<macros>
    <token name="@TOOL_VERSION@">3.0.1</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">fastq-dl</requirement>
        </requirements>
    </xml>
    <token name="@FASTQ_DL_FOR_LOOP@"><![CDATA[
        for accessionid in "\${accessionsarr[@]}"; do
            fastq-dl --accession "\$accessionid"
            --provider ena
            --only-provider
            $only_download_metadata
            $group_by_experiment
            $group_by_sample;
            exit_code=\$? ;
            if [ \$exit_code -ne 0 ]; then
                echo "fastq-dl failed for accession: \${accessionid}" >&2 ;
                exit \$exit_code ;
                break ;
            else
            mv fastq-run-info.tsv logs/"\$accessionid"-fastq-run-info.tsv > /dev/null 2>&1 || true;
            fi ;
        done
    ]]></token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                <![CDATA[
			        @software{petit2024fastq-dl,
                        author       = {Robert A. Petit III and Micheal B. Hall and Gerry Tonkin-Hill and Jie Zhu and Timothy D. Read},
                        title        = {{fastq-dl}: efficiently download FASTQ files from SRA or ENA repositories},
                        version      = {2.0.2},
                        year         = {2024},
                        url          = {https://github.com/rpetit3/fastq-dl},
                        note         = {Accessed: 2024-10-31}
                    }
			        ]]>
        </citation>
        </citations>
    </xml>
    <xml name="creators">
        <creator>
            <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" identifier="https://orcid.org/0009-0000-2501-8053" />
        </creator>
    </xml>
</macros>