view qiime2__metadata__merge.xml @ 5:1c33171f9eaf draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.10.0)
for:
    qiime2 (version: 2025.10.0)
-->
<tool name="qiime2 metadata merge" id="qiime2__metadata__merge" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Merge metadata</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.10</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>