--- a/dexseq.xml	Tue Dec 11 00:19:18 2018 -0500
+++ b/dexseq.xml	Mon Jan 14 05:02:19 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
+<tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1">
     <description>Determines differential exon usage from count tables</description>
     <macros>
         <import>macros.xml</import>
@@ -54,6 +54,7 @@
      -f '#echo json.dumps(temp_factor_names)#'
      -a $gtf
      -c $fdr_cutoff
+     -d $rds
 
      #if $report:
          -r ./html_out
@@ -93,6 +94,8 @@
         <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
             label="Visualise the analysis results?"
             help="Output an additional HTML file." />
+        <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
+            label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
         <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
     </inputs>
     <outputs>
@@ -100,6 +103,9 @@
         <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
             <filter>report is True</filter>
         </data>
+        <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}">
+            <filter>rds is True</filter>
+        </data>
     </outputs>
     <tests>
         <!-- Ensure default output works-->
@@ -151,6 +157,22 @@
             <param name="fdr_cutoff" value="0.05"/>
             <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/>
         </test>
+        <!-- Ensure rds output works-->
+        <test expect_num_outputs="2">
+            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="condition"/>
+                <param name="factorLevel1" value="knockdown"/>
+                <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
+                <param name="factorLevel2" value="control"/>
+                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
+            </repeat>
+            <param name="report" value="False"/>
+            <param name="rds" value="True"/>
+            <param name="fdr_cutoff" value="0.05"/>
+            <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
+            <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
@@ -188,7 +210,7 @@
 
 **Output**
 
-DEXSeq_ generates a tabular file containing the different columns and an optional html report.
+DEXSeq_ generates a tabular file containing the different columns and an optional html report. It can also ouput the DEXSeqResults R object that can be used with the plotDEXSeq tool to visualise individual genes.
 
 ====== ==========================================================
 Column Description