<tool name="aurora_star_site" id='aurora_star_site_report' version="2.0.1">
    <description>
        ultrafast universal RNA-seq aligner
    </description>
    <requirements>
        <requirement type="package" version="2.5">pandoc</requirement>
        <requirement type="package" version="1.20.2">r-getopt</requirement>
        <requirement type="package" version="1.10">r-rmarkdown</requirement>
        <requirement type="package" version="2.5.4a">star</requirement>
        <requirement type="package" version="1.7">samtools</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

            -A '$genomeFastaFiles'
            -B '$sjdbGTFfile'
            -C '$sjdbOverhang'
            -F '$first_reads'
            -R '$second_reads'
            -S '$sorted_bam'

    ]]></command>
    <inputs>
        <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger"/>
        <param type="data" name="second_reads" label="Second reads" optional="True" format="fastq,fastqsanger"/>
        <param type="data" name="genomeFastaFiles" argument="--genomeFastaFiles" label="Genome fasta files"
               optional="False" format="fasta,fa"/>
        <param type="data" name="sjdbGTFfile" argument="--sjdbGTFfile" label="Annotated transcripts"
               help="the file with annotated transcripts in the standard GTF format. STAR will extract splice junctions from this file and use them to greatly improve accuracy of the mapping. While this is optional, and STAR can be run without annotations, using annotations is highly recommended whenever they are available."
               optional="True" format="gtf"/>
        <param type="integer" name="sjdbOverhang" argument="--sjdbOverhang" label="sjdbOverhang"
               help="the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. Ideally, this length should be equal to the ReadLength-1, where ReadLength is the length of the reads. For instance, for Illumina 2x100b paired-end reads, the ideal value is 100-1=99. In case of reads of varying length, the ideal value is max(ReadLength)-1. In most cases, a generic value of 100 will work as well as the ideal value."
               optional="False" value="100" min="1"/>
    </inputs>
    <outputs>
        <data name="report" format="html" label="${tool.name} report on ${on_string}"/>
        <data name="sorted_bam" format="bam" label="${tool.name} sorted bam on ${on_string}"/>
    </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>
        <citation type="bibtex"><![CDATA[
            @article{dobin2013star,
            title={STAR: ultrafast universal RNA-seq aligner},
            author={Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R},
            journal={Bioinformatics},
            volume={29},
            number={1},
            pages={15--21},
            year={2013},
            publisher={Oxford University Press}
            }
        ]]></citation>
    </citations>
</tool>