<tool name="aurora_skewer_site" id='aurora_skewer_site_report' version="2.0.1">
    <description>A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads.
    </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="0.2.2">skewer</requirement>
        <requirement type="package" version="4.5.6">r-plotly</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 '$first_reads'
	        -B '$second_reads'
	        -x '$adapter_first_reads'
	        -y '$adapter_second_reads'
	        -m '$trimming_mode'
	        -r '$maximum_allowed_error_rate'
	        -D '$maximum_allowed_indel_error_rate'
	        -q '$quality_trimming_3_end'
	        -Q '$mean_quality'
	        -l '$minimum_read_length'
	        -j '$advanced_options.junction_adapter'
	        -M '$advanced_options.tab_adapter'
	        -b '$advanced_options.barcode'
	        -c '$advanced_options.cut'
	        -n '$advanced_options.filter_degenerative_reads'
	        -u '$advanced_options.filter_undetermined_mate_pair_reads'
	        -f '$advanced_options.format'
	        -z '$advanced_options.compress'
	        -E '$advanced_options.qiime'
	        -F '$advanced_options.quiet'
	        -i '$advanced_options.intelligent'
	        -1 '$trimmed_r1'
	        -2 '$trimmed_r2'
	        -3 '$trimmed_s'


    ]]></command>
    <inputs>
        <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger"
               multiple="False"/>
        <param type="data" name="second_reads" label="Second reads"
               help="If it is single end reads, ignore this input field and use the &quot;first reads&quot; field only."
               optional="True" format="fastq,fastqsanger" multiple="False"/>
        <param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads."
               optional="True" format="fasta,fa" multiple="False"/>
        <param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads"
               optional="True" format="fasta,fa" multiple="False"/>
        <param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False">
            <option value="None" selected="true">--select a model--</option>
            <option value="head" selected="false">5&#x2019; end trimming (single end reads)</option>
            <option value="tail" selected="false">3&#x2019; end trimming (single end reads)</option>
            <option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option>
            <option value="pe" selected="false">paired-end trimming</option>
            <option value="mp" selected="false">mate-pair trimming</option>
            <option value="ap" selected="false">amplicon trimming</option>
        </param>
        <param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate"
               optional="False" value="0.1" min="0" max="0.5"/>
        <param type="float" name="maximum_allowed_indel_error_rate" argument="-d"
               label="Maximum allowed indel error rate"
               help="The valid range of indel error rate is [0,  maximum allowed error rate]" optional="False"
               value="0.03" min="0"/>
        <param type="integer" name="quality_trimming_3_end" argument="-q" label="3&#x2019; end quality trimming"
               optional="False" value="0"/>
        <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality"
               optional="False" value="0"/>
        <param type="integer" name="minimum_read_length" argument="-l"
               label="Minimum read length allowed after trimming" optional="False" value="18"/>
        <section name="advanced_options" title="Advanced options" expanded="False">
            <param type="data" name="junction_adapter" argument="-j"
                   label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa"
                   multiple="False"/>
            <param type="text" name="tab_adapter" argument="-M"
                   label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/>
            <param type="boolean" name="barcode" argument="-b"
                   label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False"
                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
            <param type="text" name="cut" argument="-c"
                   label="To hard clip off the 5&#x2019; leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode"
                   optional="False" value="0, 0"/>
            <param type="boolean" name="filter_degenerative_reads" argument="-n"
                   label="Whether to filter out highly degenerative reads" optional="False" checked="False"
                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
            <param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u"
                   label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False"
                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
            <param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False"
                   multiple="False">
                <option value="sanger" selected="false">sanger</option>
                <option value="solexa" selected="false">solexa</option>
                <option value="auto" selected="true">auto</option>
            </param>
            <param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format"
                   optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
            <param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME"
                   optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
            <param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False"
                   truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
            <param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads"
                   optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
        </section>
    </inputs>
    <outputs>
        <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/>
        <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/>
        <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}"
              hidden="false"/>
        <data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}"
              hidden="false"/>
    </outputs>
    <help>
        <![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help>
    <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>