--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotdexseq.xml	Mon Jan 14 05:02:19 2019 -0500
@@ -0,0 +1,90 @@
+<tool id="plotdexseq" name="plotDEXSeq" version="@VERSION@.0">
+    <description>Visualization of the per gene DEXSeq results</description>
+    <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>