# HG changeset patch
# User bgruening
# Date 1461530109 14400
# Node ID 7b4732d497a337c3921f1f04b4389fcee499d219
# Parent  5a42d470c9f6fedfcf8f607246be8397b67fed72
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty

diff -r 5a42d470c9f6 -r 7b4732d497a3 deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Mar 18 08:47:43 2016 -0400
+++ b/deepTools_macros.xml	Sun Apr 24 16:35:09 2016 -0400
@@ -68,16 +68,22 @@
     <xml name="region_limit_operation">
         <param argument="--region" type="text" value=""
             label="Region of the genome to limit the operation to"
-            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
+            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
+            <sanitizer>
+                <valid initial="string.letters,string.digits">
+                    <add value="|"/>
+                 </valid>
+            </sanitizer>
+        </param>
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.2.2</token>
+    <token name="@WRAPPER_VERSION@">2.2.3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.2.2">deepTools</requirement>
+            <requirement type="package" version="2.2.3">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -302,7 +308,7 @@
     </token>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1093/nar/gku365</citation>
+            <citation type="doi">10.1093/nar/gkw257</citation>
             <yield />
         </citations>
     </xml>
diff -r 5a42d470c9f6 -r 7b4732d497a3 multiBigwigSummary.xml
--- a/multiBigwigSummary.xml	Fri Mar 18 08:47:43 2016 -0400
+++ b/multiBigwigSummary.xml	Sun Apr 24 16:35:09 2016 -0400
@@ -18,8 +18,8 @@
             @THREADS@
 
             --outFileName $outFile
-            --bwfiles '#echo "' '".join($files)#'
-            --labels '#echo "' '".join($labels)#'
+            --bwfiles #echo " ".join($files)#
+            --labels #echo " ".join($labels)#
 
             #if $outRawCounts:
                 --outRawCounts '$outFileRawCounts'
diff -r 5a42d470c9f6 -r 7b4732d497a3 test-data/bowtie2 test1.bam
Binary file test-data/bowtie2 test1.bam has changed
diff -r 5a42d470c9f6 -r 7b4732d497a3 test-data/bowtie2-test1.bam
Binary file test-data/bowtie2-test1.bam has changed
diff -r 5a42d470c9f6 -r 7b4732d497a3 test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular	Fri Mar 18 08:47:43 2016 -0400
+++ b/test-data/plotCoverage_result1.tabular	Sun Apr 24 16:35:09 2016 -0400
@@ -1,4 +1,4 @@
-#'chr'	'start'	'end'	'bowtie2-test1.bam'	'bowtie2-test1.bam'
+#'chr'	'start'	'end'	'bowtie2 test1.bam'	'bowtie2 test1.bam'
 chrM	0	1	23.0	23.0
 chrM	1	2	35.0	35.0
 chrM	2	3	35.0	35.0
diff -r 5a42d470c9f6 -r 7b4732d497a3 test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular	Fri Mar 18 08:47:43 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular	Sun Apr 24 16:35:09 2016 -0400
@@ -1,4 +1,4 @@
-'bowtie2-test1.bam'	'bowtie2-test1.bam'
+'bowtie2 test1.bam'	'bowtie2 test1.bam'
 68	68
 65	65
 61	61