<tool id="DESeq" name="DESeq2: DESeq" 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 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[
        ## Add tools to PATH
        export PATH=/opt/R-3.2.5/bin:\$PATH &&

        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>
</tool>