diff bamCoverage.xml @ 37:2f7edf06a5da draft

Uploaded

--- a/bamCoverage.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/bamCoverage.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -22,7 +22,11 @@
         #if $scaling.type=='rpkm':
             --normalizeUsingRPKM
         #elif $scaling.type=='1x':
-            --normalizeTo1x $scaling.normalizeTo1x
+            #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
+            #else:
+                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
+            #end if
         #elif $scaling.type=='own':
             --scaleFactor $scaling.scaleFactor
         #end if
@@ -71,9 +75,7 @@
             <when value="rpkm"/>
             <when value="no"/>
             <when value="1x">
-                <param name="normalizeTo1x" type="integer" value="2150570000"
-                    label="Genome size"
-                    help ="Enter the genome size to normalize the reads counts. Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
+                <expand macro="effectiveGenomeSize" />
             </when>
             <when value="own">
                 <param name="scaleFactor" type="float" value="1" size="3" 
@@ -141,14 +143,17 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
+You can find more details in the `bamCoverage wiki`_.
+
+.. _bamCoverage wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
+
+
 **Output files**:
 
 - coverage file either in bigWig or bedGraph format
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>