<tool id="metabolights_downloader" name="Download MetaboLights Study" version="0.1.0">
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
wget ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/i_*.txt ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/s_*.txt ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/a_*.txt ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/m_*.t*
]]></command>
        <inputs>
                <param name="study_id" type="text" label="Public Study Identifier at MetaboLights" help="This should be obtained from the MetaboLights website. For public studies, Ex. MTBLS253">
                        <validator type="empty_field" />
                </param>
                <param type="select" name="download_rawfiles" label="Download raw files" help="Downloading raw files may take a while, as the raw files can be big in size">
                        <option value="true">YES</option>
                        <option value="false" selected="true">FALSE</option>
                </param>
        </inputs>
    <outputs>
        <collection type="list" label="Assay File(s)" name="a_files">
                <discover_datasets pattern="(?P<designation>a_.+)\.txt" format="tabular"/>
          </collection>
        <collection type="list" label="Sample File(s)" name="s_files">
                <discover_datasets pattern="(?P<designation>s_.+)\.txt" format="tabular"/>
        </collection>
        <collection type="list" label="Metabolite Annotation File(s)" name="maf_files">
                <discover_datasets pattern="(?P<designation>m_.+)\.tsv" format="tabular"/>
        </collection>
        <data name="i_file" format="tabular" label="Investigation File" from_work_dir="i_Investigation.txt" visible="true"/>
    </outputs>
    <help><![CDATA[
**Overview**
 A program to download MetaboLights studies metadata.
    ]]></help>
    <citations>
        <citation type="doi">10.1002/0471250953.bi1413s53</citation>
    </citations>
</tool>