annotate original_metadata.xml @ 0:2eef3b6f1c84 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit commit d5891ffcc42b812f9e072b4c58abc5077e947db0

<tool id="mg_toolkit_original_metadata" name="Metagenomics toolkit Original Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Download original metadata for a study</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators" />
    <expand macro="biotools" />
    <expand macro="requirements" />
    <command><![CDATA[
        mkdir output_metadata &&
        mg-toolkit original_metadata -a ${accessions} &&
        mv *.csv output_metadata
    ]]></command>
    
    <inputs>
        <param name="accessions" type="text" label="Accessions" help="Study/project accessions (e.g., ERP001736 SRP000319)" optional="false">
            <validator type="regex" message="Accessions separated with white spaces">^([A-Za-z]{3,4}\d+)(\s[A-Za-z]{3,4}\d+)*$</validator>
        </param>
    </inputs>    
    <outputs>
        <collection name="output_collection" type="list" label="Original metadata">
            <discover_datasets pattern="(?P&lt;designation&gt;.+).csv" directory="output_metadata" format="csv"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="accessions" value="ERP001736 SRP000319" />
            <output_collection name="output_collection" type="list">
                <element name="ERP001736">
                    <assert_contents>
                        <has_n_lines n="250" />
                        <has_size size="185577" />
                    </assert_contents>
                </element>
                <element name="SRP000319">
                    <assert_contents>
                        <has_n_lines n="30" />
                        <has_size size="2855" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="accessions" value="ERP001736" />
            <output_collection name="output_collection" type="list">
                <element name="ERP001736">
                    <assert_contents>
                        <has_n_lines n="250" />                
                        <has_size size="185577" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help>
<![CDATA[ 
The mg-toolkit original-metadata tool is part of the EMG Toolkit provided by EBI Metagenomics.
This tool allows users to retrieve the original metadata associated with metagenomic studies and analyses.
It facilitates the extraction of detailed contextual information submitted by researchers, 
aiding in the interpretation and further analysis of metagenomic data.

License
-------
* `Apache-2.0 license <https://raw.githubusercontent.com/EBI-Metagenomics/emg-toolkit/master/LICENSE>`_

]]>
    </help>
    <expand macro="citations" />
</tool>