<tool id="plotdexseq" name="plotDEXSeq" version="@VERSION@.1" profile="@PROFILE@">
    <description>Visualization of the per gene DEXSeq results</description>
    <xrefs>
        <xref type="bio.tools">dexseq</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.20.2">r-getopt</requirement>
    </expand>
    <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/plotdexseq.R'
    -r '$rdata'
    -p '$primaryfactor'
    #if $genes.genes_select == 'list':
        -f '$genes.genefile'
    #else:
        -g '$genes.geneid'
    #end if
    -c $fdr_cutoff
    -t $transcripts
    -a $names
    -n $normcounts
    -s $splicing
    ]]></command>
    <inputs>
        <param name="rdata" type="data" format="rdata" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/>
        <param name="primaryfactor" type="text" value="FactorName" label="Specify the primary factor name in the DEXSeqResults object" help="Only letters, numbers and underscores will be retained in this field">
            <sanitizer>
                <valid initial="string.letters,string.digits"><add value="_" /></valid>
            </sanitizer>
        </param>
        <conditional name="genes">
            <param name="genes_select" type="select" label="Genes to plot" help="Select to input a single gene ID or a list of IDs. Default: single gene ID">
                <option value="single" selected="True">single</option>
                <option value="list">list</option>
            </param>
            <when value="single">
                <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize">
                    <sanitizer>
                        <valid initial="string.letters,string.digits"><add value="_" /></valid>
                    </sanitizer>
                </param>
            </when>
            <when value="list">
                <param name="genefile" type="data" format="tabular" label="List of gene IDs" help="This should be a single tabular column with one gene per row and no header." />
            </when>
        </conditional>
        <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.1" label="False Discovery Rate"/>
        <param name="transcripts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcripts" help="If Yes, the transcripts are displayed in the plot. Default: No"/>
        <param name="names" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcript names" help="If Yes, the names of the transcripts are shown. Default: No"/>
        <param name="normcounts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot count values from the individual samples" help="If yes, provides a plot of the counts normalized by the size factors. Default: No"/>
        <param name="splicing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot exon usage" help="If yes, the samples gene expression effects are averaged out, leaving only exon usage coefficients. Default: No" />
    </inputs>

    <outputs>
        <data name="dexseq_plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!-- Ensure default output works-->
        <test expect_num_outputs="1">
            <param name="rdata" ftype="rdata" value="dexseq.rds"/>
            <param name="primaryfactor" value="condition"/>
            <param name="geneid" value="FBgn0000053"/>
            <param name="fdr_cutoff" value="1"/>
            <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/>
        </test>
        <!-- Ensure plotting multiple genes works-->
        <test expect_num_outputs="1">
            <param name="rdata" ftype="rdata" value="dexseq.rds"/>
            <param name="primaryfactor" value="condition"/>
            <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/>
            <param name="fdr_cutoff" value="1"/>
            <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool enables visualization of DEXSeq results for individual genes. The input is a DEXSeqResults rds file, which can be output from the DEXSeq tool, and a single gene ID or list of IDs to plot.

.. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
    ]]></help>
    <citations>
        <citation type="doi">10.1101/gr.133744.111</citation>
    </citations>
</tool>