<tool id="DESeq" name="DESeq2: DESeq" 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 perform 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_render.R'


            ## 1. input data
            -e $echo
            ##----- code chunk to get file paths and raw file names for a multiple inputs data field ----
            #set $sep = ''
            #set $count_file_paths = ''
            #set $count_file_names = ''
            #for $count_file in $count_files:
                #set $count_file_paths += $sep + str($count_file)
                #set $count_file_names += $sep + str($count_file.name)
                #set $sep = ','
            #end for
            ##----------------- end for getting file names and file paths ------------------------------
            -P '$count_file_paths'
            -N '$count_file_names'
            -S $sample_table
            -p '$design_formula'

            ## 2. output report and report site directory
		    -r $report
		    -d $report.files_path
		    -s $sink_message
		    -w $deseq_workspace

		    ## 3. Rmd templates from the tool directory
            -t '${__tool_directory__}/DESeq.Rmd'



        ]]>
    </command>
    <inputs>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
               label="Display analysis code in report?"/>
        <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>
    </inputs>
    <outputs>
        <data name="report" format="html" label="DESeq Analysis on ${on_string}"/>
        <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
        <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis on ${on_string}"/>
    </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>