--- a/deseq-hts_1.0/galaxy/deseq.xml	Wed Jun 27 15:38:39 2012 -0400
+++ b/deseq-hts_1.0/galaxy/deseq.xml	Tue Oct 08 08:09:28 2013 -0400
@@ -1,7 +1,10 @@
-<tool id="deseq-hts" name="DESeq" version="1.6.1">
-  <description>Determines differentially expressed transcripts from read alignments</description>
-  <command> 
-deseq-hts/src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat 
+<tool id="deseq-hts" name="DESeq" version="1.12.1">
+  <description> Determines differentially expressed transcripts from read alignments</description>
+  <requirements>
+	<requirement type="package" version="0.1">oqtans</requirement>
+  </requirements>
+  <command interpreter="bash"> 
+./../src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat 
 #for $i in $replicate_groups
 #for $j in $i.replicates
 $j.bam_alignment:#slurp
@@ -19,8 +22,8 @@
   </inputs>
 
   <outputs>
-    <data format="txt" name="deseq_out" label="DESeq result"/>
-    <data format="txt" name="Log_File" label="DESeq log file"/>
+    <data format="txt" name="deseq_out" label="${tool.name} on ${on_string}: Differential Expression"/>
+    <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/>
   </outputs>
 
   <tests>
@@ -41,19 +44,15 @@
 
 **What it does** 
 
-`DESeq` is a tool for differential expression testing of RNA-Seq data.
-
+DESeq_ is a tool for differential expression testing of RNA-Seq data.
 
-**Inputs**
-
-`DESeq` requires three input files to run:
+.. _DESeq: http://bioconductor.org/packages/release/bioc/html/DESeq.html
 
-1. Annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
-2. The BAM alignment files grouped into replicate groups, each containing several replicates. BAM files store the read alignments in a compressed format. They can be generated using the `SAM-to-BAM` tool in the NGS: SAM Tools section. (The script will also work with only two groups containing only a single replicate each. However, this analysis has less statistical power and is  therefor not recommended.)
+`DESeq` requires:
 
-**Output**
+Genome annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
 
-`DESeq` generates a text file containing the gene name and the p-value.
+The BAM alignment files grouped into replicate groups, each containing several replicates. BAM files store the read alignments, The program will also work with only two groups containing only a single replicate each. However, this analysis has less statistical power and is therefore not recommended!
 
 ------
 
@@ -100,7 +99,7 @@
 
 ------
 
-DESeq-hts Wrapper Version 0.3 (Feb 2012)
+DESeq-hts Wrapper Version 0.5 (Aug 2013)
 
 </help>
 </tool>