diff bamCoverage.xml @ 5:8c6f450d266c draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

--- a/bamCoverage.xml	Mon Dec 21 19:04:49 2015 -0500
+++ b/bamCoverage.xml	Tue Dec 22 13:42:24 2015 -0500
@@ -43,9 +43,9 @@
                 @ADVANCED_OPTS_READ_PROCESSING@
                 $advancedOpt.skipNAs
 
-                if str($advancedOpt.ignoreForNormalization).strip() != '':
+                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                     --ignoreForNormalization $advancedOpt.ignoreForNormalization
-                end if
+                #end if
             #end if
 ]]>
     </command>
@@ -54,7 +54,7 @@
         <param name="bamInput" format="bam" type="data" label="BAM file"
             help="The BAM file must be sorted."/>
 
-        <param name="binSize" type="integer" value="50" min="1" 
+        <param name="binSize" type="integer" value="50" min="1"
             label="Bin size in bp"
             help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
 
@@ -149,7 +149,7 @@
         <test>
             <param name="bamInput" value="phiX.bam" ftype="bam" />
             <param name="outFileFormat" value="bedgraph" />
-            <param name="showAdvancedOpt" value="no" />
+            <param name="showAdvancedOpt" value="yes" />
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
         </test>
@@ -171,7 +171,7 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
-You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
+You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCoverage.html
 
 
 **Output files**: