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<tool name="aurora_bdss" id='aurora_bdss_report' version="1.0.0">
    <description>
        some description
    </description>
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
        <requirement type="package" version="0.6.2">parallel-fastq-dump</requirement>
    </requirements>
    <command><![CDATA[

        ######### each aurora tool generates a html file and have an files path directory associated with it.
        mkdir -p $report.files_path &&

        ######### three important paths:
        #########   1. path to tool installation directory
        #########   2. path to report html
        #########   3. path to files_path directory associated with the report output.
        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
        export REPORT='$report' &&
        export REPORT_FILES_PATH='$report.files_path' &&

        ############ create a hidden file to store r markdown rendering log
        touch $report.files_path/.r_rendering.log.txt &&

        ############ finally run the render.R script
        Rscript '${__tool_directory__}/rmarkdown_report_render.R'
        
            -o $report
            -d $report.files_path

            -s '$sra_ids_se'
            -p '$sra_ids_pe'
            -f $format


    ]]></command>
    <inputs>
        <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA"
               help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885"/>
        <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA"
               help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1748507"/>
        <param type="select" name="format" label="Output format">
            <option value="fastq" selected="true">fastq</option>
            <option value="fasta">fasta</option>
        </param>
    </inputs>
    <outputs>
        <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
        <!--list dataset collection for single end SRA data-->
        <collection type="list" name="list_collection" label="BDSS download data (single end reads)">
            <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory"/>
        </collection>
        <!--list:paired dataset collection for paired end SRA data-->
        <collection type="list:paired" name="list:paired_collection" label="BDSS download data (paired end reads)">
            <discover_datasets
                    pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"
                    directory="pe_read_files_directory"/>
        </collection>
    </outputs>
    <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation>
        <citation type="bibtex"><![CDATA[
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation>
        <citation type="bibtex"><![CDATA[
            @online{jstree,
            author={Bozhanov, Ivan},
            year = 2018,
            url = {https://www.jstree.com/}
            }
        ]]></citation>
    </citations>
</tool>