<tool name="Fastqc site" id='aurora_fastqc_site' version="2.1.0">
    <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="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.3">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="0.2">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="0.3.5">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="1.2.2">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[
        

        Rscript '${__tool_directory__}/fastqc_site_render.R'
            -e $echo
            -r $reads_1
            -n '$reads_1.name'
            -R $reads_2
            -N '$reads_2.name'
            -c $contaminants
            -l $limits

		    -o $report
		    -d $report.files_path
		    -s $sink_message

		    -t '${__tool_directory__}'
        
    ]]></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."/>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
               label="Display analysis code in report?"/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="fastqc site"/>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
    </outputs>
    <citations>
        <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>
        <citation type="bibtex"><![CDATA[
            @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"><![CDATA[
            @Book{ggplot22016,
            author = {Hadley Wickham},
            title = {ggplot2: Elegant Graphics for Data Analysis},
            publisher = {Springer-Verlag New York},
            year = {2009},
            isbn = {978-0-387-98140-6},
            url = {http://ggplot2.org},
            }
        ]]></citation>
    </citations>
</tool>