<tool id="DESeq_results" name="DESeq2: Results" 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="0.4.0">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>
        <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_results_render.R'

            ## 1. input data
            -e $echo
            -w $deseq_workspace
            -c "$contrast_group"
            -t $treatment
            -k $condition

            #set $groups = []
            #for $c_group in $clustering_groups
                #if str($c_group.group)
                    #set $groups = $groups + [str($c_group.group)]
                #end if
            #end for
            #set $groups = ','.join($groups)
            -m "$groups"

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

		    ## 3. Rmd templates sitting in the tool directory

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



        ]]>
    </command>
    <inputs>
        <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" />
        <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" />
        <param type="data_column" name="contrast_group" data_ref="sample_table" use_header_names="true"
               optional="false"
               label="Group for result contrast"
               help=""/>
        <param type="text" name="treatment" label="Treatment level" />
        <param type="text" name="condition" label="Condition level" />

        <repeat name="clustering_groups" title="Gene clustering groups" min="1">
            <param type="data_column" name="group" data_ref="sample_table" use_header_names="true"
                   optional="false"
                   label="A phenotype column from the sample table" />
        </repeat>

        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data name="deseq_results" format="html" label="DESeq Results" />
    </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>