diff bamCompare.xml @ 37:2f7edf06a5da draft

Uploaded

--- a/bamCompare.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/bamCompare.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -37,7 +37,13 @@
           #if $comparison.normalization.type=='rpkm':
             --normalizeUsingRPKM
           #elif $comparison.normalization.type=='1x':
-            --normalizeTo1x $comparison.normalization.normalizeTo1x
+
+            #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
+            #else:
+                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
+            #end if
+
           #end if
       #end if
 
@@ -123,9 +129,7 @@
                     <when value="rpkm" />
                     <when value="no" />
                     <when value="1x">
-                        <param name="normalizeTo1x" type="integer" value="2150570000"
-                            label="Report normalized coverage to 1x sequenceing depth"
-                            help ="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>
                 </conditional>
             </when>
@@ -203,13 +207,18 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
+You can find more details in the `bamCompare wiki`_.
+
+.. _bamCompare wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
+
+
 **Output files**:
 
 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.
 
 -----
 
-.. class:: infomark
+@REFERENCES@
 
     </help>
 </tool>