--- a/bigwigCompare.xml	Mon May 25 05:16:10 2015 -0400
+++ b/bigwigCompare.xml	Sat May 30 13:55:46 2015 -0400
@@ -46,12 +46,15 @@
 
         <conditional name="comparison">
             <param name="comparison_select" type="select" 
-                label="How to compare the two files" help="(--ratio)">
+                label="How to compare the two files"
+                help="The default is to output the log2ratio between the two samples.
+                The reciprocal ratio returns the negative of the inverse of the ratio if
+                the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)">
                 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
                 <option value="ratio">compute the ratio of the number of reads</option>
                 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
                 <option value="add">compute the sum over all reads</option>
-                <option value="reciprocal_ratio">compute the reciprocal ratio of the number of reads</option>
+                <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
             </param>
             <when value="log2">
                 <expand macro="pseudocount" />
@@ -61,7 +64,9 @@
             </when>
             <when value="subtract" />
             <when value="add" />
-            <when value="reciprocal_ratio" />
+            <when value="reciprocal_ratio">
+                <expand macro="pseudocount" />
+            </when>
         </conditional>
 
         <param name="outFileFormat" type="select" label="Coverage file format">
@@ -107,8 +112,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="bigwigFile1" value="1.bigwig" ftype="bigwig" />
-            <param name="bigwigFile2" value="1.bigwig" ftype="bigwig" />
+            <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
+            <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="no" />
             <param name="outFileFormat" value="bigwig" />
             <param name="binSize" value="5" />
@@ -116,8 +121,8 @@
             <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" />
         </test>
         <test>
-            <param name="bigwigFile1" value="1.bigwig" ftype="bigwig" />
-            <param name="bigwigFile2" value="1.bigwig" ftype="bigwig" />
+            <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
+            <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="no" />
             <param name="outFileFormat" value="bedgraph" />
             <param name="binSize" value="10" />