--- a/bamCoverage.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamCoverage.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">bamCoverage</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         bamCoverage
@@ -53,7 +52,9 @@
                 ##if str($advancedOpt.ignoreForNormalization).strip() != '':
                 ##    --ignoreForNormalization $advancedOpt.ignoreForNormalization
                 ##end if
-
+                #if $samFlag:
+                    --samFlag $samFlag
+                #end if
             #end if
 ]]>
     </command>
@@ -109,9 +110,8 @@
                 <expand macro="doNotExtendPairedEnds" />
                 <expand macro="ignoreDuplicates" />
                 <expand macro="minMappingQuality" />
-
                 <expand macro="missingDataAsZero" />
-
+                <expand macro="samFlag" />
              <!--   <param name="ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
                     help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />