diff bamCompare.xml @ 66:1dbd76a58d8b draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty

--- a/bamCompare.xml	Mon May 25 05:16:10 2015 -0400
+++ b/bamCompare.xml	Sat May 30 13:55:46 2015 -0400
@@ -109,10 +109,15 @@
 
         <conditional name="comparison">
             <param name="type" type="select" 
-                label="How to compare the two files">
+                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.">
                 <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 of 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" />
@@ -120,6 +125,10 @@
             <when value="ratio">
                 <expand macro="pseudocount" />
             </when>
+            <when value="add" />
+            <when value="reciprocal_ratio">
+                <expand macro="pseudocount" />
+            </when>
             <when value="subtract">
                 <conditional name="normalization">
                     <param name="type" type="select" label="Normalization method" >