<tool id="wgcna_preprocessing" name="WGCNA: preprocessing" version="1.0.0">
    <requirements>
        <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="0.4.0">r-highcharter</requirement>
        <requirement type="package" version="0.2">r-dt</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
        <requirement type="package" version="1.51">r-wgcna</requirement>
    </requirements>
    <description>
        Data clearning and preprocessing.
    </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[
        ## Add tools to PATH
        export PATH=/opt/R-3.2.5/bin:\$PATH &&

        Rscript '${__tool_directory__}/wgcna_preprocessing_render.R'

            ## 1. input data
            -e $echo
            -E $expression_data


            ## 2. output report and report site directory
		    -o $wgcna_preprocessing
		    -d $wgcna_preprocessing.files_path
		    -w $preprocessing_workspace

		    ## 3. Rmd templates sitting in the tool directory

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



        ]]>
    </command>
    <inputs>
        <param type="data" name="expression_data" format="csv" optional="false" label="Gene expression data"
               help="Each row represents a gene and each column represents a sample."/>

        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data name="wgcna_preprocessing" format="html" label="WGCNA: preprocessing" />
        <data name="preprocessing_workspace" format="rdata" label="R workspace: WGCNA preprocessing" />
    </outputs>
    <citations>
        <citation type="bibtex">
            @article{langfelder2008wgcna,
            title={WGCNA: an R package for weighted correlation network analysis},
            author={Langfelder, Peter and Horvath, Steve},
            journal={BMC bioinformatics},
            volume={9},
            number={1},
            pages={559},
            year={2008},
            publisher={BioMed Central}
            }
        </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>
    </citations>
</tool>