<tool id="rmarkdown_deseq2_count_matrix" name="DESeq2 (count matrix)" version="1.0.0">
    <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="1.3">r-rmarkdown</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
        <requirement type="package" version="0.5.0">r-dplyr</requirement>
        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
        <requirement type="package" version="0.2">r-dt</requirement>
    </requirements>
    <description>deseq2 analysis given a count matrix input</description>
    <stdio>
        <regex source="stderr" match="XXX" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[
Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
                        -e $echo
                        -c $count_data
                        -n '$count_matrix_column_names'
                        -C $col_data
                        -D '$design_formula'
                        -k $contrast_condition
                        -T $treatment
                        -K $control
                        -r $report
                        -d $report.files_path
                        -s $sink_message
                        -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
                    ]]></command>
    <inputs>
        <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
               truevalue="TRUE" falsevalue="FALSE"/>
        <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
        <param type="text" name="count_matrix_column_names" label="column names"
               help="This field is used to update the column names of count data matrix. Column names are separated by comma (,). For example, 'column_1, column_2, column_3, column_4'"
               optional="True" area="True" size="5x25"></param>
        <param type="data" name="col_data" label="column data (from file)" optional="False" format="txt,csv" multiple="False"/>
        <param type="text" name="design_formula" label="design formula"
               help="The simplest design formula for differential expression would be ~ condition, where condition&#13;&#10;                     is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"
               optional="False" value="~ condition_1 + condition_2">
            <sanitizer>
                <valid>
                    <add value="~"/>
                </valid>
            </sanitizer>
        </param>
        <param type="text" name="contrast_condition" label="condition"
               help="A condition name specified in the design formula" optional="False" value="condition_1"/>
        <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
               optional="False" value="treated"/>
        <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
               optional="False" value="untreated"/>
    </inputs>
    <outputs>
        <data name="report" format="html" label="DESeq2 report" hidden="false"/>
        <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
              hidden="false"/>
        <data name="deseq2" format="rdata" label="DESeq2 R objects" from_work_dir="deseq2.RData"
              hidden="false"/>
        <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
              hidden="false"/>
    </outputs>
    <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>
    <citations>
        <citation type="bibtex"><![CDATA[            @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"><![CDATA[            @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>
    </citations>
</tool>