<tool id="DESeq_results" name="DESeq2: Results" version="2.0.0">
    <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="1.2">r-rmarkdown</requirement>
        <requirement type="package" version="1.8.4">r-plyr</requirement>
        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
        <requirement type="package" version="1.1.0">r-stringr</requirement>
        <requirement type="package" version="0.4.0">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="1.0.8">r-pheatmap</requirement>
    </requirements>
    <description>
        An R Markdown tool to display DESeq analysis.
    </description>
    <stdio>
        <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
        <regex match="XXX"
               source="stderr"
               level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command>
        <![CDATA[

        Rscript '${__tool_directory__}/DESeq_results_render.R'

            ## 1. input data
            -e $echo
            -W $deseq_workspace
            -C '$contrast_factor'
            -T '$treatment'
            -K '$condition'

            -M '$clustering_factors'

            ## 2. output report and report site directory
		    -r $report
            -d $report.files_path
            -s $sink_message
            -R $deseq_results

		    ## 3. Rmd templates sitting in the tool directory
            -t '${__tool_directory__}/DESeq_results.Rmd'



        ]]>
    </command>
    <inputs>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
               label="Display analysis code in report?"/>
        <param type="data" name="deseq_workspace" format="rdata" multiple="false" optional="false"
               label="Workspace from tool DESeq2: DESeq"/>
        <param type="text" name="contrast_factor" label="Factor" optional="false"
               help="the name of a factor in the design formula"/>
        <param type="text" name="treatment" label="Treatment level" optional="false"
               help=" the name of the numerator level for the fold change"/>
        <param type="text" name="condition" label="Condition level" optional="false"
               help=" the name of the denominator level for the fold change"/>
        <param type="text" name="clustering_factors" title="Gene clustering factors" optional="false"
               label="factors of interest for clustering samples and PCA plot"
               help="A single factor or multiple factors from the design formula. Multiple factors are separated by comma (,)."/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="DESeq results report on ${on_string}" />
        <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
        <data format="csv" name="deseq_results" label="DESeq results on ${on_string}" from_work_dir="deseq_results.csv" />
    </outputs>
    <citations>
        <citation type="bibtex">
            @article{love2014moderated,
            title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
            author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
            journal={Genome biology},
            volume={15},
            number={12},
            pages={550},
            year={2014},
            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>