view original_metadata.xml @ 1:b613e5dd5e83 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit commit df500c27a6ef0ea25e0361feada7df8dedee98f1

<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>