# HG changeset patch
# User bgruening
# Date 1550667654 18000
# Node ID c09c23eaf1166fe5335e80dd2b57c2286a7381cc
# Parent  59cbb059cd1e97f7bdaca85bf55edf53c7e65d78
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf

diff -r 59cbb059cd1e -r c09c23eaf116 bamCompare.xml
--- a/bamCompare.xml	Tue Feb 19 10:03:16 2019 -0500
+++ b/bamCompare.xml	Wed Feb 20 08:00:54 2019 -0500
@@ -166,8 +166,8 @@
                 <expand macro="skipNAs" />
                 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
                     help="Skip bins where BOTH files lack coverage.">
-                    <option value="no" selected="true">No</option>
-                    <option value="yes">Yes, skip them.</option>
+                    <option value="" selected="true">No</option>
+                    <option value="--skipZeroOverZero">Yes, skip them.</option>
                 </param>
 
                 <param argument="--ignoreForNormalization" type="text" value="" size="50"
diff -r 59cbb059cd1e -r c09c23eaf116 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Feb 19 10:03:16 2019 -0500
+++ b/deepTools_macros.xml	Wed Feb 20 08:00:54 2019 -0500
@@ -512,7 +512,7 @@
 
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
-        #if $custom_labels_conditional.custom_labels_select == "Yes":
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
             #set custom_labels=labels
         #end if
         #set files=[]
@@ -533,7 +533,7 @@
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
-        #if $custom_labels_conditional.custom_labels_select == "Yes":
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
             #set labels=custom_labels
         #end if
 ]]>
diff -r 59cbb059cd1e -r c09c23eaf116 test-data/estimateReadFiltering.txt
--- a/test-data/estimateReadFiltering.txt	Tue Feb 19 10:03:16 2019 -0500
+++ b/test-data/estimateReadFiltering.txt	Wed Feb 20 08:00:54 2019 -0500
@@ -1,3 +1,3 @@
 Sample	Total Reads	Mapped Reads	Alignments in blacklisted regions	Estimated mapped reads filtered	Below MAPQ	Missing Flags	Excluded Flags	Internally-determined Duplicates	Marked Duplicates	Singletons	Wrong strand
-paired_chr2L.bam	12644	12589	0	1395.9	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
-paired_chr2L.bam	12644	12589	0	1395.9	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
+paired_chr2L.bam	12644	12589	0	4192.0	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
+paired_chr2L.bam	12644	12589	0	4192.0	4149.0	0.0	0.0	0.0	0.0	55.0	0.0