--- a/dexseq.xml	Tue Oct 13 17:21:57 2015 -0400
+++ b/dexseq.xml	Sun Jan 29 06:59:23 2017 -0500
@@ -1,17 +1,19 @@
-<tool id="dexseq" name="DEXSeq" version="1.0">
+<tool id="dexseq" name="DEXSeq" version="1.20.1">
     <description>Determines differential exon usage from count tables</description>
     <requirements>
-        <requirement type="package" version="1.14">dexseq</requirement>
+        <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="0.2.15">r-rjson</requirement>
     </requirements>
     <code file="dexseq_helper.py" />
     <stdio>
-        <regex match="Execution halted" 
-           source="both" 
-           level="fatal" 
+        <regex match="Execution halted"
+           source="both"
+           level="fatal"
            description="Execution halted." />
-        <regex match="Input-Error 01" 
-           source="both" 
-           level="fatal" 
+        <regex match="Input-Error 01"
+           source="both"
+           level="fatal"
            description="Error in your input parameters: Make sure you only apply factors to selected samples." />
         <regex match="Error in"
            source="both"
@@ -31,8 +33,8 @@
     <![CDATA[
         mkdir ./html_out &&
         #import json
-        Rscript $__tool_directory__/dexseq.R
-            -o "$dexseq_out"
+        Rscript '$__tool_directory__/dexseq.R'
+            -o '$dexseq_out'
             -p \${GALAXY_SLOTS:-4}
             #set $temp_factor_names = list()
             #for $factor in $rep_factorName:
@@ -57,11 +59,11 @@
             #if $report:
                 -r ./html_out
                 &&
-                mkdir $htmlreport.extra_files_path
+                mkdir '$htmlreport.extra_files_path'
                 &&
                 cp ./html_out/testForDEU.html $htmlreport
                 &&
-                cp -r ./html_out/* $htmlreport.extra_files_path
+                cp -r ./html_out/* '$htmlreport.extra_files_path'
             #end if
 
     ]]>
@@ -69,7 +71,7 @@
     <inputs>
         <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
         <repeat name="rep_factorName" title="Factor" min="1">
-            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
+            <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
                 help="Only letters, numbers and underscores will be retained in this field">
                 <sanitizer>
                     <valid initial="string.letters,string.digits"><add value="_" /></valid>
@@ -128,7 +130,7 @@
     <![CDATA[
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
 Inference of differential exon usage in RNA-Seq.
 
@@ -144,7 +146,7 @@
 The following table gives some examples of factors and their levels:
 
 ========= ============== ===============
-Factor    Factor level 1 Factor level 2 
+Factor    Factor level 1 Factor level 2
 --------- -------------- ---------------
 condition Knockdown      Wildtype
 --------- -------------- ---------------