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<tool id="aurora_deseq2" name="aurora_deseq2" version="2.2.0">
    <description>Differential analysis of count data with the DESeq2 package</description>
    <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="1.6">r-rmarkdown</requirement>
        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
        <requirement type="package" version="4.5.6">r-plotly</requirement>
        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
        <requirement type="package" version="1.0.8">r-pheatmap</requirement>
        <requirement type="package" version="0.2">r-dt</requirement>
    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[

        ######### each aurora tool generates a html file and have an files path directory associated with it.
        mkdir -p $report.files_path &&

        ######### three important paths:
        #########   1. path to tool installation directory
        #########   2. path to report html
        #########   3. path to files_path directory associated with the report output.
        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
        export REPORT='$report' &&
        export REPORT_FILES_PATH='$report.files_path' &&

        ############ create a hidden file to store r markdown rendering log
        touch $report.files_path/.r_rendering.log.txt &&


        Rscript '${__tool_directory__}/deseq2_render.R'

              -o $report
              -d $report.files_path

              -A '$count_data'
              -B '$column_data'
              -C '$design_formula'
              -D '$treatment_name'
              -E '$treated'
              -F '$untreated'
              -G '$test_type'
              -H '$fit_type'
              -I '$alpha'
              -J '$significant_genes']]></command>
    <inputs>
        <param type="data" name="count_data" label="Count data"
               help="an RData file that stores the count matrix data. The file is generated from the aurora_htseq tool."
               optional="False" format="csv"/>
        <param type="data" name="column_data" label="Column data"
               help="A table file that stores column data for DESeq2 analysis. The first column are the column names from the count data matrix. The remaining columns are experimental treatments."
               optional="False" format="csv"/>
        <param type="text" name="design_formula" label="Design formula"
               help="The design formula expresses the variables which will be used in modeling. The formula should be a tilde (~) followed by the variables with plus signs between them, e.g., ~ condition1 + condition2"
               optional="False">
            <sanitizer sanitize="true">
                <valid initial="default">
                    <add preset="string.printable"/>
                    <add value="~"/>
                </valid>
            </sanitizer>
        </param>
        <param type="text" name="treatment_name" label="Treatment name"
               help="one of the treatment column names from the column data." optional="False"/>
        <param type="text" name="treated" label="Treated"
               help="A level from the specified treatment column that will be used as the treated group in the DESeq2 analysis."
               optional="False"/>
        <param type="text" name="untreated" label="Untreated"
               help="A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis."
               optional="False"/>
        <param type="select" name="test_type" label="Test type" optional="False">
            <option value="Wald" selected="true">Wald</option>
            <option value="LRT" selected="false">Likelihood Ratio Test (LRT)</option>
        </param>
        <param type="select" name="fit_type" label="Fitting of dispersions"
               help="either &quot;parametric&quot;, &quot;local&quot;, or &quot;mean&quot; for the type of fitting of dispersions to the mean intensity"
               optional="False">
            <option value="parametric" selected="true">parametric</option>
            <option value="local" selected="false">local</option>
            <option value="mean" selected="false">mean</option>
        </param>
        <param type="float" name="alpha" label="Alpha"
               help="the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value."
               optional="False" value="0.1" min="0" max="1"/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="${tool.name} on ${on_string}"/>
        <data name="significant_genes" format="tabular" label="${tool.name} signficant genes on ${on_string} " hidden="false"/>
    </outputs>
    <citations>
        <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>
        <citation type="bibtex"><![CDATA[
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation>
        <citation type="bibtex"><![CDATA[@article{love2014differential,
  title={Differential analysis of count data--the DESeq2 package},
  author={Love, Michael and Anders, Simon and Huber, Wolfgang},
  journal={Genome Biol},
  volume={15},
  pages={550},
  year={2014}
}]]></citation>
    </citations>
</tool>