<tool name="aurora_fastqc_site" id='aurora_fastqc_site' version="2.2.1">
    <description>
        Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads
        files.
    </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="1.8.4">r-plyr</requirement>
        <requirement type="package" version="1.3.1">r-stringr</requirement>
        <requirement type="package" version="0.4">r-dt</requirement>
        <requirement type="package" version="1.4.3">r-reshape2</requirement>
        <requirement type="package" version="4.8.0">r-plotly</requirement>
        <requirement type="package" version="0.3.6">r-htmltools</requirement>
        <requirement type="package" version="0.11.5">fastqc</requirement>
        <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
        <requirement type="package" version="1.2.3">xorg-libsm</requirement>
        <requirement type="package" version="6.0">unzip</requirement>
    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <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' &&

        ############ copy jstree directory cp -r ${__tool_directory__}/vakata-jstree-3.3.5 ./ &&

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

        Rscript '${__tool_directory__}/rmarkdown_report_render.R'

		    -o $report
		    -d $report.files_path

		    -r $reads_1
            -n '$reads_1.name'
            -R $reads_2
            -N '$reads_2.name'
            -c $contaminants
            -l $limits

    ]]></command>
    <inputs>
        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
               label="Short reads before trimming"
               help="Short reads data from history. This could be reads before trimming."/>
        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data" label="Short reads after trimming"
               help="Short reads data from history. This could be reads after trimming."/>
        <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
               help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
               searched against the library. The file must contain sets of named adapters in the form name[tab]sequence.
               Lines prefixed with a hash will be ignored."/>
        <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
               help="Specifies a non-default file which contains a set of criteria which will be used to determine the
               warn/error limits for the various modules. This file can also be used to selectively remove some modules
               from the output all together. The format needs to mirror the default limits.txt file found in the
               Configuration folder."/>

    </inputs>
    <outputs>
        <data format="html" name="report" label="${tool.name} on ${on_string}"/>
    </outputs>
    <citations>
        <citation type="bibtex"><![CDATA[
            @online{jstree,
            author={Bozhanov, Ivan},
            year = 2018,
            url = {https://www.jstree.com/}
            }
        ]]></citation>
        <citation type="bibtex"><![CDATA[
            @misc{bioinformatics2014fastqc,
            title={FastQC},
            author={Bioinformatics, Babraham},
            year={2014}
            }
        ]]></citation>
        <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>
    </citations>
</tool>