<tool id="DESeq" name="DESeq2: DESeq" version="1.0.0">
    <requirements>
        <requirement type="package" version="1.19.2.1">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="0.4.0">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 perform DESeq analysis.
    </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__}/DESeq_render.R'

            ## 1. input data
            -e $echo
            -c $count_files
            -s $sample_table
            -p "$design_formula"

            ## 2. output report and report site directory
		    -o $DESeq
		    -d $DESeq.files_path
		    -w $deseq_workspace

		    ## 3. Rmd templates sitting in the tool directory

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



        ]]>
    </command>
    <inputs>
        <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" />
        <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file"
               help="The sample table file contains a table. The first column is the sample name, the second column is
                    the count file name and the rest of columns are treatment columns. The file names in this table have
                    to be in the same order as the count files uploaded in the previous step. "/>
        <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
               help="The simplest design formula for differential expression would be ~ condition, where condition
                     is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
            <sanitizer>
                <valid initial="default">
                    <add preset="string.printable"/>
                    <add value="~"/>
                </valid>
            </sanitizer>
        </param>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data name="DESeq" format="html" label="DESeq Analysis" />
        <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" />
    </outputs>
    <citations>
        <citation>
            @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>
        <citation>
            @misc{pheatmap2015,
            title = {pheatmap: Pretty Heatmaps},
            author = {Raivo Kolde},
            year = {2015},
            note = {R package version 1.0.8},
            url = {https://CRAN.R-project.org/package=pheatmap},
            }
        </citation>
        <citation>
            @misc{dt2016,
            title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
            author = {Yihui Xie},
            year = {2016},
            note = {R package version 0.2},
            url = {https://CRAN.R-project.org/package=DT},
            }
        </citation>
    </citations>
</tool>