diff bamCoverage.xml @ 40:20f8dafb554f draft

Uploaded

--- a/bamCoverage.xml	Sat Feb 01 08:09:18 2014 -0500
+++ b/bamCoverage.xml	Mon Feb 03 12:38:00 2014 -0500
@@ -31,14 +31,15 @@
             --scaleFactor $scaling.scaleFactor
         #end if
 
+        #if str(region).strip() != '':
+            --region 'region'
+        #end if
+
         #if $advancedOpt.showAdvancedOpt == "yes":
             #if $advancedOpt.smoothLength:
                 --smoothLength '$advancedOpt.smoothLength'
             #end if
 
-            #if str($advancedOpt.region.value) != '':
-                --region '$advancedOpt.region'
-            #end if
             $advancedOpt.doNotExtendPairedEnds
             $advancedOpt.ignoreDuplicates
 
@@ -88,6 +89,8 @@
             <option value="bedgraph">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>
@@ -99,10 +102,6 @@
                     label="Smooth values using the following length (in bp)"
                     help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
 
-                <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="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
                     label="Do not extend paired ends"
                     help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>