</option>
                    <option value="qza">Metadata from Artifact</option>
                </param>
                <when value="tsv">
                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                </when>
                <when value="qza">
                    <param name="source" type="data" format="qza" label="Metadata Source"/>
                </when>
            </conditional>
        </repeat>
        <repeat name="metadata2" min="1" help="[required]  Second metadata file to merge." title="metadata2: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__metadata2__">
                <param name="type" type="select" label="metadata2: Metadata">
                    <option value="tsv" selected="true">Metadata from TSV</option>
                    <option value="qza">Metadata from Artifact</option>
                </param>
                <when value="tsv">
                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                </when>
                <when value="qza">
                    <param name="source" type="data" format="qza" label="Metadata Source"/>
                </when>
            </conditional>
        </repeat>
    </inputs>
    <outputs>
        <data name="merged_metadata" format="qza" label="${tool.name} on ${on_string}: merged_metadata.qza" from_work_dir="merged_metadata.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: metadata merge
=======================
Merge metadata


Outputs:
--------
:merged_metadata.qza: The merged metadata.

|  

Description:
------------
Merge metadata that contains overlapping ids or overlapping columns, but not both overlapping ids and overlapping columns. The result will be the union (i.e., outer join) of the ids and columns from the two metadata inputs.

Attemping to merge metadata with both overlapping ids and overlapping columns will currently fail because we don't resolve conflicting column values for a sample. Merging metadata with neither overlapping ids or overlapping columns is possible with this action.

To merge more than two metadata objects, run this command multiple times, iteratively using the output of the previous run as one of the metadata inputs.

The output, an ImmutableMetadata artifact, can be used anywhere that a metadata file can be used, or can be exported to a metadata tsv file in the typical format.


|  

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