diff correctGCBias.xml @ 40:20f8dafb554f draft

Uploaded

--- a/correctGCBias.xml	Sat Feb 01 08:09:18 2014 -0500
+++ b/correctGCBias.xml	Mon Feb 03 12:38:00 2014 -0500
@@ -33,10 +33,11 @@
             --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
         #end if
 
+        #if str(region).strip() != '':
+            --region 'region'
+        #end if
+
         #if $advancedOpt.showAdvancedOpt == "yes":
-            #if str($advancedOpt.region.value) != '':
-                --region '$advancedOpt.region'
-            #end if
             --binSize '$advancedOpt.binSize'  
         #end if
 
@@ -57,6 +58,8 @@
             <option value="bg">bedgraph</option>
         </param>
 
+        <expand macro="region_limit_operation" />
+
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -64,10 +67,6 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="region" type="text" value=""
-                    label="Region of the genome to limit the operation to"
-                    help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
-
                 <param name="binSize" type="integer" value="50" min="1" 
                     label="Bin size in bp"
                     help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>