# HG changeset patch
# User bgruening
# Date 1461526645 14400
# Node ID 36947e3103a09c0a1e0685ef660f96124af309dc
# Parent  eb83a15755dddf1b4a056fab0a26539f88a6b740
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty

diff -r eb83a15755dd -r 36947e3103a0 deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Mar 18 08:37:56 2016 -0400
+++ b/deepTools_macros.xml	Sun Apr 24 15:37:25 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 eb83a15755dd -r 36947e3103a0 plotProfiler.xml
--- a/plotProfiler.xml	Fri Mar 18 08:37:56 2016 -0400
+++ b/plotProfiler.xml	Sun Apr 24 15:37:25 2016 -0400
@@ -129,6 +129,7 @@
                     <option value="fill">fill</option>
                     <option value="se">add standard error</option>
                     <option value="overlapped_lines">overlapped lines</option>
+                    <option value="heatmap">heatmap</option>
                 </param>
                 <param argument="--samplesLabel" type="text" size="30"
                     label="Labels for the samples (each bigwig) plotted"
diff -r eb83a15755dd -r 36947e3103a0 test-data/bowtie2 test1.bam
Binary file test-data/bowtie2 test1.bam has changed
diff -r eb83a15755dd -r 36947e3103a0 test-data/bowtie2-test1.bam
Binary file test-data/bowtie2-test1.bam has changed
diff -r eb83a15755dd -r 36947e3103a0 test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular	Fri Mar 18 08:37:56 2016 -0400
+++ b/test-data/plotCoverage_result1.tabular	Sun Apr 24 15:37:25 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 eb83a15755dd -r 36947e3103a0 test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular	Fri Mar 18 08:37:56 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular	Sun Apr 24 15:37:25 2016 -0400
@@ -1,4 +1,4 @@
-'bowtie2-test1.bam'	'bowtie2-test1.bam'
+'bowtie2 test1.bam'	'bowtie2 test1.bam'
 68	68
 65	65
 61	61