# HG changeset patch
# User bgruening
# Date 1461523665 14400
# Node ID 582a05c586ba9a77d766561b8cd9ac0d4499b174
# Parent  8fefd05b0e3f1ec8716eb73d02d7c324f24165cc
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty

diff -r 8fefd05b0e3f -r 582a05c586ba deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Mar 18 08:35:01 2016 -0400
+++ b/deepTools_macros.xml	Sun Apr 24 14:47:45 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 8fefd05b0e3f -r 582a05c586ba plotCoverage.xml
--- a/plotCoverage.xml	Fri Mar 18 08:35:01 2016 -0400
+++ b/plotCoverage.xml	Sun Apr 24 14:47:45 2016 -0400
@@ -17,8 +17,8 @@
             @THREADS@
 
             --plotFile '$outFileName'
-            --bamfiles '#echo "' '".join($files)#'
-            --labels '#echo "' '".join($labels)#'
+            --bamfiles #echo " ".join($files)#
+            --labels #echo " ".join($labels)#
             --plotFileFormat "$outFileFormat"
 
             #if $outRawCounts:
@@ -76,13 +76,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
+            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <!--param name="outFileFormat" value="png" /-->
             <param name="showAdvancedOpt" value="yes" />
             <param name="plotTitle" value="Test Title from Galaxy" />
             <param name="outRawCounts" value="True" />
             <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2200" />
+            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
         </test>
     </tests>
     <help>
diff -r 8fefd05b0e3f -r 582a05c586ba test-data/bowtie2 test1.bam
Binary file test-data/bowtie2 test1.bam has changed
diff -r 8fefd05b0e3f -r 582a05c586ba test-data/bowtie2-test1.bam
Binary file test-data/bowtie2-test1.bam has changed
diff -r 8fefd05b0e3f -r 582a05c586ba test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular	Fri Mar 18 08:35:01 2016 -0400
+++ b/test-data/plotCoverage_result1.tabular	Sun Apr 24 14:47:45 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 8fefd05b0e3f -r 582a05c586ba test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular	Fri Mar 18 08:35:01 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular	Sun Apr 24 14:47:45 2016 -0400
@@ -1,4 +1,4 @@
-'bowtie2-test1.bam'	'bowtie2-test1.bam'
+'bowtie2 test1.bam'	'bowtie2 test1.bam'
 68	68
 65	65
 61	61