--- a/htseq.xml	Thu Sep 13 00:50:59 2012 -0400
+++ b/htseq.xml	Thu Sep 13 00:51:13 2012 -0400
@@ -1,5 +1,5 @@
 <tool id="htseq-count" name="Count reads in features with htseq-count" version="1.0.0">
-  
+  <description> - Create a digital expression matrix by counting reads in features with htseq-count</description>
   <command interpreter="perl">
   	htseq.pl -m $MODE -s $STRANDED -a $MINAQUAL -t $FEATURETYPE -i $IDATTR -g $gff_file -o $output -r $report $REDUCE
 	## Inputs.
@@ -70,7 +70,7 @@
 
 The following figure illustrates the effect of these three modes:
 
-.. image:: ./static/operation_icons/count_modes.png
+.. image:: http://www-huber.embl.de/users/anders/HTSeq/doc/_images/count_modes.png
 
 The strandedness of the assay may also be set. For stranded=no, a read is considered overlapping with a feature regardless of whether it is mapped to the same or the opposite strand as the feature. For stranded=yes and single-end reads, the read has to be mapped to the same strand as the feature. For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed.
 
@@ -90,6 +90,12 @@
     * not_aligned: reads in the Sam/Bam file without alignment
     * alignment_not_unique: reads with more than one reported alignment. These reads are recognized from the NH optional SAM field tag. (If the aligner does not set this field, multiply aligned reads will be counted multiple times.)
 
+**Reference**
+
+http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
+
+
+
   </help>  
   
 </tool>