diff bamCompare.xml @ 55:51c21e40ec5c draft

Uploaded

--- a/bamCompare.xml	Mon Dec 22 19:00:50 2014 -0500
+++ b/bamCompare.xml	Wed Jan 21 09:29:46 2015 -0500
@@ -69,7 +69,7 @@
             --missingDataAsZero $advancedOpt.missingDataAsZero
 
             #if str($advancedOpt.ignoreForNormalization).strip() != '':
-                --ignoreForNormalization $advancedOpt.ignoreForNormalization
+                --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
             #end if
 
         #end if
@@ -109,9 +109,9 @@
         <conditional name="comparison">
             <param name="type" type="select" 
                 label="How to compare the two files">
-                <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="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>
             </param>
             <when value="log2">
                 <expand macro="pseudocount" />