<tool id="fastqc_site" name="Fastqc Site" version="1.0.0">
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.2">r-rmarkdown</requirement>
        <requirement type="package" version="1.8.4">r-plyr</requirement>
        <requirement type="package" version="1.1.0">r-stringr</requirement>
        <requirement type="package" version="0.5.0">r-highcharter</requirement>
        <requirement type="package" version="0.2">r-dt</requirement>
        <requirement type="package" version="1.4.2">r-reshape2</requirement>
        <requirement type="package" version="4.5.6">r-plotly</requirement>
        <requirement type="package" version="0.2.0.1">r-formattable</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
        <requirement type="package" version="0.11.5">fastqc</requirement>
    </requirements>
    <description>
        Implements FastQC analysis and display results in R Markdown website.
    </description>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"
               description="Execution halted." />
        <regex match="Error in"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
        <regex match="Fatal error"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <command>
        <![CDATA[

        Rscript '${__tool_directory__}/fastqc_site_render.R'

            ## 1. input data
            -r $reads
            -e $echo

            ## 2. output report and report site directory
		    -o $fastqc_site
		    -d $fastqc_site.files_path

		    ## 3. Rmd templates sitting in the tool directory

		        ## _site.yml and index.Rmd template files
                -s '${__tool_directory__}/_site.yml'
                -i '${__tool_directory__}/index.Rmd'

                ## other Rmd body template files
		        -p  '${__tool_directory__}/01_evaluation_overview.Rmd'
		        -a  '${__tool_directory__}/02_fastqc_original_reports.Rmd'
		        -b  '${__tool_directory__}/1_per_base_quality_scores.Rmd'
		        -c  '${__tool_directory__}/2_per_base_N_content.Rmd'
		        -f  '${__tool_directory__}/3_per_sequence_quality_scores.Rmd'
		        -g  '${__tool_directory__}/4_per_sequence_GC_content.Rmd'
		        -h  '${__tool_directory__}/5_per_base_sequence_content.Rmd'

        ]]>
    </command>
    <inputs>
        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" multiple="true" name="reads" type="data" label="Short reads data from history" />
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data format="html" name="fastqc_site" label="fastqc site" />
    </outputs>
    <citations>
        <citation type="bibtex">
            @misc{bioinformatics2014fastqc,
            title={FastQC},
            author={Bioinformatics, Babraham},
            year={2014}
            }
        </citation>
        <citation type="bibtex">
            @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">
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        </citation>
        <citation type="bibtex">
            @misc{plotly2017,
            title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
            author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
            year = {2017},
            note = {R package version 4.6.0},
            url = {https://CRAN.R-project.org/package=plotly},
            }
        </citation>
        <citation type="bibtex">
            @misc{highcharter2017,
            title = {highcharter: A Wrapper for the 'Highcharts' Library},
            author = {Joshua Kunst},
            year = {2017},
            note = {R package version 0.5.0},
            url = {https://CRAN.R-project.org/package=highcharter},
            }
        </citation>
        <citation type="bibtex">
            @misc{formattable2016,
            title = {formattable: Create 'Formattable' Data Structures},
            author = {Kun Ren and Kenton Russell},
            year = {2016},
            note = {R package version 0.2.0.1},
            url = {https://CRAN.R-project.org/package=formattable},
            }
        </citation>
    </citations>
</tool>