<tool id="DESeq_visualization" name="DESeq2: Visualization" version="1.0.0">
    <requirements>
        <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>
    </requirements>
    <description>
        An R Markdown tool to visualize DESeq analysis results.
    </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__}/DESeq_visualization_render.R'

            ## 1. input data
            -e $echo
            -w $deseq_workspace
            
            #set $pca_groups = []
            #for $group in $intgroups_pca
                #if str($group.intgroup)
                    #set $pca_groups = $pca_groups + [str($group.intgroup)]
                #end if
            #end for
            #set $pca_groups = ','.join($pca_groups)
            -p "$pca_groups"
            
            #set $mds_groups = []
            #for $group in $intgroups_mds
                #if str($group.intgroup)
                    #set $mds_groups = $mds_groups + [str($group.intgroup)]
                #end if
            #end for
            #set $mds_groups = ','.join($mds_groups)
            -m "$mds_groups"

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


		    ## 3. Rmd templates sitting in the tool directory

		        ## _site.yml and index.Rmd template files
                -D '${__tool_directory__}/DESeq_visualization.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" />
        <repeat name="intgroups_pca" title="Interest groups for PCA plot" min="1">
            <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
                   optional="false"
                   label="Interest group for PCA plot"
                   help=""/>
        </repeat>
        <repeat name="intgroups_mds" title="Interest groups for MDS plot" min="1">
            <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
                   optional="false"
                   label="Interest group for MDS plot"
                   help=""/>
        </repeat>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data name="deseq_visualization" format="html" label="DESeq Visualization" />
    </outputs>
</tool>