--- a/rDiff/galaxy/rdiff.xml	Thu Feb 14 23:38:36 2013 -0500
+++ b/rDiff/galaxy/rdiff.xml	Tue Oct 08 07:15:44 2013 -0400
@@ -1,19 +1,27 @@
 <tool id="rdiff-web" name="rDiff" version="0.3">
     <description>Determines differentially expressed transcripts from read alignments</description>
     <command interpreter="bash"> 
-        rdiff_run.sh $test_meth $anno_input $read_length $rdiff_out $rdiff_out.extra_files_path
-        #for $i in $replicate_groups
-        #for $j in $i.replicates
-        $j.bam_alignment?
-        #end for
-        :
-        #end for
+        rdiff_run.sh
+        $test_meth 
+        $anno_input 
+        $read_length 
+        $rdiff_out $rdiff_out.extra_files_path
+##
+## replicate groups 
+##
+#for $i in $replicate_groups
+#for $j in $i.replicates
+$j.bam_alignment?
+#end for
+:
+#end for
+
         >> $Log_File 
     </command>
   <inputs>
 
     <!-- genome annotation in GFF format -->
-	<param format="gff3" name="anno_input" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
+	<param format="gff,gtf,gff3" name="anno_input" type="data" label="Genome annotation file" help="A tab delimited format for storing sequence features and annotations(GFF/GTF/GFF3)"/>
 
     <!-- RNA-seq samples and corresponding replicates -->
    <repeat name="replicate_groups" title="Sample" min="2" max="2">
@@ -22,19 +30,21 @@
      </repeat>
    </repeat>
 
-    
+    <!-- rDiff test method --> 
      <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." >
             <option value="poisson">Poisson</option>
             <option value="param">Parametric</option>
             <option value="nonparam">Nonparametric</option>
     </param>
+
+    <!-- read length uesd in the experiment-->
     <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/>
 
   </inputs>
 
   <outputs>
-    <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Testing Result" />
-    <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/>
+    <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Expression" />
+    <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: Log"/>
   </outputs>
   
   <help>